Wed May 29 09:24:26 UTC 2024 I: starting to build sra-sdk/experimental/amd64 on jenkins on '2024-05-29 09:24' Wed May 29 09:24:26 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/9150/console.log Wed May 29 09:24:26 UTC 2024 I: Downloading source for experimental/sra-sdk=3.0.9+dfsg-3 --2024-05-29 09:24:26-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sra-sdk/sra-sdk_3.0.9%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3001 (2.9K) [text/prs.lines.tag] Saving to: ‘sra-sdk_3.0.9+dfsg-3.dsc’ 0K .. 100% 314M=0s 2024-05-29 09:24:26 (314 MB/s) - ‘sra-sdk_3.0.9+dfsg-3.dsc’ saved [3001/3001] Wed May 29 09:24:26 UTC 2024 I: sra-sdk_3.0.9+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sra-sdk Binary: sra-toolkit, libngs-c++3, libngs-c++-dev, libncbi-ngs3, libncbi-ngs-dev, libngs-java, libngs-jni, libngs-java-doc, python3-ngs Architecture: amd64 arm64 all Version: 3.0.9+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Aaron M. Ucko Homepage: https://github.com/ncbi/sra-tools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, d-shlibs, dh-python, javahelper, libabsl-dev, libncbi-vdb-dev (>= 3.0.9+dfsg~), libfuse-dev, libhdf5-dev, libmagic-dev, libre2-dev, libxml2-dev, libzstd-dev, liblzma-dev, libsam-extract-dev, markdown | libtext-markdown-perl | discount , maven-repo-helper, python3-all, default-jdk, flex, bison Package-List: libncbi-ngs-dev deb libdevel optional arch=amd64,arm64 libncbi-ngs3 deb libs optional arch=amd64,arm64 libngs-c++-dev deb libdevel optional arch=amd64,arm64 libngs-c++3 deb libs optional arch=amd64,arm64 libngs-java deb java optional arch=amd64,arm64 libngs-java-doc deb doc optional arch=all libngs-jni deb java optional arch=amd64,arm64 python3-ngs deb python optional arch=all sra-toolkit deb science optional arch=amd64,arm64 Checksums-Sha1: 376e5faec7d5b5330ca98b7cda5dafc4b47afe2a 34555404 sra-sdk_3.0.9+dfsg.orig.tar.xz 17ab684c176f54008d31904806d636324a8d19dc 3791512 sra-sdk_3.0.9+dfsg-3.debian.tar.xz Checksums-Sha256: 64644c082b02294f65a554e1428dabce095f165941af0997d5106c0c74e9f28e 34555404 sra-sdk_3.0.9+dfsg.orig.tar.xz f8e21a36ee630e7a16210509d8a7fd6b0da126a3a88ab8e19e9b8e3542380ae7 3791512 sra-sdk_3.0.9+dfsg-3.debian.tar.xz Files: 3d70afe02290c05e8d09bc1097f1ae41 34555404 sra-sdk_3.0.9+dfsg.orig.tar.xz d088594605289fc209b445000a2ab324 3791512 sra-sdk_3.0.9+dfsg-3.debian.tar.xz Dgit: 35d07ab0df3d7660656ea982cdfe875e9f19cb9a debian archive/debian/3.0.9+dfsg-3 https://git.dgit.debian.org/sra-sdk -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmY4RigACgkQHnCRsfFK ZKKXYw//Rjn5iDeHwELgu7GSNkdttol2TmZrA8hFW5ZNm3D8ElkDNz1d3tWOYXWj GoPdRQugM2K3A/c4f2VhFxwdqurJ0oGhIpPiCKr3IZir00F5eBs+r94CjMM4B90p fJJOmTl7vFeXfZyWin9lcMaRyx/4B1z/gP2Xlv0oOzo/w9YUhZMf+GxpNRyJ+R8P vUSTq4oDc4c8c3uMzK6n9bS2T/8N560AtRqmktM64zSdKe0S6yYlZ05rI0dMojFd gtGhOH2bQbM32HMa2jgCrnfDgpFkFusr99I8e2BkG+lh8YuQa07VacAyMKb6B2iG ezHiZHQTye8agRF0TmhS0Fx3UU3R7SZpfP1A2Rql6QfQ8gtwcjrJcT7gidofj4Nh lo/KDFtNUn8qMObNGNT3Glg1cf606idRB0w4oqd+JbQT5wjEVWWUvcdIC9vEszOQ JLmyb4gOeLGh+hUvGNDQhkHEc0AH4mHhTVn/k7zAXJ4wjCYRSMkD1yGSP/fCkIUd 7quIStUB6ithlPAlRee3uHW1kGGrd8qOSt8YmQjtRft0653XsFlt7Dt2lp1TNdv7 Vj2fmRDHOGjyzF+GexTHw999LD5VmkKJ4WTRiOk9CfQcG2TCUKp8ZYmiF8XdRiK+ LVg5umO/YUfeJX80prTTjfNmcuAIik5c/2j6r0onJ0EIMpUni+0= =Ulou -----END PGP SIGNATURE----- Wed May 29 09:24:26 UTC 2024 I: Checking whether the package is not for us Wed May 29 09:24:26 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed May 29 09:24:26 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed May 29 09:35:40 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 28 21:24:30 -12 2024 I: pbuilder-time-stamp: 1716974670 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [sra-sdk_3.0.9+dfsg-3.dsc] I: copying [./sra-sdk_3.0.9+dfsg.orig.tar.xz] I: copying [./sra-sdk_3.0.9+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Mon May 6 02:53:28 2024 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.9+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting sra-sdk in sra-sdk-3.0.9+dfsg dpkg-source: info: unpacking sra-sdk_3.0.9+dfsg.orig.tar.xz dpkg-source: info: unpacking sra-sdk_3.0.9+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying set_explicit_path_to_schemata.patch dpkg-source: info: applying python3 dpkg-source: info: applying skip_test_using_lots_of_memory.patch dpkg-source: info: applying find_ncbi-vdb-interfaces.patch dpkg-source: info: applying link_vdb_dynamically.patch dpkg-source: info: applying use_debian_packaged_re2.patch dpkg-source: info: applying use_debian_packaged_compression_libs.patch dpkg-source: info: applying use_soversions.patch dpkg-source: info: applying label_online_tests.patch dpkg-source: info: applying prefer_dynamic_libraries.patch dpkg-source: info: applying fix_ngs-c++-underlinkage.patch dpkg-source: info: applying use_c_locale_for_comma.patch dpkg-source: info: applying no_sse4.2.patch dpkg-source: info: applying fix_arm64_build.patch dpkg-source: info: applying support_libre2-11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3289361/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c59451e9fca7407dbc68691057bbc1bf' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3289361' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QerUu8PE/pbuilderrc_xrrG --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QerUu8PE/b1 --logfile b1/build.log sra-sdk_3.0.9+dfsg-3.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 07:34 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3289361/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, d-shlibs, dh-python, javahelper, libabsl-dev, libncbi-vdb-dev (>= 3.0.9+dfsg~), libfuse-dev, libhdf5-dev, libmagic-dev, libre2-dev, libxml2-dev, libzstd-dev, liblzma-dev, libsam-extract-dev, markdown | libtext-markdown-perl | discount, maven-repo-helper, python3-all, default-jdk, flex, bison dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19716 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on libabsl-dev; however: Package libabsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libncbi-vdb-dev (>= 3.0.9+dfsg~); however: Package libncbi-vdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libfuse-dev; however: Package libfuse-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libmagic-dev; however: Package libmagic-dev is not installed. pbuilder-satisfydepends-dummy depends on libre2-dev; however: Package libre2-dev is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libsam-extract-dev; however: Package libsam-extract-dev is not installed. pbuilder-satisfydepends-dummy depends on markdown | libtext-markdown-perl | discount; however: Package markdown is not installed. Package libtext-markdown-perl is not installed. Package discount is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison 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} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bison{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cmake{a} cmake-data{a} d-shlibs{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-python{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hdf5-helpers{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} libabsl-dev{a} libabsl20230802{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libcups2t64{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{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} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libfuse-dev{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu-dev{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-dev{a} libmagic-mgc{a} libmagic1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnpth0t64{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libre2-11{a} libre2-dev{a} libreadline8t64{a} librhash0{a} librole-tiny-perl{a} librtmp1{a} libsam-extract-dev{a} libsam-extract3{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol-dev{a} libsharpyuv0{a} libssh2-1t64{a} libssl-dev{a} libsub-quote-perl{a} libsz2{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvulkan1{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{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} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxml2-dev{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} markdown{a} maven-repo-helper{a} media-types{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tzdata{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 curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfl-dev libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgmock-dev libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace unzip wget xdg-user-dirs 0 packages upgraded, 284 newly installed, 0 to remove and 0 not upgraded. Need to get 263 MB of archives. After unpacking 881 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libncbi-vdb-dev (>= 3.0.9+dfsg~) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) libbz2-dev [1.0.8-5.1 (unstable)] 2) libmbedcrypto16 [3.6.0-2 (experimental)] 3) libmbedtls21 [3.6.0-2 (experimental)] 4) libmbedx509-7 [3.6.0-2 (experimental)] 5) libncbi-vdb-dev [3.0.9+dfsg-1 (experimental)] 6) libncbi-vdb3 [3.0.9+dfsg-1 (experimental)] 7) libncbi-wvdb-dev [3.0.9+dfsg-1 (experimental)] 8) libncbi-wvdb3 [3.0.9+dfsg-1 (experimental)] 9) ncbi-vdb-data [3.0.9+dfsg-1 (experimental)] The following NEW packages will be installed: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bison{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cmake{a} cmake-data{a} d-shlibs{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-python{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hdf5-helpers{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} libabsl-dev{a} libabsl20230802{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libcups2t64{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{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} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libfuse-dev{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu-dev{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-dev{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libmodule-runtime-perl{a} libmoo-perl{a} libncbi-vdb-dev{a} libncbi-vdb3{a} libncbi-wvdb-dev{a} libncbi-wvdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnpth0t64{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libre2-11{a} libre2-dev{a} libreadline8t64{a} librhash0{a} librole-tiny-perl{a} librtmp1{a} libsam-extract-dev{a} libsam-extract3{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol-dev{a} libsharpyuv0{a} libssh2-1t64{a} libssl-dev{a} libsub-quote-perl{a} libsz2{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvulkan1{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{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} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxml2-dev{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} markdown{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tzdata{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 bzip2-doc curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfl-dev libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgmock-dev libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace unzip wget xdg-user-dirs 0 packages upgraded, 293 newly installed, 0 to remove and 0 not upgraded. Need to get 269 MB of archives. After unpacking 905 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b2 [426 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 17 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-2 [94.2 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1+b1 [10.7 MB] Get: 78 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 86 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 93 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.100-1 [1406 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.3-1 [54.9 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 98 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 99 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 143 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.8-1 [36.5 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 154 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.8-1 [8284 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.8-1 [151 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get: 177 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 178 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.17-75 [1068 B] Get: 181 http://deb.debian.org/debian unstable/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.43-6 [119 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.43-6 [363 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.43-6 [701 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 gnupg-utils amd64 2.2.43-6 [500 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.43-6 [523 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.43-6 [248 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 gpg-wks-client amd64 2.2.43-6 [100 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.43-6 [250 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.43-6 [374 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 195 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 198 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 226 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.23.7 [1068 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 javahelper all 0.79 [84.6 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libabsl-dev amd64 20230802.1-4 [1208 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 250 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.8.0-1 [548 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.5-2+b1 [351 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.5-2+b2 [158 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libfuse-dev amd64 2.9.9-8.1 [1021 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 273 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libmagic-dev amd64 1:5.45-3 [118 kB] Get: 275 http://deb.debian.org/debian experimental/main amd64 libmbedcrypto16 amd64 3.6.0-2 [349 kB] Get: 276 http://deb.debian.org/debian experimental/main amd64 libmbedx509-7 amd64 3.6.0-2 [144 kB] Get: 277 http://deb.debian.org/debian experimental/main amd64 libmbedtls21 amd64 3.6.0-2 [231 kB] Get: 278 http://deb.debian.org/debian experimental/main amd64 ncbi-vdb-data all 3.0.9+dfsg-1 [74.0 kB] Get: 279 http://deb.debian.org/debian experimental/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-1 [1176 kB] Get: 280 http://deb.debian.org/debian experimental/main amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-1 [1177 kB] Get: 281 http://deb.debian.org/debian experimental/main amd64 libncbi-wvdb-dev amd64 3.0.9+dfsg-1 [1298 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 283 http://deb.debian.org/debian experimental/main amd64 libncbi-vdb-dev amd64 3.0.9+dfsg-1 [1599 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libre2-11 amd64 20240501-3 [194 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libre2-dev amd64 20240501-3 [249 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libsam-extract3 amd64 3.0.2+dfsg-2+b1 [43.4 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libsam-extract-dev amd64 3.0.2+dfsg-2+b1 [44.8 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg-2 [145 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Fetched 269 MB in 9s (28.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19716 files and directories currently installed.) Preparing to unpack .../0-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../1-binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package m4. Preparing to unpack .../2-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 29 09:28:44 UTC 2024. Universal Time is now: Wed May 29 09:28:44 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.11-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-2) ... No schema files found: doing nothing. Setting up libasound2t64:amd64 (1.2.11-1+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.43-6) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.2.1-3) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b1) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-4+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up d-shlibs (0.106) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libsepol-dev:amd64 (3.5-2+b1) ... Setting up libpcsclite1:amd64 (2.2.3-1) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libglapi-mesa:amd64 (24.0.8-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14.1.0-1) ... Setting up libvulkan1:amd64 (1.3.280.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up at-spi2-common (2.52.0-1) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up bison (2:3.8.2+dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up librole-tiny-perl (2.002004-1) ... Setting up ncbi-vdb-data (3.0.9+dfsg-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libsam-extract3:amd64 (3.0.2+dfsg-2+b1) ... Setting up cmake-data (3.29.3-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libmbedcrypto16:amd64 (3.6.0-2) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up liburi-perl (5.28-1) ... Setting up libsam-extract-dev:amd64 (3.0.2+dfsg-2+b1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up markdown (1.0.1-12) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... 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 (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libre2-11:amd64 (20240501-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up flex (2.6.4-8.2+b2) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up libselinux1-dev:amd64 (3.5-2+b2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.17.0-2) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libaec-dev:amd64 (1.1.3-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libnss3:amd64 (2:3.100-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libfuse-dev:amd64 (2.9.9-8.1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.17.0-2) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libxml2-dev:amd64 (2.12.7+dfsg-2) ... Setting up libmbedx509-7:amd64 (3.6.0-2) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.17.0-2) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libabsl-dev:amd64 (20230802.1-4) ... Setting up libmbedtls21:amd64 (3.6.0-2) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.17.0-2) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.43-6) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libre2-dev:amd64 (20240501-3) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.43-6) ... Setting up gnupg-utils (2.2.43-6) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up gpg-agent (2.2.43-6) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.43-6) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.8-1) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.43-6) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libcurl4-openssl-dev:amd64 (8.8.0-1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... 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 cmake (3.29.3-1+b1) ... Setting up libncbi-wvdb-dev:amd64 (3.0.9+dfsg-1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libglx-mesa0:amd64 (24.0.8-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.43-6) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.3) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up gnupg (2.2.43-6) ... Setting up libncbi-vdb-dev:amd64 (3.0.9+dfsg-1) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-3.1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-all (3.11.8-1) ... Setting up libhdf5-dev (1.10.10+repack-3.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up dh-python (6.20240422) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up javahelper (0.79) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian: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:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... 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 default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.17-75) ... Setting up default-jdk (2:1.17-75) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../sra-sdk_3.0.9+dfsg-3_source.changes dpkg-buildpackage: info: source package sra-sdk dpkg-buildpackage: info: source version 3.0.9+dfsg-3 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Aaron M. Ucko dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake \ --with python3,javahelper,jh_maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_auto_clean rm -rf ngs/ngs-java/x86_64-linux-gnu rm -rf ngs/ngs-bam/x86_64-linux-gnu rm -f ngs/ngs-bam/Makefile.config rm -f ngs/ngs-bam/Makefile.config.install.linux.x86_64.prl rm -f ngs/ngs-bam/Makefile.config.linux.x86_64 rm -f ngs/ngs-bam/reconfigure rm -rf ngs/ngs-sdk/ngs/unix/generic rm -rf ngs/ngs-sdk/x86_64-linux-gnu rm -rf ngs/ngs-python/build ngs/ngs-python/dist rm -rf ngs/ngs-python/ngs.egg-info find test tools -name actual -type d | xargs -rt rm -rf rm -rf ngs/ngs-*/examples/actual/* rm -fv test/*/*/tmp.kfg rm -rf libs/ngs-vdb/test/data/SparseFragmentBlobs rm -rf test/external/vdb-dump/data test/loaders/bam-load/out.sra find tools/loaders/general-loader/test -name input | xargs -rt rm -rf rm -f ngs/ngs-sdk/examples/actual.txt rm debian/libngs-jni.links rm: cannot remove 'debian/libngs-jni.links': No such file or directory make[1]: [debian/rules:45: override_dh_auto_clean] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_autoreconf_clean -O--buildsystem=cmake jh_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake \ --with python3,javahelper,jh_maven_repo_helper dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_auto_configure -- -DVDB_LIBDIR=/usr/lib/x86_64-linux-gnu \ -DVDB_INCDIR=/usr/include/ncbi-vdb -DBUILD_TOOLS_LOADERS=ON \ -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON \ -DCMAKE_SKIP_RPATH=ON -DTOOLS_ONLY=OFF \ -DCOMPILER_OPTION_SSE42_SUPPORTED=FALSE cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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 -DVDB_LIBDIR=/usr/lib/x86_64-linux-gnu -DVDB_INCDIR=/usr/include/ncbi-vdb -DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON -DCMAKE_SKIP_RPATH=ON -DTOOLS_ONLY=OFF -DCOMPILER_OPTION_SSE42_SUPPORTED=FALSE .. CMAKE_VERSION=3.29.3 -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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 CMake Deprecation Warning at build/env.cmake:32 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:62 (include) BUILD_TOOLS_INTERNAL=ON BUILD_TOOLS_LOADERS=ON BUILD_TOOLS_TEST_TOOLS=ON TOOLS_ONLY=OFF VERSION=3.0.9 -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /usr/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.12.7") LIBXML2_INCLUDE_DIR=/usr/include/libxml2 LIBXML2_LIBRARIES=/usr/lib/x86_64-linux-gnu/libxml2.so -- Found Java: /usr/bin/java (found version "17.0.11") found components: Development -- Found Python3: /usr/bin/python3 (found version "3.11.9") found components: Interpreter Using ncbi-vdb interfaces: /usr/include/ncbi-vdb Using ncbi-vdb binary libraries: /usr/lib/x86_64-linux-gnu -- Looking for C++ include mbedtls/md.h -- Looking for C++ include mbedtls/md.h - not found RUN_SANITIZER_TESTS: OFF -- Found JNI: /usr/lib/jvm/default-java/include found components: AWT JVM -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE RE2_FOUND=FALSE SharQ is not built: ZLIB_FOUND=TRUE BZip2_FOUND=TRUE Threads_FOUND=TRUE RE2_FOUND=FALSE -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.10") found components: C RE2_FOUND=FALSE -- Configuring done (2.7s) -- Generating done (1.3s) 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/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' jh_linkjars -O--buildsystem=cmake dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sra-sdk-3.0.9+dfsg -B/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/depend make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/depend make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/depend make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/depend make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/shared /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/shared /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/shared/CMakeFiles/tk-version.dir/DependInfo.cmake "--color=" make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/depend make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/depend make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/DependInfo.cmake "--color=" make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs/CMakeFiles/ngs.dir/DependInfo.cmake "--color=" make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/depend make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake "--color=" make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/depend make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/kxml /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/kxml 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ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build make -f 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o [ 0%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o [ 0%] Building C object shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o [ 0%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o [ 0%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o [ 0%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"shared\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o -MF CMakeFiles/tk-version.dir/toolkit.vers.c.o.d -o CMakeFiles/tk-version.dir/toolkit.vers.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/shared/toolkit.vers.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o -MF CMakeFiles/ngs.dir/NCBI-NGS.c.o.d -o CMakeFiles/ngs.dir/NCBI-NGS.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NCBI-NGS.c make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/build make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build [ 0%] Building C object ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o -MF CMakeFiles/ngs-jni.dir/jni_Manager.c.o.d -o CMakeFiles/ngs-jni.dir/jni_Manager.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni/jni_Manager.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o -MF CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_PileupEvent.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-py\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o -MF CMakeFiles/ngs-py.dir/py_Manager.c.o.d -o CMakeFiles/ngs-py.dir/py_Manager.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py/py_Manager.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && /usr/bin/javadoc -d /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/build [ 0%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 0%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -MF CMakeFiles/ngs.dir/CSRA1_Pileup.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_Pileup.c [ 0%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -MF CMakeFiles/ngs.dir/CSRA1_Alignment.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_Alignment.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ReadCollectionItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -MF CMakeFiles/ngs.dir/CSRA1_Reference.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Reference.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_Reference.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_ReadCollection.c [ 0%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o [ 0%] Building C object libs/kxml/CMakeFiles/kxml.dir/xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ReadCollectionItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/libxml2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/kxml/CMakeFiles/kxml.dir/xml.c.o -MF CMakeFiles/kxml.dir/xml.c.o.d -o CMakeFiles/kxml.dir/xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/kxml/xml.c [ 1%] Building C object libs/loader/CMakeFiles/loader.dir/progressbar.c.o [ 2%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o cd 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/progressbar.c [ 2%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp [ 2%] Building Java objects for ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib -d /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -h ./jni @/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources [ 2%] Linking C static library ../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -P CMakeFiles/tk-version.dir/cmake_clean_target.cmake [ 2%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o -MF CMakeFiles/ngs.dir/CSRA1_Read.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/CSRA1_Read.c [ 2%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o -MF CMakeFiles/ngs-jni.dir/jni_String.c.o.d -o CMakeFiles/ngs-jni.dir/jni_String.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni/jni_String.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -E cmake_link_script CMakeFiles/tk-version.dir/link.txt --verbose=1 [ 2%] Building C object libs/loader/CMakeFiles/loader.dir/loader-file.c.o /usr/bin/ar qc ../ilib/libtk-version.a "CMakeFiles/tk-version.dir/toolkit.vers.c.o" cd 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CMakeFiles/ngs-py.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-py.dir/link.txt --verbose=1 [ 2%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk 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-D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -MF CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o.d -o CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni/jni_ErrorMsg.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 2%] Built target ngs-py make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/DependInfo.cmake "--color=" [ 2%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/PileupItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/EBI_ReferenceSequence.c make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o [ 3%] Linking C static library ../../../ilib/libngs-jni.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -MF CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o.d -o CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_makedb.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -P CMakeFiles/ngs-jni.dir/cmake_clean_target.cmake [ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o cd 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object libs/loader/CMakeFiles/loader.dir/loader-meta.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/loader-meta.c.o -MF CMakeFiles/loader.dir/loader-meta.c.o.d -o CMakeFiles/loader.dir/loader-meta.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/loader-meta.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-jni.dir/link.txt --verbose=1 [ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/SRA_DB_ReadCollection.c /usr/bin/ar qc ../../../ilib/libngs-jni.a "CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "CMakeFiles/ngs-jni.dir/jni_String.c.o" "CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" [ 3%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp /usr/bin/ranlib ../../../ilib/libngs-jni.a [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o -MF CMakeFiles/ngs.dir/SRA_Read.c.o.d -o CMakeFiles/ngs.dir/SRA_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/SRA_Read.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-jni make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake "--color=" [ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o [ 4%] Building C object libs/loader/CMakeFiles/loader.dir/queue-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/libxml2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o -MF CMakeFiles/kxml.dir/xtoc-parsexml.c.o.d -o CMakeFiles/kxml.dir/xtoc-parsexml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/kxml/xtoc-parsexml.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/queue-file.c.o -MF CMakeFiles/loader.dir/queue-file.c.o.d -o CMakeFiles/loader.dir/queue-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/queue-file.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 4%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3vdb.c [ 4%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -MF CMakeFiles/ascp.dir/ascp.c.o.d -o CMakeFiles/ascp.dir/ascp.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp/ascp.c [ 4%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/FragmentBlobIterator.cpp [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/SRA_ReadGroup.c [ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/PileupEventItf.cpp [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/SRA_ReadGroupInfo.c [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o cd 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4%] Building C object libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o [ 4%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o [ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -MF CMakeFiles/kxml.dir/xtoc.c.o.d -o CMakeFiles/kxml.dir/xtoc.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/kxml/xtoc.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/SRA_ReferenceSequence.c [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o cd 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files for package gov.nih.nlm.ncbi.ngs... [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -MF CMakeFiles/ngs.dir/NGS_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ReadCollection.c [ 6%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/FragmentBlob.cpp [ 6%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -MF CMakeFiles/ngs.dir/NGS_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_PileupEvent.c Loading source files for package ngs... [ 6%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -MF CMakeFiles/ngs.dir/NGS_Pileup.c.o.d -o CMakeFiles/ngs.dir/NGS_Pileup.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Pileup.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -Wno-unused-result -MD -MT libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o -MF CMakeFiles/ascp.dir/unix/connect.c.o.d -o CMakeFiles/ascp.dir/unix/connect.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp/unix/connect.c [ 6%] Building C object libs/loader/CMakeFiles/loader.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/common-reader.c.o -MF CMakeFiles/loader.dir/common-reader.c.o.d -o CMakeFiles/loader.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/common-reader.c [ 6%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp [ 6%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ReferenceItf.cpp [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -MF CMakeFiles/ngs.dir/NGS_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ReadGroup.c [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb 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-D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -MF CMakeFiles/ngs.dir/NGS_Reference.c.o.d -o CMakeFiles/ngs.dir/NGS_Reference.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Reference.c [ 6%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o cd 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ReferenceSequence.c [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -MF CMakeFiles/ngs.dir/NGS_Read.c.o.d -o CMakeFiles/ngs.dir/NGS_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Read.c [ 6%] Building C object libs/loader/CMakeFiles/loader.dir/common-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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[ 7%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o [ 7%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/VdbReference.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC 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-fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp [ 8%] Building C object libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o -MF CMakeFiles/ascp.dir/linux/ascp-path.c.o.d -o CMakeFiles/ascp.dir/linux/ascp-path.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ascp/linux/ascp-path.c [ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o -MF CMakeFiles/ngs.dir/NGS_Fragment.c.o.d -o CMakeFiles/ngs.dir/NGS_Fragment.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Fragment.c [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o cd 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Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -MF CMakeFiles/ngs.dir/NGS_Cursor.c.o.d -o CMakeFiles/ngs.dir/NGS_Cursor.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Cursor.c [ 9%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o [ 9%] Linking C static library ../../ilib/libascp.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 [ 10%] Linking CXX executable ../../../test-bin/ngs-makedb cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-makedb.dir/link.txt --verbose=1 [ 10%] Linking C static library ../../ilib/libkxml.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o" -o ../../../test-bin/ngs-makedb -Wl,-Bstatic -lktst -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm /usr/bin/ar qc ../../ilib/libascp.a CMakeFiles/ascp.dir/ascp.c.o CMakeFiles/ascp.dir/unix/connect.c.o "CMakeFiles/ascp.dir/linux/ascp-path.c.o" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 /usr/bin/ranlib ../../ilib/libascp.a /usr/bin/ar qc ../../ilib/libkxml.a CMakeFiles/kxml.dir/xml.c.o "CMakeFiles/kxml.dir/xtoc-parsexml.c.o" CMakeFiles/kxml.dir/xtoc.c.o [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o -MF CMakeFiles/ngs.dir/NGS_String.c.o.d -o CMakeFiles/ngs.dir/NGS_String.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_String.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/ranlib ../../ilib/libkxml.a [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -MF CMakeFiles/ngs.dir/NGS_Refcount.c.o.d -o CMakeFiles/ngs.dir/NGS_Refcount.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Refcount.c [ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp [ 10%] Built target ascp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/diagnose /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake "--color=" [ 10%] Built target kxml make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 10%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp [ 10%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 10%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/diagnose/diagnose.c [ 10%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o -MF CMakeFiles/general-writer.dir/general-writer.cpp.o.d -o CMakeFiles/general-writer.dir/general-writer.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/general-writer.cpp [ 10%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o -MF CMakeFiles/diagnose.dir/endpoint.c.o.d -o CMakeFiles/diagnose.dir/endpoint.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/diagnose/endpoint.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o -MF CMakeFiles/ngs.dir/NGS_Id.c.o.d -o CMakeFiles/ngs.dir/NGS_Id.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_Id.c [ 11%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp [ 11%] Built target ngs-makedb make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch/CMakeFiles/prefetch.dir/DependInfo.cmake "--color=" [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -MF CMakeFiles/ngs.dir/NGS_ErrBlock.c.o.d -o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ErrBlock.c [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/ReferenceBlob.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/DependInfo.cmake "--color=" [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o [ 11%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_FragmentBlob.c [ 11%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o -MF CMakeFiles/prefetch.dir/kfile-no-q.c.o.d -o CMakeFiles/prefetch.dir/kfile-no-q.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch/kfile-no-q.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/ReferenceBlobIterator.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/VdbAlignment.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -MF CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o.d -o CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_cpp.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -MF CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o.d -o CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/NGS-VDB.cpp [ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_FragmentBlobIterator.c [ 12%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o -MF CMakeFiles/prefetch.dir/PrfMain.c.o.d -o CMakeFiles/prefetch.dir/PrfMain.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch/PrfMain.c [ 12%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/AlignmentItf.cpp [ 12%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp [ 12%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui.dir/DependInfo.cmake "--color=" [ 12%] Building C object libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -MF CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o.d -o CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/utf8-like-int-codec.c [ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlob.c [ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/fastq-dump.dir/DependInfo.cmake "--color=" [ 13%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o -MF CMakeFiles/tui.dir/dir_dlg.c.o.d -o CMakeFiles/tui.dir/dir_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/dir_dlg.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' Creating destination directory: "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/" [ 13%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o -MF CMakeFiles/fastq-dump.dir/factory.c.o.d -o CMakeFiles/fastq-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/factory.c [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o [ 13%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/mmarray.c.o -MF CMakeFiles/loader.dir/mmarray.c.o.d -o CMakeFiles/loader.dir/mmarray.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/mmarray.c [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlobIterator.c Building index for all the packages and classes... [ 13%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/reference-writer.c.o -MF CMakeFiles/loader.dir/reference-writer.c.o.d -o CMakeFiles/loader.dir/reference-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/reference-writer.c Standard Doclet version 17.0.11+9-Debian-1 Building tree for all the packages and classes... [ 13%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o -MF CMakeFiles/prefetch.dir/prefetch.c.o.d -o CMakeFiles/prefetch.dir/prefetch.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch/prefetch.c [ 14%] Building C object libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -MF CMakeFiles/loader.dir/sequence-writer.c.o.d -o CMakeFiles/loader.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/loader/sequence-writer.c [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o -MF CMakeFiles/ngs.dir/VByteBlob.c.o.d -o CMakeFiles/ngs.dir/VByteBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs/VByteBlob.c [ 15%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ReadGroupItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... [ 15%] Linking CXX static library ../../ilib/libngs-vdb.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -P CMakeFiles/ngs-vdb.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-vdb.dir/link.txt --verbose=1 [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp [ 15%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o -MF CMakeFiles/tui.dir/eventring.c.o.d -o CMakeFiles/tui.dir/eventring.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/eventring.c /usr/bin/ar qc ../../ilib/libngs-vdb.a "CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o" "CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o" [ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp /usr/bin/ranlib ../../ilib/libngs-vdb.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 16%] Built target ngs-vdb /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend static int all = primaryAlignment | secondaryAlignment; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/depend /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ [ 16%] Linking C static library ../../../ilib/libngs.a /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/illumina-dump.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs.dir/link.txt --verbose=1 [ 16%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o -MF CMakeFiles/sff-dump.dir/factory.c.o.d -o CMakeFiles/sff-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/factory.c /usr/bin/ar qc ../../../ilib/libngs.a "CMakeFiles/ngs.dir/NCBI-NGS.c.o" CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o CMakeFiles/ngs.dir/CSRA1_Reference.c.o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o CMakeFiles/ngs.dir/CSRA1_Read.c.o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o CMakeFiles/ngs.dir/SRA_Statistics.c.o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_Read.c.o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Statistics.c.o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o CMakeFiles/ngs.dir/NGS_Pileup.c.o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o CMakeFiles/ngs.dir/NGS_Alignment.c.o CMakeFiles/ngs.dir/NGS_Reference.c.o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Read.c.o CMakeFiles/ngs.dir/NGS_Fragment.c.o CMakeFiles/ngs.dir/NGS_Cursor.c.o CMakeFiles/ngs.dir/NGS_Refcount.c.o CMakeFiles/ngs.dir/NGS_String.c.o CMakeFiles/ngs.dir/NGS_Id.c.o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o CMakeFiles/ngs.dir/VByteBlob.c.o [ 16%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o -MF CMakeFiles/illumina-dump.dir/factory.c.o.d -o CMakeFiles/illumina-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/factory.c make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/abi-dump.dir/DependInfo.cmake "--color=" [ 16%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o -MF CMakeFiles/fastq-dump.dir/fasta_dump.c.o.d -o CMakeFiles/fastq-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/fasta_dump.c make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/DependInfo.cmake "--color=" [ 16%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o -MF CMakeFiles/tui.dir/file_dlg.c.o.d -o CMakeFiles/tui.dir/file_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/file_dlg.c [ 16%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o /usr/bin/ranlib ../../../ilib/libngs.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 17%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o -MF CMakeFiles/sra-pileup.dir/dyn_string.c.o.d -o CMakeFiles/sra-pileup.dir/dyn_string.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/dyn_string.c [ 17%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o -MF CMakeFiles/abi-dump.dir/factory.c.o.d -o CMakeFiles/abi-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/factory.c [ 17%] Built target ngs make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/depend [ 18%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ReadItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sam-dump.dir/DependInfo.cmake "--color=" [ 18%] Linking C static library ../../ilib/libloader.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o [ 18%] Linking CXX static library ../../../../ilib/libtui_cpp.a [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o /usr/bin/ar qc ../../ilib/libloader.a CMakeFiles/loader.dir/progressbar.c.o "CMakeFiles/loader.dir/loader-file.c.o" "CMakeFiles/loader.dir/loader-meta.c.o" "CMakeFiles/loader.dir/queue-file.c.o" "CMakeFiles/loader.dir/alignment-writer.c.o" "CMakeFiles/loader.dir/common-reader.c.o" "CMakeFiles/loader.dir/common-writer.c.o" CMakeFiles/loader.dir/mmarray.c.o "CMakeFiles/loader.dir/reference-writer.c.o" "CMakeFiles/loader.dir/sequence-writer.c.o" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui_cpp.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o -MF CMakeFiles/tui.dir/line_policy.c.o.d -o CMakeFiles/tui.dir/line_policy.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/line_policy.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o -MF CMakeFiles/sam-dump.dir/inputfiles.c.o.d -o CMakeFiles/sam-dump.dir/inputfiles.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/inputfiles.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... /usr/bin/ranlib ../../ilib/libloader.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui_cpp.dir/link.txt --verbose=1 [ 18%] Built target loader make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/depend /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ [ 18%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /usr/bin/ar qc ../../../../ilib/libtui_cpp.a CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ /usr/bin/ranlib ../../../../ilib/libtui_cpp.a Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 18%] Built target tui_cpp make -f tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build.make tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 18%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o -MF CMakeFiles/fasterq-dump.dir/helper.c.o.d -o CMakeFiles/fasterq-dump.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/helper.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build.make tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/build Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -MF CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o.d -o CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/cmdline_cmn.c public final static String NCBI_VDB = "ncbi-ngs"; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o [ 18%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o -MF CMakeFiles/tui.dir/screen.c.o.d -o CMakeFiles/tui.dir/screen.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/screen.c [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-context.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o -MF CMakeFiles/sam-dump.dir/perf_log.c.o.d -o CMakeFiles/sam-dump.dir/perf_log.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/perf_log.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ [ 18%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o -MF CMakeFiles/fastq-dump.dir/core.c.o.d -o CMakeFiles/fastq-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... [ 18%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o -MF CMakeFiles/sff-dump.dir/fasta_dump.c.o.d -o CMakeFiles/sff-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/fasta_dump.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... [ 18%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o -MF CMakeFiles/illumina-dump.dir/fasta_dump.c.o.d -o CMakeFiles/illumina-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/fasta_dump.c [ 18%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/FragmentItf.cpp [ 18%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o -MF CMakeFiles/abi-dump.dir/fasta_dump.c.o.d -o CMakeFiles/abi-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/fasta_dump.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c:1011:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1011 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... [ 18%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o -MF CMakeFiles/sam-dump.dir/rna_splice_log.c.o.d -o CMakeFiles/sam-dump.dir/rna_splice_log.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/rna_splice_log.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o -MF CMakeFiles/tui.dir/string_cache.c.o.d -o CMakeFiles/tui.dir/string_cache.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/string_cache.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... [ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp [ 18%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Read.java:79: warning: no comment cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp static int aligned = fullyAligned | partiallyAligned; ^ [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -MF CMakeFiles/sra-pileup.dir/out_redir.c.o.d -o CMakeFiles/sra-pileup.dir/out_redir.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/out_redir.c [ 18%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp [ 18%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o -MF CMakeFiles/illumina-dump.dir/core.c.o.d -o CMakeFiles/illumina-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o -MF CMakeFiles/sra-pileup.dir/perf_log.c.o.d -o CMakeFiles/sra-pileup.dir/perf_log.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/perf_log.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c:1011:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1011 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 18%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/StatisticsItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -MF CMakeFiles/sam-dump.dir/sam-dump-opts.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump-opts.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-dump-opts.c [ 18%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o -MF CMakeFiles/fasterq-dump.dir/arg_helper.c.o.d -o CMakeFiles/fasterq-dump.dir/arg_helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/arg_helper.c [ 18%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o -MF CMakeFiles/abi-dump.dir/core.c.o.d -o CMakeFiles/abi-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c [ 18%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o -MF CMakeFiles/sra-pileup.dir/reref.c.o.d -o CMakeFiles/sra-pileup.dir/reref.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/reref.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... [ 18%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o -MF CMakeFiles/sff-dump.dir/core.c.o.d -o CMakeFiles/sff-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... [ 18%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o -MF CMakeFiles/tui.dir/tui.c.o.d -o CMakeFiles/tui.dir/tui.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui.c [ 18%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c:1011:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1011 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... [ 19%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/core.c:1011:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1011 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Note: ngs/itf/Refcount.java uses or overrides a deprecated API. Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index.html... Note: Recompile with -Xlint:deprecation for details. [ 19%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o -MF CMakeFiles/fastq-dump.dir/fastq.c.o.d -o CMakeFiles/fastq-dump.dir/fastq.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/fastq.c Building index for all classes... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o [ 19%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o -MF CMakeFiles/tui.dir/tui_dlg.c.o.d -o CMakeFiles/tui.dir/tui_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_dlg.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -MF CMakeFiles/fasterq-dump.dir/dflt_defline.c.o.d -o CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/dflt_defline.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... [ 19%] Generating CMakeFiles/ngs-java.dir/java_class_filelist Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index-all.html... cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp [ 19%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o -MF CMakeFiles/illumina-dump.dir/illumina.c.o.d -o CMakeFiles/illumina-dump.dir/illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/illumina.c [ 19%] Creating Java archive ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar @java_class_filelist [ 19%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -MF CMakeFiles/fasterq-dump.dir/tool_ctx.c.o.d -o CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/tool_ctx.c Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... [ 19%] Linking CXX static library ../../ilib/libgeneral-writer.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -P CMakeFiles/general-writer.dir/cmake_clean_target.cmake [ 19%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o 44 warnings [ 19%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/StringItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o -MF CMakeFiles/sra-pileup.dir/cg_tools.c.o.d -o CMakeFiles/sra-pileup.dir/cg_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/cg_tools.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-writer.dir/link.txt --verbose=1 [ 19%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp /usr/bin/ar qc ../../ilib/libgeneral-writer.a "CMakeFiles/general-writer.dir/general-writer.cpp.o" "CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o" /usr/bin/ranlib ../../ilib/libgeneral-writer.a /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/tool_ctx.c: In function 'tctx_extract_short_accession': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/tool_ctx.c:348:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 348 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 19%] Linking C static library ../../ilib/libdiagnose.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -P CMakeFiles/diagnose.dir/cmake_clean_target.cmake [ 19%] Built target general-writer make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o -MF CMakeFiles/abi-dump.dir/abi.c.o.d -o CMakeFiles/abi-dump.dir/abi.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-dump/abi.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -E cmake_link_script CMakeFiles/diagnose.dir/link.txt --verbose=1 [ 19%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp [ 19%] Built target ngs-doc_javadoc /usr/bin/ar qc ../../ilib/libdiagnose.a CMakeFiles/diagnose.dir/diagnose.c.o CMakeFiles/diagnose.dir/endpoint.c.o make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/DependInfo.cmake "--color=" [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp /usr/bin/ranlib ../../ilib/libdiagnose.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG 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tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/DependInfo.cmake "--color=" [ 19%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/main.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/Refcount.cpp [ 19%] Building CXX object tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -MF CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o.d -o CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-validate/check-corrupt.cpp [ 19%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 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-I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp [ 19%] Built target ngs-java [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-hdr.c [ 20%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o [ 20%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o cd 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-std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/check-redact.c.o -MF CMakeFiles/vdb-validate.dir/check-redact.c.o.d -o CMakeFiles/vdb-validate.dir/check-redact.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-validate/check-redact.c [ 20%] Linking C executable ../../../bin/illumina-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-dump.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-dump.dir/factory.c.o" "CMakeFiles/illumina-dump.dir/fasta_dump.c.o" "CMakeFiles/illumina-dump.dir/core.c.o" "CMakeFiles/illumina-dump.dir/illumina.c.o" -o ../../../bin/illumina-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o -MF CMakeFiles/sra-pileup.dir/report_deletes.c.o.d -o CMakeFiles/sra-pileup.dir/report_deletes.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/report_deletes.c [ 20%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ErrorMsg.cpp [ 20%] Linking C executable ../../../bin/abi-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-dump.dir/link.txt --verbose=1 [ 20%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-dump.3.0.9 /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/inspector.c: In function 'insp_report': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/inspector.c:1165:14: warning: 'res' may be used uninitialized [-Wmaybe-uninitialized] 1165 | rc = KOutMsg( "... is %s\n", s_acc_type ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/inspector.c:248:18: note: 'res' was declared here 248 | const char * res; | ^~~ /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-dump.dir/factory.c.o" "CMakeFiles/abi-dump.dir/fasta_dump.c.o" "CMakeFiles/abi-dump.dir/core.c.o" "CMakeFiles/abi-dump.dir/abi.c.o" -o ../../../bin/abi-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-dump illumina-dump.3.0.9 [ 20%] Linking C executable ../../../bin/sff-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3.0.9 illumina-dump.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-dump.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3 illumina-dump /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-dump.dir/factory.c.o" "CMakeFiles/sff-dump.dir/fasta_dump.c.o" "CMakeFiles/sff-dump.dir/core.c.o" "CMakeFiles/sff-dump.dir/sff.c.o" -o ../../../bin/sff-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 20%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o [ 20%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o [ 20%] Built target illumina-dump make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg 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-ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o -MF CMakeFiles/prefetch.dir/PrfRetrier.c.o.d -o CMakeFiles/prefetch.dir/PrfRetrier.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch/PrfRetrier.c [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o -MF CMakeFiles/sra-pileup.dir/ref_regions.c.o.d -o CMakeFiles/sra-pileup.dir/ref_regions.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/ref_regions.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-dump.3.0.9 [ 20%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv abi-dump abi-dump.3.0.9 cd 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/sbuffer.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr1.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr1.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-hdr1.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3.0.9 abi-dump.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3 abi-dump make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-dump.3.0.9 [ 20%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o [ 20%] Built target abi-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -MF CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o.d -o CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-decrypt/vdb-decrypt.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sff-dump sff-dump.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3.0.9 sff-dump.3 [ 21%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3 sff-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp [ 21%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Read.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Read.cpp [ 21%] Built target sff-dump make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 22%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o -MF CMakeFiles/fasterq-dump.dir/err_msg.c.o.d -o CMakeFiles/fasterq-dump.dir/err_msg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/err_msg.c make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build [ 22%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o -MF CMakeFiles/prefetch.dir/PrfOutFile.c.o.d -o CMakeFiles/prefetch.dir/PrfOutFile.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/prefetch/PrfOutFile.c [ 22%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -MF CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o.d -o CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-decrypt/vdb-encrypt.c [ 22%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o -MF CMakeFiles/tui.dir/tui_dlg_helper.c.o.d -o CMakeFiles/tui.dir/tui_dlg_helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_dlg_helper.c [ 22%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/adapter/ErrBlock.cpp [ 22%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp [ 22%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp [ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o -MF CMakeFiles/sra-pileup.dir/4na_ascii.c.o.d -o CMakeFiles/sra-pileup.dir/4na_ascii.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/4na_ascii.c [ 22%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb 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CMakeFiles/fasterq-dump.dir/file_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/file_tools.c [ 22%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp [ 23%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o -MF CMakeFiles/tui.dir/tui_menu.c.o.d -o CMakeFiles/tui.dir/tui_menu.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_menu.c [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker_0.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/ref_walker_0.c [ 24%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp [ 25%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PackageItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp [ 25%] Linking C executable ../../../bin/fastq-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-dump.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-dump.dir/factory.c.o" "CMakeFiles/fastq-dump.dir/fasta_dump.c.o" "CMakeFiles/fastq-dump.dir/core.c.o" "CMakeFiles/fastq-dump.dir/fastq.c.o" -o ../../../bin/fastq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 25%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp [ 25%] Linking C executable ../../../bin/vdb-decrypt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-decrypt.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o" "CMakeFiles/vdb-decrypt.dir/shared.c.o" -o ../../../bin/vdb-decrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 25%] Linking CXX executable ../../../bin/check-corrupt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/check-corrupt.dir/link.txt --verbose=1 [ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o -MF CMakeFiles/fasterq-dump.dir/var_fmt.c.o.d -o CMakeFiles/fasterq-dump.dir/var_fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/var_fmt.c [ 25%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o" -o ../../../bin/check-corrupt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-adapt-c++.dir/link.txt --verbose=1 [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/ref_walker.c /usr/bin/ar qc ../../../ilib/libngs-adapt-c++.a "CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o -MF CMakeFiles/sam-dump.dir/sam-aligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-aligned.c [ 25%] Linking C executable ../../../bin/vdb-encrypt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-encrypt.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-decrypt.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-decrypt vdb-decrypt.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3.0.9 vdb-decrypt.3 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o" "CMakeFiles/vdb-encrypt.dir/shared.c.o" -o ../../../bin/vdb-encrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a [ 25%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3 vdb-decrypt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-dump.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-dump fastq-dump.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 25%] Built target vdb-decrypt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3.0.9 fastq-dump.3 make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/srapath /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath/CMakeFiles/srapath.dir/DependInfo.cmake "--color=" [ 25%] Linking C executable ../../../bin/prefetch [ 25%] Built target ngs-adapt-c++ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/prefetch.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3 fastq-dump make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 fastq-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 25%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/prefetch.dir/kfile-no-q.c.o" CMakeFiles/prefetch.dir/PrfMain.c.o CMakeFiles/prefetch.dir/prefetch.c.o CMakeFiles/prefetch.dir/PrfRetrier.c.o CMakeFiles/prefetch.dir/PrfOutFile.c.o -o ../../../bin/prefetch ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 25%] Built target fastq-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o -MF CMakeFiles/srapath.dir/helper.c.o.d -o CMakeFiles/srapath.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/srapath/helper.c make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat/CMakeFiles/sra-stat.dir/DependInfo.cmake "--color=" [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o -MF CMakeFiles/sra-pileup.dir/walk_debug.c.o.d -o CMakeFiles/sra-pileup.dir/walk_debug.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/walk_debug.c [ 25%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f check-corrupt.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-py -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv check-corrupt check-corrupt.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3.0.9 check-corrupt.3 [ 25%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/assembly-statistics.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration 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'/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-encrypt.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-encrypt vdb-encrypt.3.0.9 [ 25%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3.0.9 vdb-encrypt.3 [ 25%] Built target check-corrupt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc 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-I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o -MF CMakeFiles/sra-pileup.dir/pileup_counters.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_counters.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/pileup_counters.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/rcexplain/CMakeFiles/rcexplain.dir/build.make tools/external/rcexplain/CMakeFiles/rcexplain.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd 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Building C object tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/util\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o -MF CMakeFiles/rcexplain.dir/rcexplain.c.o.d -o 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ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': [ 26%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o [ 26%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o -MF CMakeFiles/tui.dir/tui_std_dlg.c.o.d -o CMakeFiles/tui.dir/tui_std_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_std_dlg.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 26%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o 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[-Wmisleading-indentation] 102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o -MF CMakeFiles/fasterq-dump.dir/temp_dir.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_dir.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/temp_dir.c [ 26%] Building C object tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o [ 27%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/align-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o -MF CMakeFiles/align-info.dir/align-info.c.o.d -o CMakeFiles/align-info.dir/align-info.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/align-info/align-info.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o -MF CMakeFiles/srapath.dir/line_iter.c.o.d -o CMakeFiles/srapath.dir/line_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/srapath/line_iter.c [ 27%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o [ 27%] Linking C executable ../../../bin/rcexplain cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cmake -E cmake_link_script CMakeFiles/rcexplain.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/rcexplain.dir/rcexplain.c.o -o ../../../bin/rcexplain /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c:11540: /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c:102377:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~~~~~ [ 27%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb 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[-Wmisleading-indentation] 102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~ [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o -MF CMakeFiles/sra-pileup.dir/pileup_indels.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_indels.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/pileup_indels.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c:102378:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~~~~~ [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -MF CMakeFiles/sra-pileup.dir/pileup_varcount.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_varcount.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/pileup_varcount.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f rcexplain.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv rcexplain rcexplain.3.0.9 [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o -MF CMakeFiles/sra-pileup.dir/pileup_stat.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_stat.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/pileup_stat.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3.0.9 rcexplain.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3 rcexplain [ 28%] Linking C executable ../../../bin/vdb-validate cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-validate.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 28%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o -MF CMakeFiles/srapath.dir/repository-mgr.c.o.d -o CMakeFiles/srapath.dir/repository-mgr.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/srapath/repository-mgr.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget.c.o -MF CMakeFiles/tui.dir/tui_widget.c.o.d -o CMakeFiles/tui.dir/tui_widget.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget.c [ 28%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o -MF CMakeFiles/sra-pileup.dir/pileup_v2.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_v2.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/pileup_v2.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/test-sra/CMakeFiles/test-sra.dir/build.make tools/external/test-sra/CMakeFiles/test-sra.dir/build make[3]: Entering directory 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-I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/test-sra/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -MF CMakeFiles/test-sra.dir/unix/PrintOS.c.o.d -o CMakeFiles/test-sra.dir/unix/PrintOS.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/test-sra/unix/PrintOS.c [ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb 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vdb-validate.3.0.9 vdb-validate.3 [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3 vdb-validate cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/DependInfo.cmake "--color=" [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o -MF CMakeFiles/fasterq-dump.dir/index.c.o.d -o CMakeFiles/fasterq-dump.dir/index.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/index.c [ 29%] Linking CXX static library ../../../../ilib/libngs-bind-python.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build [ 29%] Linking C executable ../../../bin/align-info [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-info.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -MF CMakeFiles/fasterq-dump.dir/lookup_writer.c.o.d -o CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/lookup_writer.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-info.dir/align-info.c.o" -o ../../../bin/align-info /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-python.dir/link.txt --verbose=1 [ 30%] Linking C executable ../../../bin/kdbmeta [ 30%] Building C object tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /usr/bin/cmake -E cmake_link_script CMakeFiles/kdbmeta.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cache-mgr\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o -MF CMakeFiles/cache-mgr.dir/cache-mgr.c.o.d -o CMakeFiles/cache-mgr.dir/cache-mgr.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c /usr/bin/ar qc ../../../../ilib/libngs-bind-python.a "CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" [ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/kdbmeta.dir/kdbmeta.c.o -o ../../../bin/kdbmeta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o -MF CMakeFiles/fasterq-dump.dir/lookup_reader.c.o.d -o CMakeFiles/fasterq-dump.dir/lookup_reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/lookup_reader.c [ 31%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp /usr/bin/ranlib ../../../../ilib/libngs-bind-python.a make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/depend [ 31%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool/CMakeFiles/sratools.dir/DependInfo.cmake "--color=" [ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o -MF CMakeFiles/sam-dump.dir/md_flag.c.o.d -o CMakeFiles/sam-dump.dir/md_flag.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/md_flag.c [ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_report': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:702:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 702 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:699:17: note: 'data' declared here 699 | report_data data; | ^~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:696:41: note: 'octx' declared here 696 | static rc_t perform_report( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_unlock': [ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:905:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 905 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:902:17: note: 'data' declared here 902 | unlock_data data; | ^~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o -MF CMakeFiles/fasterq-dump.dir/locked_value.c.o.d -o CMakeFiles/fasterq-dump.dir/locked_value.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/locked_value.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:899:41: note: 'octx' declared here 899 | static rc_t perform_unlock( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_clear': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:990:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 990 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:987:16: note: 'data' declared here 987 | clear_data data; | ^~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/cache-mgr/cache-mgr.c:984:40: note: 'octx' declared here 984 | static rc_t perform_clear( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o -MF CMakeFiles/fasterq-dump.dir/locked_file_list.c.o.d -o CMakeFiles/fasterq-dump.dir/locked_file_list.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/locked_file_list.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o -MF CMakeFiles/sam-dump.dir/cg_tools.c.o.d -o CMakeFiles/sam-dump.dir/cg_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/cg_tools.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-info.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv align-info align-info.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdbmeta.3.0.9 [ 31%] Built target ngs-bind-python make -f tools/external/sra-info/CMakeFiles/sra-info.dir/build.make tools/external/sra-info/CMakeFiles/sra-info.dir/depend [ 31%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv kdbmeta kdbmeta.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong 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"--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_printer.c.o -MF CMakeFiles/fasterq-dump.dir/file_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/file_printer.c.o -c 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o -MF CMakeFiles/sam-dump.dir/sam-dump.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-dump.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE 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-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o -MF CMakeFiles/tui.dir/tui_widget_button.c.o.d -o CMakeFiles/tui.dir/tui_widget_button.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_button.c [ 32%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o -MF CMakeFiles/samview.dir/bam.c.o.d -o CMakeFiles/samview.dir/bam.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SAM_Dump_Main': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/sam-dump.c:4387:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4387 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o -MF CMakeFiles/fasterq-dump.dir/sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/sorter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/sorter.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o [ 32%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o -MF CMakeFiles/tui.dir/tui_widget_checkbox.c.o.d -o CMakeFiles/tui.dir/tui_widget_checkbox.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_checkbox.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp [ 32%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/sra-info.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-info && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-info/CMakeFiles/sra-info.dir/sra-info.cpp.o -MF CMakeFiles/sra-info.dir/sra-info.cpp.o.d -o CMakeFiles/sra-info.dir/sra-info.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-info/sra-info.cpp [ 32%] Linking C executable ../../../bin/cache-mgr cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cmake -E cmake_link_script CMakeFiles/cache-mgr.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/cache-mgr.dir/cache-mgr.c.o" -o ../../../bin/cache-mgr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 32%] Linking C executable ../../../bin/sra-pileup cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-pileup.dir/link.txt --verbose=1 [ 33%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp [ 33%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o [ 33%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o [ 33%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-pileup.dir/dyn_string.c.o" "CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o" "CMakeFiles/sra-pileup.dir/out_redir.c.o" "CMakeFiles/sra-pileup.dir/perf_log.c.o" "CMakeFiles/sra-pileup.dir/reref.c.o" "CMakeFiles/sra-pileup.dir/cg_tools.c.o" "CMakeFiles/sra-pileup.dir/report_deletes.c.o" "CMakeFiles/sra-pileup.dir/ref_regions.c.o" "CMakeFiles/sra-pileup.dir/4na_ascii.c.o" "CMakeFiles/sra-pileup.dir/ref_walker_0.c.o" "CMakeFiles/sra-pileup.dir/ref_walker.c.o" "CMakeFiles/sra-pileup.dir/walk_debug.c.o" "CMakeFiles/sra-pileup.dir/pileup_counters.c.o" "CMakeFiles/sra-pileup.dir/pileup_index.c.o" "CMakeFiles/sra-pileup.dir/pileup_indels.c.o" "CMakeFiles/sra-pileup.dir/pileup_varcount.c.o" "CMakeFiles/sra-pileup.dir/pileup_stat.c.o" "CMakeFiles/sra-pileup.dir/pileup_v2.c.o" "CMakeFiles/sra-pileup.dir/sra-pileup.c.o" -o ../../../bin/sra-pileup /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o -MF CMakeFiles/tui.dir/tui_widget_grid.c.o.d -o CMakeFiles/tui.dir/tui_widget_grid.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_grid.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-helper.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ErrBlock.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f cache-mgr.3.0.9 [ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -MF CMakeFiles/fasterq-dump.dir/cmn_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/cmn_iter.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv cache-mgr cache-mgr.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3.0.9 cache-mgr.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3 cache-mgr make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 33%] Built target cache-mgr make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar 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-I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o -MF CMakeFiles/srapath.dir/srapath.c.o.d -o CMakeFiles/srapath.dir/srapath.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/srapath/srapath.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3.0.9 sra-pileup.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3 sra-pileup cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 sra-pileup-driver [ 34%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time 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-I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_inputline.c.o -MF CMakeFiles/tui.dir/tui_widget_inputline.c.o.d -o CMakeFiles/tui.dir/tui_widget_inputline.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_inputline.c [ 34%] Built target sra-pileup make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/depend [ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -MF CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/raw_read_iter.c [ 34%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam.c.o -MF CMakeFiles/bam-load.dir/bam.c.o.d -o CMakeFiles/bam-load.dir/bam.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c [ 34%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/build [ 34%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-jni -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 34%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/dispatch/ErrorMsg.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-c++.dir/link.txt --verbose=1 [ 34%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o -MF CMakeFiles/kar+.dir/kar-path.c.o.d -o CMakeFiles/kar+.dir/kar-path.c.o -c 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"CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" [ 34%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o -MF CMakeFiles/sam-dump.dir/dyn_string.c.o.d -o CMakeFiles/sam-dump.dir/dyn_string.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-pileup/dyn_string.c /usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a [ 34%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o -MF CMakeFiles/kar.dir/kar-args.c.o.d -o CMakeFiles/kar.dir/kar-args.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar-args.c [ 34%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o -MF CMakeFiles/fasterq-dump.dir/special_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/special_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/special_iter.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 34%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o -MF CMakeFiles/tui.dir/tui_widget_label.c.o.d -o CMakeFiles/tui.dir/tui_widget_label.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_label.c [ 34%] Built target ngs-bind-c++ make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+meta.dir/DependInfo.cmake "--color=" [ 34%] Linking C executable ../../../bin/srapath [ 35%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cmake -E cmake_link_script CMakeFiles/srapath.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o -MF CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/fq_seq_ua_iter.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/srapath.dir/helper.c.o CMakeFiles/srapath.dir/line_iter.c.o "CMakeFiles/srapath.dir/repository-mgr.c.o" CMakeFiles/srapath.dir/services.c.o CMakeFiles/srapath.dir/cgi_request.c.o CMakeFiles/srapath.dir/srapath.c.o -o ../../../bin/srapath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 35%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o [ 35%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+args.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o -MF CMakeFiles/kar+meta.dir/kar+util.c.o.d -o CMakeFiles/kar+meta.dir/kar+util.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar+util.c [ 35%] Linking CXX static library ../../../../ilib/libngs-bind-java.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+args.c.o -MF CMakeFiles/kar+.dir/kar+args.c.o.d -o CMakeFiles/kar+.dir/kar+args.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar+args.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -P CMakeFiles/ngs-bind-java.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-java.dir/link.txt --verbose=1 [ 35%] Building C object tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -MF CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o.d -o CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/dump-blob-boundaries.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 36%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o -MF CMakeFiles/tui.dir/tui_widget_progress.c.o.d -o CMakeFiles/tui.dir/tui_widget_progress.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_progress.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/ar qc ../../../../ilib/libngs-bind-java.a "CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" [ 36%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o -MF CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/fq_seq_csra_iter.c [ 36%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o [ 37%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o -MF CMakeFiles/sra-sort.dir/caps.c.o.d -o CMakeFiles/sra-sort.dir/caps.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/caps.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-formats.c [ 37%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o /usr/bin/ranlib ../../../../ilib/libngs-bind-java.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o -MF CMakeFiles/kar.dir/kar.c.o.d -o CMakeFiles/kar.dir/kar.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f srapath.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv srapath srapath.3.0.9 [ 37%] Linking CXX static library ../../../ilib/libngs-disp.a [ 37%] Built target ngs-bind-java make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3.0.9 srapath.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3 srapath cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake [ 37%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o -MF CMakeFiles/tui.dir/tui_widget_radiobox.c.o.d -o CMakeFiles/tui.dir/tui_widget_radiobox.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_radiobox.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 srapath-driver cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-disp.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/ar qc ../../../ilib/libngs-disp.a "CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "CMakeFiles/ngs-disp.dir/VTable.cpp.o" "CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" [ 37%] Built target srapath make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/DependInfo.cmake "--color=" /usr/bin/ranlib ../../../ilib/libngs-disp.a [ 37%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o -MF CMakeFiles/sra-sort-cg.dir/caps.c.o.d -o CMakeFiles/sra-sort-cg.dir/caps.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/caps.c [ 37%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o -MF CMakeFiles/kar+.dir/kar+print.c.o.d -o CMakeFiles/kar+.dir/kar+print.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar+print.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 38%] Linking C executable ../../../bin/dump-blob-boundaries [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/dump-blob-boundaries.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c:1777:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1777 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c:1697:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1697 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ [ 38%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o -MF CMakeFiles/sra-sort.dir/mem.c.o.d -o CMakeFiles/sra-sort.dir/mem.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/mem.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o -MF CMakeFiles/fastqloader.dir/spot-assembler.c.o.d -o CMakeFiles/fastqloader.dir/spot-assembler.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/spot-assembler.c [ 38%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o [ 38%] Built target ngs-disp /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -Wl,-z,relro -Wl,-z,now "CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o" -o ../../../bin/dump-blob-boundaries /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -MF CMakeFiles/tui.dir/tui_widget_spin_edit.c.o.d -o CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_spin_edit.c make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/sff-load.dir/DependInfo.cmake "--color=" [ 38%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-redir.c [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o -MF CMakeFiles/kar+meta.dir/kar+meta.c.o.d -o CMakeFiles/kar+meta.dir/kar+meta.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar+meta.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/build [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/align_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/align_iter.c.o -MF CMakeFiles/fasterq-dump.dir/align_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/align_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/align_iter.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o -MF CMakeFiles/sra-sort-cg.dir/mem.c.o.d -o CMakeFiles/sra-sort-cg.dir/mem.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/mem.c [ 38%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o -MF CMakeFiles/tui.dir/tui_widget_string_list.c.o.d -o CMakeFiles/tui.dir/tui_widget_string_list.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_string_list.c [ 39%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o -MF CMakeFiles/sff-load.dir/pstring.c.o.d -o CMakeFiles/sff-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/pstring.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f dump-blob-boundaries.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv dump-blob-boundaries dump-blob-boundaries.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3.0.9 dump-blob-boundaries.3 [ 39%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o -MF CMakeFiles/sra-sort.dir/membank.c.o.d -o CMakeFiles/sra-sort.dir/membank.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/membank.c [ 39%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-fastq.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3 dump-blob-boundaries make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 39%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o -MF CMakeFiles/sra-sort-cg.dir/membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/membank.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/membank.c [ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o -MF CMakeFiles/kar+.dir/kar+util.c.o.d -o CMakeFiles/kar+.dir/kar+util.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/kar/kar+util.c [ 40%] Built target dump-blob-boundaries make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/fastq-load.dir/DependInfo.cmake "--color=" [ 40%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o -MF CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/simple_fasta_iter.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 40%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -MF CMakeFiles/tui.dir/tui_widget_tabhdr.c.o.d -o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/tui_widget_tabhdr.c [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 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tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o -MF CMakeFiles/sra-sort.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort.dir/paged-membank.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/paged-membank.c [ 41%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o -MF CMakeFiles/fasterq-dump.dir/db_join.c.o.d -o CMakeFiles/fasterq-dump.dir/db_join.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/db_join.c [ 41%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o -MF CMakeFiles/fastqloader.dir/common-writer.c.o.d -o CMakeFiles/fastqloader.dir/common-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/common-writer.c [ 41%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/.. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o -MF CMakeFiles/tui.dir/linux/systui.c.o.d -o CMakeFiles/tui.dir/linux/systui.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/tui/linux/systui.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/paged-mmapbank.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o -MF CMakeFiles/sra-sort-cg.dir/except.c.o.d -o CMakeFiles/sra-sort-cg.dir/except.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/except.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/paged-mmapbank.c [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o -MF CMakeFiles/fastq-load.dir/common-xml.c.o.d -o CMakeFiles/fastq-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c:1777:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1777 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/bam.c:1697:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1697 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ [ 41%] Linking C executable ../../../bin/kar+meta cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+meta.dir/link.txt --verbose=1 [ 41%] Linking C executable ../../../bin/sra-stat cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-stat.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/kar+meta.dir/kar+util.c.o CMakeFiles/kar+meta.dir/kar+meta.c.o -o ../../../bin/kar+meta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/idx-mapping.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-stat.dir/assembly-statistics.c.o" "CMakeFiles/sra-stat.dir/sra.c.o" "CMakeFiles/sra-stat.dir/sra-stat.c.o" -o ../../../bin/sra-stat ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o cd 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-f -s sra-stat.3 sra-stat [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o -MF CMakeFiles/sra-sort.dir/except.c.o.d -o CMakeFiles/sra-sort.dir/except.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/except.c [ 42%] Built target kar+meta make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/srf-load.dir/DependInfo.cmake "--color=" [ 42%] Built target sra-stat [ 42%] Linking C static library ../../../../ilib/libtui.a make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/abi-load.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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CMakeFiles/tui.dir/tui_widget_spin_edit.c.o CMakeFiles/tui.dir/tui_widget_string_list.c.o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o CMakeFiles/tui.dir/linux/systui.c.o [ 43%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function 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-Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/col-pair.c /usr/bin/ranlib ../../../../ilib/libtui.a [ 43%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort.dir/idx-mapping.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/idx-mapping.c [ 43%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o -MF CMakeFiles/samview.dir/sam.c.o.d -o CMakeFiles/samview.dir/sam.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/sam.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 44%] Linking C executable ../../../bin/test-sra cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra.dir/link.txt --verbose=1 [ 44%] Built target tui make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/illumina-load.dir/DependInfo.cmake "--color=" /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra.dir/test-sra.c.o" "CMakeFiles/test-sra.dir/unix/PrintOS.c.o" -o ../../../bin/test-sra ../../../ilib/libascp.a ../../../ilib/libdiagnose.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 44%] Linking C executable ../../../bin/sam-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-dump.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build [ 44%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sam-dump.dir/inputfiles.c.o" "CMakeFiles/sam-dump.dir/perf_log.c.o" "CMakeFiles/sam-dump.dir/rna_splice_log.c.o" "CMakeFiles/sam-dump.dir/sam-dump-opts.c.o" "CMakeFiles/sam-dump.dir/out_redir.c.o" "CMakeFiles/sam-dump.dir/sam-hdr.c.o" "CMakeFiles/sam-dump.dir/sam-hdr1.c.o" "CMakeFiles/sam-dump.dir/matecache.c.o" "CMakeFiles/sam-dump.dir/read_fkt.c.o" "CMakeFiles/sam-dump.dir/sam-aligned.c.o" "CMakeFiles/sam-dump.dir/sam-unaligned.c.o" "CMakeFiles/sam-dump.dir/md_flag.c.o" "CMakeFiles/sam-dump.dir/cg_tools.c.o" "CMakeFiles/sam-dump.dir/sam-dump.c.o" "CMakeFiles/sam-dump.dir/sam-dump3.c.o" "CMakeFiles/sam-dump.dir/dyn_string.c.o" -o ../../../bin/sam-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o -MF CMakeFiles/fastqloader.dir/sequence-writer.c.o.d -o CMakeFiles/fastqloader.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/sequence-writer.c [ 44%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-inspect.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-inspect.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-inspect.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-inspect.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-inspect.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/pstring.c.o -MF CMakeFiles/illumina-load.dir/pstring.c.o.d -o CMakeFiles/illumina-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/pstring.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o -MF CMakeFiles/abi-load.dir/common-xml.c.o.d -o CMakeFiles/abi-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c [ 45%] Linking C executable ../../../bin/kar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar.dir/link.txt --verbose=1 [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o -MF CMakeFiles/srf-load.dir/common-xml.c.o.d -o CMakeFiles/srf-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar.dir/kar-path.c.o" "CMakeFiles/kar.dir/kar-args.c.o" CMakeFiles/kar.dir/kar.c.o -o ../../../bin/kar /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-sra.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv test-sra test-sra.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3.0.9 test-sra.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3 test-sra make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o -MF CMakeFiles/fastq-load.dir/experiment-xml.c.o.d -o CMakeFiles/fastq-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/experiment-xml.c [ 45%] Built target test-sra make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/helicos-load.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sam-dump.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sam-dump sam-dump.3.0.9 make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3.0.9 sam-dump.3 [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o -MF CMakeFiles/sra-sort.dir/map-file.c.o.d -o CMakeFiles/sra-sort.dir/map-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/map-file.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/pstring.c.o -MF CMakeFiles/helicos-load.dir/pstring.c.o.d -o CMakeFiles/helicos-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/pstring.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3 sam-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 sam-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar.3.0.9 [ 45%] Built target sam-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv kar kar.3.0.9 make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3.0.9 kar.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3 kar make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o [ 46%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o -MF CMakeFiles/fastqloader.dir/common-reader.c.o.d -o CMakeFiles/fastqloader.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/common-reader.c make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o -MF CMakeFiles/illumina-load.dir/common-xml.c.o.d -o CMakeFiles/illumina-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/DependInfo.cmake "--color=" [ 46%] Built target kar make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load/CMakeFiles/cg-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/build [ 46%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/row-set.c [ 46%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o [ 46%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o -MF CMakeFiles/pacbio-loadxml.dir/pstring.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/pstring.c [ 46%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o -MF CMakeFiles/vdb-dump.dir/vdb_info.c.o.d -o CMakeFiles/vdb-dump.dir/vdb_info.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o -MF CMakeFiles/fasterq-dump.dir/tbl_join.c.o.d -o CMakeFiles/fasterq-dump.dir/tbl_join.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/tbl_join.c [ 47%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/cg-load.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/cg-load.c.o -MF CMakeFiles/cg-load.dir/cg-load.c.o.d -o CMakeFiles/cg-load.dir/cg-load.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/cg-load.c [ 47%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/hdf5/hdf5arrayfile.c [ 47%] Linking C executable ../../../bin/kar+ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar+.dir/kar-path.c.o" CMakeFiles/kar+.dir/kar+args.c.o CMakeFiles/kar+.dir/kar+print.c.o CMakeFiles/kar+.dir/kar+util.c.o CMakeFiles/kar+.dir/kar+.c.o -o ../../../bin/kar+ /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o -MF CMakeFiles/helicos-load.dir/common-xml.c.o.d -o CMakeFiles/helicos-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c [ 47%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o -MF CMakeFiles/sratools.dir/config.cpp.o.d -o CMakeFiles/sratools.dir/config.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/config.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/cg-load.c: In function 'DB_Fini': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/cg-load.c:229:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 229 | if( (rc = KLoaderMeta_Write(node, p->argv0, __DATE__, "Complete Genomics", KAppVersion())) != 0 ) { | ^~~~~~~~ [ 47%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o -MF CMakeFiles/fastqloader.dir/fastq-reader.c.o.d -o CMakeFiles/fastqloader.dir/fastq-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/fastq-reader.c [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/common-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/common-xml.c [ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/simple-row-set.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv kar+ kar+.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3.0.9 kar+.3 [ 47%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o -MF CMakeFiles/bam-load.dir/sam.c.o.d -o CMakeFiles/bam-load.dir/sam.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/sam.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3 kar+ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 48%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/hdf5/hdf5dir.c [ 48%] Built target kar+ make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/CMakeFiles/general-loader.dir/DependInfo.cmake "--color=" [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o -MF CMakeFiles/sff-load.dir/run-xml.c.o.d -o CMakeFiles/sff-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o -MF CMakeFiles/srf-load.dir/experiment-xml.c.o.d -o CMakeFiles/srf-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/experiment-xml.c [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o -MF CMakeFiles/abi-load.dir/experiment-xml.c.o.d -o CMakeFiles/abi-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/experiment-xml.c In function 'inspect_line', inlined from 'parse_buffer' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c:521:29, inlined from 'get_meta_bam_hdr' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c:550:21, inlined from 'get_meta_info' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c:589:5: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c:496:38: warning: 'line' may be used uninitialized [-Wmaybe-uninitialized] 496 | if ( ( len > 3 ) && ( '@' == line[ 0 ] ) ) { | ~~~~^~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c: In function 'get_meta_info': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb_info.c:507:12: note: 'line' was declared here 507 | char * line; | ^~~~ make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/mapping-row-set.c [ 48%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o -MF CMakeFiles/general-loader.dir/general-loader.cpp.o.d -o CMakeFiles/general-loader.dir/general-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/general-loader.cpp [ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o -MF CMakeFiles/sra-sort.dir/col-pair.c.o.d -o CMakeFiles/sra-sort.dir/col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/col-pair.c [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o -MF CMakeFiles/illumina-load.dir/experiment-xml.c.o.d -o CMakeFiles/illumina-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/experiment-xml.c [ 48%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/hdf5/hdf5file.c [ 48%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c [ 48%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o -MF CMakeFiles/fastq-load.dir/run-xml.c.o.d -o CMakeFiles/fastq-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o -MF CMakeFiles/fasterq-dump.dir/temp_registry.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_registry.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/temp_registry.c [ 48%] Linking C executable ../../../bin/samview cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview.dir/link.txt --verbose=1 [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o -MF CMakeFiles/helicos-load.dir/experiment-xml.c.o.d -o CMakeFiles/helicos-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/experiment-xml.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/samview.dir/bam.c.o CMakeFiles/samview.dir/sam.c.o CMakeFiles/samview.dir/samview.c.o -o ../../../bin/samview /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lz [ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/sorting-row-set.c [ 49%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-evidence-intervals.c [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump.c [ 49%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o -MF CMakeFiles/fasterq-dump.dir/copy_machine.c.o.d -o CMakeFiles/fasterq-dump.dir/copy_machine.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/copy_machine.c [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o -MF CMakeFiles/sff-load.dir/loader-file.c.o.d -o CMakeFiles/sff-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview.3.0.9 [ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG 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tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv samview samview.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o -MF CMakeFiles/sra-sort.dir/row-set.c.o.d -o CMakeFiles/sra-sort.dir/row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/row-set.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3.0.9 samview.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3 samview make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 50%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o -MF CMakeFiles/pacbio-load.dir/pl-tools.c.o.d -o CMakeFiles/pacbio-load.dir/pl-tools.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-tools.c [ 50%] Built target samview make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/DependInfo.cmake "--color=" [ 50%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o -MF CMakeFiles/bam-load.dir/alignment-writer.c.o.d -o CMakeFiles/bam-load.dir/alignment-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/alignment-writer.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f 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-ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o -MF CMakeFiles/abi-load.dir/run-xml.c.o.d -o CMakeFiles/abi-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -MF CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o.d -o CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp [ 51%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/multi_writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/multi_writer.c.o -MF CMakeFiles/fasterq-dump.dir/multi_writer.c.o.d -o CMakeFiles/fasterq-dump.dir/multi_writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/multi_writer.c [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o [ 51%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o -MF CMakeFiles/srf-load.dir/run-xml.c.o.d -o CMakeFiles/srf-load.dir/run-xml.c.o -c 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CMakeFiles/sra-sort.dir/simple-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/simple-row-set.c [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o -MF CMakeFiles/fastq-load.dir/loader-file.c.o.d -o CMakeFiles/fastq-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c [ 51%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o -MF CMakeFiles/sratools.dir/command-line.cpp.o.d -o CMakeFiles/sratools.dir/command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/command-line.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o -MF CMakeFiles/illumina-load.dir/run-xml.c.o.d -o CMakeFiles/illumina-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c [ 51%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/../database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); | ^~~~~~~~ [ 51%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o [ 51%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk 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tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o [ 51%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char 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-ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o -MF CMakeFiles/sff-load.dir/sra-writer.c.o.d -o CMakeFiles/sff-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c [ 51%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix 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tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o -MF CMakeFiles/abi-load.dir/loader-file.c.o.d -o CMakeFiles/abi-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c [ 52%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/ref_inventory.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/run-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c [ 52%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix 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-D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o -MF CMakeFiles/helicos-load.dir/run-xml.c.o.d -o CMakeFiles/helicos-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/run-xml.c [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o cd 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tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o -MF CMakeFiles/fastq-load.dir/sra-writer.c.o.d -o CMakeFiles/fastq-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c [ 52%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o [ 52%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/tbl-pair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort.dir/sorting-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/sorting-row-set.c [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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--verbose=1 [ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o -MF CMakeFiles/bam-load.dir/sequence-writer.c.o.d -o CMakeFiles/bam-load.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/sequence-writer.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-view-spec.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-inspect.c.o" "CMakeFiles/vdb-dump.dir/vdb_info.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump.c.o" -o ../../../bin/vdb-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o -MF CMakeFiles/illumina-load.dir/loader-file.c.o.d -o CMakeFiles/illumina-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c [ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o -MF CMakeFiles/sra-sort.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort.dir/meta-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/meta-pair.c [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o cd 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53%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o -MF CMakeFiles/srf-load.dir/loader-fmt.c.o.d -o CMakeFiles/srf-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-fmt.c [ 53%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -MF CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o.d -o CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-basecalls_cmn.c [ 53%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -MF CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o.d -o CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/fasterq-dump/fasterq-dump.c [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o -MF CMakeFiles/abi-load.dir/sra-writer.c.o.d -o CMakeFiles/abi-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c [ 53%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o -MF CMakeFiles/fastqloader.dir/id2name.c.o.d -o CMakeFiles/fastqloader.dir/id2name.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/id2name.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-dump.3.0.9 [ 53%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o -MF CMakeFiles/pacbio-load.dir/pl-sequence.c.o.d -o CMakeFiles/pacbio-load.dir/pl-sequence.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-sequence.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-dump vdb-dump.3.0.9 [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o [ 53%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o -MF CMakeFiles/illumina-load.dir/loader-fmt.c.o.d -o CMakeFiles/illumina-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-fmt.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o -MF CMakeFiles/cg-load.dir/factory-mappings.c.o.d -o CMakeFiles/cg-load.dir/factory-mappings.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3.0.9 vdb-dump.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3 vdb-dump [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o -MF CMakeFiles/srf-load.dir/sra-writer.c.o.d -o CMakeFiles/srf-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 vdb-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 54%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o -MF CMakeFiles/bam-load.dir/loader-imp.c.o.d -o CMakeFiles/bam-load.dir/loader-imp.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/loader-imp.c [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-file.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/db-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/db-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/db-pair.c [ 56%] Built target vdb-dump cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o -MF CMakeFiles/helicos-load.dir/loader-file.c.o.d -o CMakeFiles/helicos-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-file.c make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 56%] Linking C static library ../../../ilib/libfastqloader.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -P CMakeFiles/fastqloader.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o -MF CMakeFiles/illumina-load.dir/sra-writer.c.o.d -o CMakeFiles/illumina-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastqloader.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o -MF CMakeFiles/sra-sort.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort.dir/dir-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/dir-pair.c [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o [ 56%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o -MF CMakeFiles/abi-load.dir/loader.c.o.d -o CMakeFiles/abi-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -MF CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o.d -o CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/test-gw-dumper.cpp /usr/bin/ar qc ../../../ilib/libfastqloader.a "CMakeFiles/fastqloader.dir/spot-assembler.c.o" "CMakeFiles/fastqloader.dir/common-writer.c.o" "CMakeFiles/fastqloader.dir/sequence-writer.c.o" "CMakeFiles/fastqloader.dir/common-reader.c.o" "CMakeFiles/fastqloader.dir/fastq-reader.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o" CMakeFiles/fastqloader.dir/id2name.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings15_Read': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:248:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 248 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:225:14: note: 'tmp' declared here 225 | char tmp[2]; | ^~~ /usr/bin/ranlib ../../../ilib/libfastqloader.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 56%] Linking C executable ../../../bin/fasterq-dump [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-fmt.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fasterq-dump.dir/link.txt --verbose=1 [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o -MF CMakeFiles/helicos-load.dir/loader-fmt.c.o.d -o CMakeFiles/helicos-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader-fmt.c [ 56%] Built target fastqloader /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/fasterq-dump.dir/helper.c.o" "CMakeFiles/fasterq-dump.dir/arg_helper.c.o" "CMakeFiles/fasterq-dump.dir/dflt_defline.c.o" "CMakeFiles/fasterq-dump.dir/tool_ctx.c.o" "CMakeFiles/fasterq-dump.dir/inspector.c.o" "CMakeFiles/fasterq-dump.dir/sbuffer.c.o" "CMakeFiles/fasterq-dump.dir/err_msg.c.o" "CMakeFiles/fasterq-dump.dir/file_tools.c.o" "CMakeFiles/fasterq-dump.dir/var_fmt.c.o" "CMakeFiles/fasterq-dump.dir/flex_printer.c.o" "CMakeFiles/fasterq-dump.dir/temp_dir.c.o" "CMakeFiles/fasterq-dump.dir/progress_thread.c.o" "CMakeFiles/fasterq-dump.dir/cleanup_task.c.o" "CMakeFiles/fasterq-dump.dir/index.c.o" "CMakeFiles/fasterq-dump.dir/lookup_writer.c.o" "CMakeFiles/fasterq-dump.dir/lookup_reader.c.o" "CMakeFiles/fasterq-dump.dir/locked_file_list.c.o" "CMakeFiles/fasterq-dump.dir/locked_value.c.o" "CMakeFiles/fasterq-dump.dir/file_printer.c.o" "CMakeFiles/fasterq-dump.dir/merge_sorter.c.o" "CMakeFiles/fasterq-dump.dir/sorter.c.o" "CMakeFiles/fasterq-dump.dir/cmn_iter.c.o" "CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o" "CMakeFiles/fasterq-dump.dir/special_iter.c.o" "CMakeFiles/fasterq-dump.dir/fq_seq_ua_iter.c.o" "CMakeFiles/fasterq-dump.dir/fq_seq_csra_iter.c.o" "CMakeFiles/fasterq-dump.dir/align_iter.c.o" "CMakeFiles/fasterq-dump.dir/simple_fasta_iter.c.o" "CMakeFiles/fasterq-dump.dir/db_join.c.o" "CMakeFiles/fasterq-dump.dir/tbl_join.c.o" "CMakeFiles/fasterq-dump.dir/temp_registry.c.o" "CMakeFiles/fasterq-dump.dir/copy_machine.c.o" "CMakeFiles/fasterq-dump.dir/multi_writer.c.o" "CMakeFiles/fasterq-dump.dir/concatenator.c.o" "CMakeFiles/fasterq-dump.dir/ref_inventory.c.o" "CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o" -o ../../../bin/fasterq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/depend [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o -MF CMakeFiles/srf-load.dir/loader.c.o.d -o CMakeFiles/srf-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings22_Read': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:311:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 311 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:287:14: note: 'tmp' declared here 287 | char tmp[2]; | ^~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 56%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/makeinputs.cpp.o [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/makeinputs.cpp.o -MF CMakeFiles/makeinputs.dir/makeinputs.cpp.o.d -o CMakeFiles/makeinputs.dir/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/makeinputs.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o -MF CMakeFiles/sff-load.dir/writer-454.c.o.d -o CMakeFiles/sff-load.dir/writer-454.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-454.c [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -MF CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o.d -o CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-stringop-truncation -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o -MF CMakeFiles/helicos-load.dir/sra-writer.c.o.d -o CMakeFiles/helicos-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f fasterq-dump.3.0.9 /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings25_Read': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:382:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 382 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-mappings.c:358:14: note: 'tmp' declared here 358 | char tmp[2]; | ^~~ [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o -MF CMakeFiles/illumina-load.dir/loader.c.o.d -o CMakeFiles/illumina-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv fasterq-dump fasterq-dump.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3.0.9 fasterq-dump.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3 fasterq-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 fasterq-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort.dir/tbl-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/tbl-pair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/glob-poslen.c [ 56%] Built target fasterq-dump make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 56%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/formatter.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-info && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-info/CMakeFiles/sra-info.dir/formatter.cpp.o -MF CMakeFiles/sra-info.dir/formatter.cpp.o.d -o CMakeFiles/sra-info.dir/formatter.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-info/formatter.cpp [ 57%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o -MF CMakeFiles/sratools.dir/run-source.cpp.o.d -o CMakeFiles/sratools.dir/run-source.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/run-source.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 57%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o -MF CMakeFiles/fastq-load.dir/writer-illumina.c.o.d -o CMakeFiles/fastq-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-illumina.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/loader-imp.c:3453:44: warning: "/*" within comment [-Wcomment] 3453 | int const logLevel = klogWarn; /*G.assembleWithSecondary ? klogWarn : klogErr; | /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/loader-imp.c:4163:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4163 | rc = KLoaderMeta_Write(node, progName, __DATE__, "BAM", KAppVersion()); | ^~~~~~~~ [ 57%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o -MF CMakeFiles/pacbio-load.dir/pl-consensus.c.o.d -o CMakeFiles/pacbio-load.dir/pl-consensus.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-consensus.c [ 57%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o [ 57%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o -MF CMakeFiles/cg-load.dir/factory-reads.c.o.d -o CMakeFiles/cg-load.dir/factory-reads.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-reads.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -MF CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o.d -o CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/sff-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-ion-torrent.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/poslen-col-pair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o -MF CMakeFiles/helicos-load.dir/loader.c.o.d -o CMakeFiles/helicos-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/loader.c:889:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 889 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 58%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o -MF CMakeFiles/pacbio-load.dir/pl-passes.c.o.d -o CMakeFiles/pacbio-load.dir/pl-passes.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-passes.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o -MF CMakeFiles/sff-load.dir/sff-fmt.c.o.d -o CMakeFiles/sff-load.dir/sff-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/sff-fmt.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o -MF CMakeFiles/sra-sort.dir/db-pair.c.o.d -o CMakeFiles/sra-sort.dir/db-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/db-pair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o -MF CMakeFiles/fastq-load.dir/writer-454.c.o.d -o CMakeFiles/fastq-load.dir/writer-454.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-454.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/ref-alignid-col.c [ 59%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -MF CMakeFiles/cg-load.dir/factory-tag-lfr.c.o.d -o CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/factory-tag-lfr.c [ 59%] Linking CXX executable ../../../../test-bin/test-gw-dumper cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-gw-dumper.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o" -o ../../../../test-bin/test-gw-dumper ../../../../ilib/libgeneral-writer.a [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o -MF CMakeFiles/srf-load.dir/srf.c.o.d -o CMakeFiles/srf-load.dir/srf.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/srf.c [ 60%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o -MF CMakeFiles/pacbio-load.dir/pl-metrics.c.o.d -o CMakeFiles/pacbio-load.dir/pl-metrics.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-metrics.c [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-ion-torrent.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o -MF CMakeFiles/abi-load.dir/writer-absolid.c.o.d -o CMakeFiles/abi-load.dir/writer-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-absolid.c [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o -MF CMakeFiles/srf-load.dir/srf-fmt.c.o.d -o CMakeFiles/srf-load.dir/srf-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/srf-fmt.c [ 60%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o [ 60%] Linking C executable ../../../bin/sff-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-load.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort.dir/glob-poslen.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/glob-poslen.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-load.dir/pstring.c.o" "CMakeFiles/sff-load.dir/common-xml.c.o" "CMakeFiles/sff-load.dir/experiment-xml.c.o" "CMakeFiles/sff-load.dir/run-xml.c.o" "CMakeFiles/sff-load.dir/loader-file.c.o" "CMakeFiles/sff-load.dir/loader-fmt.c.o" "CMakeFiles/sff-load.dir/sra-writer.c.o" "CMakeFiles/sff-load.dir/loader.c.o" "CMakeFiles/sff-load.dir/writer-454.c.o" "CMakeFiles/sff-load.dir/writer-ion-torrent.c.o" "CMakeFiles/sff-load.dir/sff-fmt.c.o" -o ../../../bin/sff-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 60%] Built target test-gw-dumper make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp: In function 'void run(const char*, bool, const int32_t*, const int32_t*, const int8_t*, int)': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:76:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 76 | delete gw; | ^~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:45:20: note: 'gw' was declared here 45 | GeneralWriter *gw; | ^~ [ 60%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -MF CMakeFiles/sra-sort-cg.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/buff-writer.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 60%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o -MF CMakeFiles/cg-load.dir/f1_3.c.o.d -o CMakeFiles/cg-load.dir/f1_3.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f1_3.c [ 60%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o -MF CMakeFiles/makeinputs.dir/testsource.cpp.o.d -o CMakeFiles/makeinputs.dir/testsource.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp [ 60%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -MF CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o.d -o CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o -MF CMakeFiles/illumina-load.dir/writer-illumina.c.o.d -o CMakeFiles/illumina-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-illumina.c [ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/poslen-col-pair.c [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o -MF CMakeFiles/srf-load.dir/writer-illumina.c.o.d -o CMakeFiles/srf-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-illumina.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sff-load sff-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3.0.9 sff-load.3 [ 61%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o -MF CMakeFiles/cg-load.dir/f1_5.c.o.d -o CMakeFiles/cg-load.dir/f1_5.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f1_5.c [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3 sff-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/pacbio-fmt.c [ 61%] Linking CXX executable ../../../../../test-bin/bio-end-makeinputs make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/bio-end-makeinputs.dir/link.txt --verbose=1 [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o -MF CMakeFiles/fastq-load.dir/fastq-fmt.c.o.d -o CMakeFiles/fastq-load.dir/fastq-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/fastq-fmt.c [ 61%] Built target sff-load /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o" -o ../../../../../test-bin/bio-end-makeinputs ../../../../../ilib/libgeneral-writer.a make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/DependInfo.cmake "--color=" [ 62%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o -MF CMakeFiles/abi-load.dir/absolid-fmt.c.o.d -o CMakeFiles/abi-load.dir/absolid-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/absolid-fmt.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build [ 62%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o -MF CMakeFiles/cg-load.dir/f1_7.c.o.d -o CMakeFiles/cg-load.dir/f1_7.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f1_7.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 63%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -MF CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o.d -o CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/checklookup.cpp [ 63%] Linking C executable ../../../bin/pacbio-loadxml cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-loadxml.dir/link.txt --verbose=1 [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/ref-alignid-col.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/id-mapper-col.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-loadxml.dir/pstring.c.o" "CMakeFiles/pacbio-loadxml.dir/common-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/run-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-file.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o" "CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o" "CMakeFiles/pacbio-loadxml.dir/loader.c.o" "CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o" -o ../../../bin/pacbio-loadxml ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 63%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o -MF CMakeFiles/helicos-load.dir/writer-helicos.c.o.d -o CMakeFiles/helicos-load.dir/writer-helicos.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-helicos.c [ 63%] Built target bio-end-makeinputs make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/vdb-lock /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build [ 64%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o -MF CMakeFiles/cg-load.dir/f2_0.c.o.d -o CMakeFiles/cg-load.dir/f2_0.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f2_0.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o -MF CMakeFiles/illumina-load.dir/illumina-fmt.c.o.d -o CMakeFiles/illumina-load.dir/illumina-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/illumina-fmt.c [ 65%] Building C object tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-lock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o -MF CMakeFiles/vdb-lock.dir/vdb-lock.c.o.d -o CMakeFiles/vdb-lock.dir/vdb-lock.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/vdb-lock/vdb-lock.c [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o [ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o -MF CMakeFiles/pacbio-load.dir/pl-regions.c.o.d -o CMakeFiles/pacbio-load.dir/pl-regions.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-regions.c [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o -MF CMakeFiles/srf-load.dir/ztr-illumina.c.o.d -o CMakeFiles/srf-load.dir/ztr-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/ztr-illumina.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-loadxml.3.0.9 [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-loadxml pacbio-loadxml.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o -MF CMakeFiles/cg-load.dir/f2_2.c.o.d -o CMakeFiles/cg-load.dir/f2_2.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f2_2.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3.0.9 pacbio-loadxml.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3 pacbio-loadxml [ 65%] Linking C executable ../../../bin/abi-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-load.dir/link.txt --verbose=1 [ 65%] Linking C executable ../../../bin/vdb-lock cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-lock.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-load.dir/pstring.c.o" "CMakeFiles/abi-load.dir/common-xml.c.o" "CMakeFiles/abi-load.dir/experiment-xml.c.o" "CMakeFiles/abi-load.dir/run-xml.c.o" "CMakeFiles/abi-load.dir/loader-file.c.o" "CMakeFiles/abi-load.dir/loader-fmt.c.o" "CMakeFiles/abi-load.dir/sra-writer.c.o" "CMakeFiles/abi-load.dir/loader.c.o" "CMakeFiles/abi-load.dir/writer-absolid.c.o" "CMakeFiles/abi-load.dir/absolid-fmt.c.o" -o ../../../bin/abi-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 65%] Built target pacbio-loadxml [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o -MF CMakeFiles/helicos-load.dir/helicos-fmt.c.o.d -o CMakeFiles/helicos-load.dir/helicos-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/helicos-fmt.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/vdb-unlock /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/DependInfo.cmake "--color=" /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-lock.dir/vdb-lock.c.o" -o ../../../bin/vdb-lock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o -MF CMakeFiles/sra-sort-cg.dir/run.c.o.d -o CMakeFiles/sra-sort-cg.dir/run.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/run.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o -MF CMakeFiles/sra-sort.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort.dir/buff-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/buff-writer.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o -MF CMakeFiles/cg-load.dir/f2_4.c.o.d -o CMakeFiles/cg-load.dir/f2_4.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f2_4.c [ 65%] Building C object tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-unlock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -MF CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o.d -o CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/vdb-unlock/vdb-unlock.c [ 65%] Linking C executable ../../../bin/fastq-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-lock.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-load.dir/link.txt --verbose=1 [ 65%] Linking C executable ../../../bin/illumina-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-load.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-lock vdb-lock.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3.0.9 vdb-lock.3 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-load.dir/pstring.c.o" "CMakeFiles/illumina-load.dir/common-xml.c.o" "CMakeFiles/illumina-load.dir/experiment-xml.c.o" "CMakeFiles/illumina-load.dir/run-xml.c.o" "CMakeFiles/illumina-load.dir/loader-file.c.o" "CMakeFiles/illumina-load.dir/loader-fmt.c.o" "CMakeFiles/illumina-load.dir/sra-writer.c.o" "CMakeFiles/illumina-load.dir/loader.c.o" "CMakeFiles/illumina-load.dir/writer-illumina.c.o" "CMakeFiles/illumina-load.dir/illumina-fmt.c.o" -o ../../../bin/illumina-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-load.dir/pstring.c.o" "CMakeFiles/fastq-load.dir/common-xml.c.o" "CMakeFiles/fastq-load.dir/experiment-xml.c.o" "CMakeFiles/fastq-load.dir/run-xml.c.o" "CMakeFiles/fastq-load.dir/loader-file.c.o" "CMakeFiles/fastq-load.dir/loader-fmt.c.o" "CMakeFiles/fastq-load.dir/sra-writer.c.o" "CMakeFiles/fastq-load.dir/loader.c.o" "CMakeFiles/fastq-load.dir/writer-illumina.c.o" "CMakeFiles/fastq-load.dir/writer-454.c.o" "CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o" "CMakeFiles/fastq-load.dir/fastq-fmt.c.o" -o ../../../bin/fastq-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3 vdb-lock make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp: In constructor 'TestSource::Buffer::Buffer(const std::string&, uint32_t, uint32_t, bool)': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp:52:13: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 8 equals destination size [-Wstringop-truncation] 52 | strncpy ( m_header . dad . signature, p_signature . c_str(), sizeof m_header . dad . signature ); | ^ In file included from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc/general-writer/general-writer.hpp:34, from /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:30: In static member function 'static std::size_t std::char_traits::length(const char_type*)', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:648:49, inlined from 'void run(const char*, TestCaseType, const std::string*, int)' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:77:25: /usr/include/c++/13/bits/char_traits.h:399:32: warning: 'db_schema' may be used uninitialized [-Wmaybe-uninitialized] 399 | return __builtin_strlen(__s); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:57:21: note: 'db_schema' was declared here 57 | const char* db_schema; | ^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:101:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 101 | delete gw; | ^~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:54:20: note: 'gw' was declared here 54 | GeneralWriter *gw; | ^~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-load.3.0.9 [ 65%] Built target vdb-lock cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv abi-load abi-load.3.0.9 make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/align-cache /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache/CMakeFiles/align-cache.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3.0.9 abi-load.3 [ 65%] Linking C executable ../../../bin/vdb-unlock cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-unlock.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3 abi-load make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Linking C executable ../../../bin/helicos-load /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o" -o ../../../bin/vdb-unlock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/helicos-load.dir/link.txt --verbose=1 [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o [ 65%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o [ 65%] Built target abi-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o -MF CMakeFiles/align-cache.dir/align-cache.cpp.o.d -o CMakeFiles/align-cache.dir/align-cache.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/align-cache/align-cache.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o -MF CMakeFiles/cg-load.dir/f2_5.c.o.d -o CMakeFiles/cg-load.dir/f2_5.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/f2_5.c make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/depend /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/helicos-load.dir/pstring.c.o" "CMakeFiles/helicos-load.dir/common-xml.c.o" "CMakeFiles/helicos-load.dir/experiment-xml.c.o" "CMakeFiles/helicos-load.dir/run-xml.c.o" "CMakeFiles/helicos-load.dir/loader-file.c.o" "CMakeFiles/helicos-load.dir/loader-fmt.c.o" "CMakeFiles/helicos-load.dir/sra-writer.c.o" "CMakeFiles/helicos-load.dir/loader.c.o" "CMakeFiles/helicos-load.dir/writer-helicos.c.o" "CMakeFiles/helicos-load.dir/helicos-fmt.c.o" -o ../../../bin/helicos-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/ccextract /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract/CMakeFiles/ccextract.dir/DependInfo.cmake "--color=" [ 65%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o -MF CMakeFiles/general-loader.dir/database-loader.cpp.o.d -o CMakeFiles/general-loader.dir/database-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/database-loader.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-load.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-unlock.3.0.9 [ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-load fastq-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o -MF CMakeFiles/pacbio-load.dir/pl-progress.c.o.d -o CMakeFiles/pacbio-load.dir/pl-progress.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pl-progress.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3.0.9 fastq-load.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3 fastq-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-unlock vdb-unlock.3.0.9 [ 65%] Building C object tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ccextract\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o -MF CMakeFiles/ccextract.dir/ccextract.c.o.d -o CMakeFiles/ccextract.dir/ccextract.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/ccextract/ccextract.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3.0.9 vdb-unlock.3 [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o -MF CMakeFiles/cg-load.dir/file.c.o.d -o CMakeFiles/cg-load.dir/file.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/file.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3 vdb-unlock [ 65%] Built target fastq-load [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -MF CMakeFiles/sra-sort-cg.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/sra-sort.c make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat/CMakeFiles/copycat.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-load.3.0.9 [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o -MF CMakeFiles/srf-load.dir/srf-illumina.c.o.d -o CMakeFiles/srf-load.dir/srf-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/srf-illumina.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-load illumina-load.3.0.9 [ 65%] Built target vdb-unlock make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3.0.9 illumina-load.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3 illumina-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o -MF CMakeFiles/copycat.dir/copycat.c.o.d -o CMakeFiles/copycat.dir/copycat.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/copycat.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o [ 65%] Built target illumina-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o -MF CMakeFiles/pacbio-load.dir/pacbio-load.c.o.d -o CMakeFiles/pacbio-load.dir/pacbio-load.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pacbio-load.c [ 65%] Building C object tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-unused-result -MD -MT tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o -MF CMakeFiles/make-read-filter.dir/make-read-filter.c.o.d -o CMakeFiles/make-read-filter.dir/make-read-filter.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/make-read-filter/make-read-filter.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/md5cp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp/CMakeFiles/md5cp.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f helicos-load.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv helicos-load helicos-load.3.0.9 make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o -MF CMakeFiles/md5cp.dir/md5cp.c.o.d -o CMakeFiles/md5cp.dir/md5cp.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/md5cp/md5cp.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3.0.9 helicos-load.3 /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pacbio-load.c: In function 'pacbio_meta_entry': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/pacbio-load/pacbio-load.c:219:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 219 | rc = KLoaderMeta_Write( node, toolname, __DATE__, "PacBio HDF5", KAppVersion() ); | ^~~~~~~~ [ 65%] Linking CXX executable ../../../../../test-bin/idx-text-makeinputs cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3 helicos-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-makeinputs.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o" -o ../../../../../test-bin/idx-text-makeinputs ../../../../../ilib/libgeneral-writer.a [ 65%] Built target helicos-load make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-cmp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/DependInfo.cmake "--color=" [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o -MF CMakeFiles/srf-load.dir/writer-absolid.c.o.d -o CMakeFiles/srf-load.dir/writer-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/writer-absolid.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build [ 66%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c [ 67%] Building C object tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-cmp\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o -MF CMakeFiles/meta-cmp.dir/meta-cmp.c.o.d -o CMakeFiles/meta-cmp.dir/meta-cmp.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-cmp/meta-cmp.c [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort.dir/id-mapper-col.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/id-mapper-col.c [ 67%] Linking C executable ../../../bin/pacbio-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-load.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o" "CMakeFiles/pacbio-load.dir/pl-context.c.o" "CMakeFiles/pacbio-load.dir/pl-tools.c.o" "CMakeFiles/pacbio-load.dir/pl-zmw.c.o" "CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o" "CMakeFiles/pacbio-load.dir/pl-sequence.c.o" "CMakeFiles/pacbio-load.dir/pl-consensus.c.o" "CMakeFiles/pacbio-load.dir/pl-passes.c.o" "CMakeFiles/pacbio-load.dir/pl-metrics.c.o" "CMakeFiles/pacbio-load.dir/pl-regions.c.o" "CMakeFiles/pacbio-load.dir/pl-progress.c.o" "CMakeFiles/pacbio-load.dir/pacbio-load.c.o" -o ../../../bin/pacbio-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 67%] Built target idx-text-makeinputs make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy/CMakeFiles/meta-copy.dir/DependInfo.cmake "--color=" [ 67%] Linking C executable ../../../bin/md5cp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cmake -E cmake_link_script CMakeFiles/md5cp.dir/link.txt --verbose=1 [ 67%] Linking CXX executable ../../../../test-bin/makeinputs cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/makeinputs.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 67%] Linking C executable ../../../bin/ccextract make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cmake -E cmake_link_script CMakeFiles/ccextract.dir/link.txt --verbose=1 [ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/md5cp.dir/md5cp.c.o -o ../../../bin/md5cp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o -MF CMakeFiles/cg-load.dir/file-version-factory.c.o.d -o CMakeFiles/cg-load.dir/file-version-factory.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/file-version-factory.c /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/makeinputs.dir/makeinputs.cpp.o CMakeFiles/makeinputs.dir/testsource.cpp.o -o ../../../../test-bin/makeinputs ../../../../ilib/libgeneral-writer.a -lncbi-vdb /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/ccextract.dir/ccextract.c.o -o ../../../bin/ccextract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libxml2.so [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o [ 67%] Building C object tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o -MF CMakeFiles/meta-copy.dir/meta-copy.c.o.d -o CMakeFiles/meta-copy.dir/meta-copy.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-copy/meta-copy.c [ 67%] Linking CXX executable ../../../../../test-bin/idx-text-checklookup [ 67%] Linking C executable ../../../bin/meta-cmp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-checklookup.dir/link.txt --verbose=1 [ 67%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-cmp.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o -MF CMakeFiles/align-cache.dir/helper.cpp.o.d -o CMakeFiles/align-cache.dir/helper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/align-cache/helper.cpp [ 67%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o -MF CMakeFiles/copycat.dir/ccfileformat.c.o.d -o CMakeFiles/copycat.dir/ccfileformat.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccfileformat.c /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o" -o ../../../../../test-bin/idx-text-checklookup /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-cmp.dir/meta-cmp.c.o" -o ../../../bin/meta-cmp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/csra-tbl.c [ 67%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o -MF CMakeFiles/srf-load.dir/ztr-absolid.c.o.d -o CMakeFiles/srf-load.dir/ztr-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/ztr-absolid.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o -MF CMakeFiles/sra-sort.dir/run.c.o.d -o CMakeFiles/sra-sort.dir/run.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/run.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f md5cp.3.0.9 [ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o -MF CMakeFiles/cg-load.dir/formats.c.o.d -o CMakeFiles/cg-load.dir/formats.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/formats.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv md5cp md5cp.3.0.9 [ 67%] Built target makeinputs make -f tools/internal/meta-repair/CMakeFiles/meta-repair.dir/build.make tools/internal/meta-repair/CMakeFiles/meta-repair.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3.0.9 md5cp.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-repair /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-repair 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3 ccextract make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/meta-repair/CMakeFiles/meta-repair.dir/build.make tools/internal/meta-repair/CMakeFiles/meta-repair.dir/build /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccfileformat.c: In function 'CCFileFormatIsFastq': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccfileformat.c:275:27: warning: 'seq_len' may be used uninitialized [-Wmaybe-uninitialized] 275 | if(quality_values_len != seq_len) | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccfileformat.c:193:12: note: 'seq_len' was declared here 193 | size_t seq_len,quality_values_len,seq_id_len; | ^~~~~~~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o -MF CMakeFiles/cg-load.dir/writer-algn.c.o.d -o CMakeFiles/cg-load.dir/writer-algn.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/writer-algn.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 67%] Building C object tools/internal/meta-repair/CMakeFiles/meta-repair.dir/meta-repair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-repair && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/meta-repair\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/meta-repair/CMakeFiles/meta-repair.dir/meta-repair.c.o -MF CMakeFiles/meta-repair.dir/meta-repair.c.o.d -o CMakeFiles/meta-repair.dir/meta-repair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/meta-repair/meta-repair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-cmp.3.0.9 [ 68%] Building C object tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv meta-cmp meta-cmp.3.0.9 [ 68%] Built target ccextract cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -MF CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o.d -o CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact/test-read-write-cursor.c make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3.0.9 meta-cmp.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3 meta-cmp [ 68%] Built target idx-text-checklookup make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build [ 68%] Linking C executable ../../../bin/make-read-filter [ 68%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/csra-pair.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/make-read-filter.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 68%] Linking C executable 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-D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o -MF CMakeFiles/sra-sort.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort.dir/sra-sort.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/sra-sort.c [ 68%] Building C object tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -MF CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o.d -o CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c [ 68%] Built target meta-cmp /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/make-read-filter.dir/make-read-filter.c.o" -o ../../../bin/make-read-filter /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/depend [ 68%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o -MF CMakeFiles/vdb-copy.dir/context.c.o.d -o CMakeFiles/vdb-copy.dir/context.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/context.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/DependInfo.cmake "--color=" [ 69%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-copy.dir/meta-copy.c.o" -o ../../../bin/meta-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o -MF CMakeFiles/copycat.dir/cccat.c.o.d -o CMakeFiles/copycat.dir/cccat.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/cccat.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o -MF CMakeFiles/srf-load.dir/ztr-huffman.c.o.d -o CMakeFiles/srf-load.dir/ztr-huffman.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/ztr-huffman.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o -MF CMakeFiles/vdb-diff.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-diff.dir/namelist_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff/namelist_tools.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-load.3.0.9 /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c: In function 'enter_date_name_vers': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c:755:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 755 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ [ 70%] Linking C executable ../../../bin/sra-sort-cg cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort-cg.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-load pacbio-load.3.0.9 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort-cg.dir/caps.c.o" "CMakeFiles/sra-sort-cg.dir/mem.c.o" "CMakeFiles/sra-sort-cg.dir/membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort-cg.dir/except.c.o" "CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o" "CMakeFiles/sra-sort-cg.dir/map-file.c.o" "CMakeFiles/sra-sort-cg.dir/col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/row-set.c.o" "CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/meta-pair.c.o" "CMakeFiles/sra-sort-cg.dir/dir-pair.c.o" "CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o" "CMakeFiles/sra-sort-cg.dir/db-pair.c.o" "CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o" "CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort-cg.dir/buff-writer.c.o" "CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort-cg.dir/run.c.o" "CMakeFiles/sra-sort-cg.dir/sra-sort.c.o" "CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o" "CMakeFiles/sra-sort-cg.dir/csra-pair.c.o" -o ../../../bin/sra-sort-cg /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3.0.9 pacbio-load.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f make-read-filter.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3 pacbio-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-copy.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv make-read-filter make-read-filter.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv meta-copy meta-copy.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3.0.9 make-read-filter.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3.0.9 meta-copy.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3 make-read-filter make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3 meta-copy [ 70%] Built target pacbio-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/check-redact/CMakeFiles/check-redact.dir/build.make tools/internal/check-redact/CMakeFiles/check-redact.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/check-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/check-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/check-redact/CMakeFiles/check-redact.dir/DependInfo.cmake "--color=" [ 70%] Built target make-read-filter make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/crc32sum /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/DependInfo.cmake "--color=" [ 70%] Built target meta-copy make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort-cg.3.0.9 make -f tools/internal/check-redact/CMakeFiles/check-redact.dir/build.make tools/internal/check-redact/CMakeFiles/check-redact.dir/build [ 70%] Linking C executable ../../../bin/test-read-write-cursor cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort-cg sra-sort-cg.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/test-download /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download/CMakeFiles/test-download.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3.0.9 sra-sort-cg.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-read-write-cursor.dir/link.txt --verbose=1 make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3 sra-sort-cg make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o -MF CMakeFiles/vdb-diff.dir/coldefs.c.o.d -o CMakeFiles/vdb-diff.dir/coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff/coldefs.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o" -o ../../../bin/test-read-write-cursor /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 70%] Building C object tools/internal/check-redact/CMakeFiles/check-redact.dir/check-redact.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/check-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/check-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/check-redact/CMakeFiles/check-redact.dir/check-redact.c.o -MF CMakeFiles/check-redact.dir/check-redact.c.o.d -o CMakeFiles/check-redact.dir/check-redact.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/check-redact/check-redact.c [ 70%] Building C object tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o -MF CMakeFiles/crc32sum.dir/crc32sum.c.o.d -o CMakeFiles/crc32sum.dir/crc32sum.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/crc32sum/crc32sum.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 70%] Built target sra-sort-cg make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/kdb-index /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/DependInfo.cmake "--color=" [ 70%] Building C object tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o -MF CMakeFiles/test-download.dir/test-download.c.o.d -o CMakeFiles/test-download.dir/test-download.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/test-download/test-download.c [ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o -MF CMakeFiles/vdb-copy.dir/helper.c.o.d -o CMakeFiles/vdb-copy.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/helper.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-read-write-cursor.3.0.9 [ 70%] Building C object tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o -MF CMakeFiles/kdb-index.dir/kdb-index.c.o.d -o CMakeFiles/kdb-index.dir/kdb-index.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/kdb-index/kdb-index.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv test-read-write-cursor test-read-write-cursor.3.0.9 [ 71%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff/vdb-diff-context.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3.0.9 test-read-write-cursor.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3 test-read-write-cursor make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 71%] Linking C executable ../../../bin/read-filter-redact cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/read-filter-redact.dir/link.txt --verbose=1 [ 71%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort.dir/csra-tbl.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/csra-tbl.c [ 71%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o -MF CMakeFiles/srf-load.dir/srf-absolid.c.o.d -o CMakeFiles/srf-load.dir/srf-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-load/srf-absolid.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o" -o ../../../bin/read-filter-redact /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 71%] Built target test-read-write-cursor [ 71%] Linking C executable ../../../bin/crc32sum cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cmake -E cmake_link_script CMakeFiles/crc32sum.dir/link.txt --verbose=1 [ 71%] Linking C executable ../../../bin/meta-repair cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-repair && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-repair.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/crc32sum.dir/crc32sum.c.o -o ../../../bin/crc32sum /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-repair.dir/meta-repair.c.o" -o ../../../bin/meta-repair /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 71%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG 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tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o [ 71%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/writer-evidence-dnbs.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv read-filter-redact read-filter-redact.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o -MF CMakeFiles/vdb-diff.dir/row_by_row.c.o.d -o CMakeFiles/vdb-diff.dir/row_by_row.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff/row_by_row.c [ 71%] Linking C executable ../../../bin/kdb-index cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cmake -E cmake_link_script CMakeFiles/kdb-index.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3.0.9 read-filter-redact.3 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/kdb-index.dir/kdb-index.c.o" -o ../../../bin/kdb-index /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3 read-filter-redact make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f crc32sum.3.0.9 [ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o -MF CMakeFiles/vdb-copy.dir/coldefs.c.o.d -o CMakeFiles/vdb-copy.dir/coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/coldefs.c [ 71%] Built target read-filter-redact make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-repair.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv crc32sum crc32sum.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/pacbio-correct /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/DependInfo.cmake "--color=" [ 71%] Linking CXX executable ../../../bin/align-cache cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv meta-repair meta-repair.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-cache.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3.0.9 crc32sum.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-repair.3.0.9 meta-repair.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3 crc32sum make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-cache.dir/align-cache.cpp.o" "CMakeFiles/align-cache.dir/helper.cpp.o" -o ../../../bin/align-cache /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-repair.3 meta-repair cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdb-index.3.0.9 [ 71%] Built target crc32sum cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv kdb-index kdb-index.3.0.9 make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/depend [ 71%] Building C object tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdb-index.3.0.9 kdb-index.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 71%] Linking C executable ../../../bin/check-redact cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o -MF CMakeFiles/vdb-diff.dir/col_by_col.c.o.d -o CMakeFiles/vdb-diff.dir/col_by_col.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-diff/col_by_col.c [ 71%] Linking C executable ../../../bin/test-download make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 71%] Built target meta-repair cd 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-Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-download.dir/test-download.c.o" -o ../../../bin/test-download /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build.make tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build [ 72%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/writer-evidence-intervals.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build [ 72%] Building C object tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 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-MD -MT tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o -MF CMakeFiles/rowwritetest.dir/rowwritetest.c.o.d -o CMakeFiles/rowwritetest.dir/rowwritetest.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/rowwritetest/rowwritetest.c [ 73%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -std=c11 -rdynamic -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o -MF CMakeFiles/sra-sort.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort.dir/csra-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/sra-sort/csra-pair.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 73%] Linking C executable ../../../bin/pacbio-correct cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-cache.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-correct.dir/link.txt --verbose=1 [ 73%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o -MF CMakeFiles/vdb-copy.dir/get_platform.c.o.d -o CMakeFiles/vdb-copy.dir/get_platform.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/get_platform.c [ 74%] Building C object tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv align-cache align-cache.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3.0.9 align-cache.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3 align-cache cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o -MF CMakeFiles/samview-util.dir/samview.c.o.d -o CMakeFiles/samview-util.dir/samview.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/samview-util/samview.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 74%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o" -o ../../../bin/pacbio-correct /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f check-redact.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o -MF CMakeFiles/copycat.dir/cctree.c.o.d -o CMakeFiles/copycat.dir/cctree.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/cctree.c In file included from /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/loader-imp.c:113: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/hashing.hpp:214:7: warning: 'sha1_filter' has a base 'sha_filter' which has internal linkage [-Wsubobject-linkage] 214 | class sha1_filter : public sha_filter | ^~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/hashing.hpp:218:7: warning: 'sha224_filter' has a base 'sha_filter' which has internal linkage [-Wsubobject-linkage] 218 | class sha224_filter : public sha_filter | ^~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/hashing.hpp:222:7: warning: 'sha256_filter' has a base 'sha_filter' which has internal linkage [-Wsubobject-linkage] 222 | class sha256_filter : public sha_filter | ^~~~~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv check-redact check-redact.3.0.9 [ 74%] Built target align-cache make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/testld /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld/CMakeFiles/testld.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-redact.3.0.9 check-redact.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-redact.3 check-redact cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-download.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 74%] Linking C executable ../../../bin/sortreadtest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortreadtest.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv test-download test-download.3.0.9 [ 74%] Linking CXX executable ../../../bin/sra-info make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3.0.9 test-download.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-info.dir/link.txt --verbose=1 [ 74%] Built target check-redact cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-correct.3.0.9 [ 74%] Linking C executable ../../../bin/srf-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3 test-download make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/srf-load.dir/link.txt --verbose=1 make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/txt2kdb /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/DependInfo.cmake "--color=" /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/sortreadtest.dir/sortreadtest.c.o -o ../../../bin/sortreadtest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 74%] Linking C executable ../../../bin/schema-replace /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-info.dir/main.cpp.o" "CMakeFiles/sra-info.dir/sra-info.cpp.o" "CMakeFiles/sra-info.dir/formatter.cpp.o" -o ../../../bin/sra-info /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /usr/bin/cmake -E cmake_link_script CMakeFiles/schema-replace.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-correct pacbio-correct.3.0.9 [ 74%] Building C object tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o -MF CMakeFiles/testld.dir/testld.c.o.d -o CMakeFiles/testld.dir/testld.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/testld/testld.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/srf-load.dir/pstring.c.o" "CMakeFiles/srf-load.dir/common-xml.c.o" "CMakeFiles/srf-load.dir/experiment-xml.c.o" "CMakeFiles/srf-load.dir/run-xml.c.o" "CMakeFiles/srf-load.dir/loader-file.c.o" "CMakeFiles/srf-load.dir/loader-fmt.c.o" "CMakeFiles/srf-load.dir/sra-writer.c.o" "CMakeFiles/srf-load.dir/loader.c.o" "CMakeFiles/srf-load.dir/srf.c.o" "CMakeFiles/srf-load.dir/srf-fmt.c.o" "CMakeFiles/srf-load.dir/writer-illumina.c.o" "CMakeFiles/srf-load.dir/ztr-illumina.c.o" "CMakeFiles/srf-load.dir/srf-illumina.c.o" "CMakeFiles/srf-load.dir/writer-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-huffman.c.o" "CMakeFiles/srf-load.dir/srf-absolid.c.o" -o ../../../bin/srf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3.0.9 pacbio-correct.3 [ 74%] Built target test-download /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/schema-replace.dir/schema-replace.c.o" -o ../../../bin/schema-replace /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 74%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o make -f tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/build.make tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o -MF CMakeFiles/cg-load.dir/writer-seq.c.o.d -o CMakeFiles/cg-load.dir/writer-seq.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/cg-load/writer-seq.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/sam-factory /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-factory /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/DependInfo.cmake "--color=" [ 74%] Linking C executable ../../../bin/vdb-diff cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3 pacbio-correct make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-diff.dir/link.txt --verbose=1 make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 74%] Linking C executable ../../../bin/sra-sort cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort.dir/link.txt --verbose=1 [ 74%] Linking C executable ../../../bin/samview-util make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/build.make tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview-util.dir/link.txt --verbose=1 [ 75%] Building C object tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o [ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o -MF CMakeFiles/txt2kdb.dir/txt2kdb.c.o.d -o CMakeFiles/txt2kdb.dir/txt2kdb.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/txt2kdb/txt2kdb.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o -MF CMakeFiles/vdb-copy.dir/copy_meta.c.o.d -o CMakeFiles/vdb-copy.dir/copy_meta.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/copy_meta.c /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-diff.dir/namelist_tools.c.o" "CMakeFiles/vdb-diff.dir/coldefs.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o" "CMakeFiles/vdb-diff.dir/cmn.c.o" "CMakeFiles/vdb-diff.dir/row_by_row.c.o" "CMakeFiles/vdb-diff.dir/col_by_col.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff.c.o" -o ../../../bin/vdb-diff /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 75%] Built target pacbio-correct make -f tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/build.make tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f schema-replace.3.0.9 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/samview-util.dir/samview.c.o" -o ../../../bin/samview-util /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 75%] Building CXX object tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/sam-factory.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-factory && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/test-tools/sam-factory/CMakeFiles/sam-factory.dir/sam-factory.cpp.o -MF CMakeFiles/sam-factory.dir/sam-factory.cpp.o.d -o CMakeFiles/sam-factory.dir/sam-factory.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/sam-factory/sam-factory.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wno-unused-const-variable -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort.dir/caps.c.o" "CMakeFiles/sra-sort.dir/mem.c.o" "CMakeFiles/sra-sort.dir/membank.c.o" "CMakeFiles/sra-sort.dir/paged-membank.c.o" "CMakeFiles/sra-sort.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort.dir/except.c.o" "CMakeFiles/sra-sort.dir/idx-mapping.c.o" "CMakeFiles/sra-sort.dir/map-file.c.o" "CMakeFiles/sra-sort.dir/col-pair.c.o" "CMakeFiles/sra-sort.dir/row-set.c.o" "CMakeFiles/sra-sort.dir/simple-row-set.c.o" "CMakeFiles/sra-sort.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort.dir/meta-pair.c.o" "CMakeFiles/sra-sort.dir/dir-pair.c.o" "CMakeFiles/sra-sort.dir/tbl-pair.c.o" "CMakeFiles/sra-sort.dir/db-pair.c.o" "CMakeFiles/sra-sort.dir/glob-poslen.c.o" "CMakeFiles/sra-sort.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort.dir/buff-writer.c.o" "CMakeFiles/sra-sort.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort.dir/run.c.o" "CMakeFiles/sra-sort.dir/sra-sort.c.o" "CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort.dir/csra-tbl.c.o" "CMakeFiles/sra-sort.dir/csra-pair.c.o" -o ../../../bin/sra-sort /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/sam-analyze /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-analyze /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv schema-replace schema-replace.3.0.9 [ 76%] Linking C executable ../../../bin/rowwritetest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cmake -E cmake_link_script CMakeFiles/rowwritetest.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sortreadtest.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3.0.9 schema-replace.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sortreadtest sortreadtest.3.0.9 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/rowwritetest.dir/rowwritetest.c.o -o ../../../bin/rowwritetest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3 schema-replace [ 76%] Linking C executable ../../../bin/cg-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/cg-load.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3.0.9 sortreadtest.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/build.make tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/copy_meta.c: In function 'enter_date_name_vers': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/copy_meta.c:301:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 301 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ [ 76%] Built target schema-replace [ 76%] Linking C executable ../../../bin/testld make -f tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/build.make tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cmake -E cmake_link_script CMakeFiles/testld.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3 sortreadtest [ 76%] Building CXX object tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/main.cpp.o /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/cg-load.dir/cg-load.c.o" "CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/factory-mappings.c.o" "CMakeFiles/cg-load.dir/factory-reads.c.o" "CMakeFiles/cg-load.dir/factory-tag-lfr.c.o" "CMakeFiles/cg-load.dir/f1_3.c.o" "CMakeFiles/cg-load.dir/f1_5.c.o" "CMakeFiles/cg-load.dir/f1_7.c.o" "CMakeFiles/cg-load.dir/f2_0.c.o" "CMakeFiles/cg-load.dir/f2_2.c.o" "CMakeFiles/cg-load.dir/f2_4.c.o" "CMakeFiles/cg-load.dir/f2_5.c.o" "CMakeFiles/cg-load.dir/file.c.o" "CMakeFiles/cg-load.dir/file-version-factory.c.o" "CMakeFiles/cg-load.dir/formats.c.o" "CMakeFiles/cg-load.dir/writer-algn.c.o" "CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/writer-seq.c.o" -o ../../../bin/cg-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-analyze && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/main.cpp.o -MF CMakeFiles/sam-analyze.dir/main.cpp.o.d -o CMakeFiles/sam-analyze.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/sam-analyze/main.cpp /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/testld.dir/testld.c.o -o ../../../bin/testld /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-diff.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/build.make tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/build [ 76%] Built target sortreadtest make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-diff vdb-diff.3.0.9 make -f test/vdb/CMakeFiles/test-vdb.dir/build.make test/vdb/CMakeFiles/test-vdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/vdb /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/vdb /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/vdb/CMakeFiles/test-vdb.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3.0.9 vdb-diff.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3 vdb-diff make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f srf-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-info.3.0.9 [ 76%] Building CXX object tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/main.cpp.o -MF CMakeFiles/qa-stats.dir/main.cpp.o.d -o CMakeFiles/qa-stats.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/main.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sra-info sra-info.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv srf-load srf-load.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-info.3.0.9 sra-info.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3.0.9 srf-load.3 make -f test/vdb/CMakeFiles/test-vdb.dir/build.make test/vdb/CMakeFiles/test-vdb.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview-util.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-info.3 sra-info make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3 srf-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv samview-util samview-util.3.0.9 [ 76%] Built target vdb-diff [ 76%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o -MF CMakeFiles/copycat.dir/cctree-dump.c.o.d -o CMakeFiles/copycat.dir/cctree-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/cctree-dump.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o -MF CMakeFiles/general-loader.dir/main.cpp.o.d -o CMakeFiles/general-loader.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/main.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3.0.9 samview-util.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3 samview-util make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build [ 77%] Building CXX object test/vdb/CMakeFiles/test-vdb.dir/test-vdb.cpp.o [ 77%] Built target sra-info cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f rowwritetest.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/vdb/CMakeFiles/test-vdb.dir/test-vdb.cpp.o -MF CMakeFiles/test-vdb.dir/test-vdb.cpp.o.d -o CMakeFiles/test-vdb.dir/test-vdb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/vdb/test-vdb.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv rowwritetest rowwritetest.3.0.9 make -f test/external/align-info/CMakeFiles/Build-align-info.dir/build.make test/external/align-info/CMakeFiles/Build-align-info.dir/depend [ 77%] Building Java objects for test-ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f cg-load.3.0.9 [ 77%] Built target srf-load make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/align-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/align-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/align-info/CMakeFiles/Build-align-info.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort sra-sort.3.0.9 make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f testld.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv cg-load cg-load.3.0.9 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3.0.9 rowwritetest.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3.0.9 sra-sort.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/align-info/CMakeFiles/Build-align-info.dir/build.make test/external/align-info/CMakeFiles/Build-align-info.dir/build [ 77%] Built target samview-util cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv testld testld.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3.0.9 cg-load.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3 sra-sort cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3 cg-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3 rowwritetest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3.0.9 testld.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/align-info/CMakeFiles/Build-align-info.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3 testld make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java/junit-4.11.jar:/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java/junit-4.11.jar -d /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir @/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_sources make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Build-align-info [ 77%] Linking C executable ../../../bin/txt2kdb [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o -MF CMakeFiles/sratools.dir/proc.cpp.o.d -o CMakeFiles/sratools.dir/proc.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/proc.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target rowwritetest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/txt2kdb.dir/link.txt --verbose=1 make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/depend [ 77%] Built target cg-load [ 77%] Built target testld make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/DependInfo.cmake "--color=" make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/depend [ 77%] Built target sra-sort [ 77%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/DependInfo.cmake "--color=" make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o -MF CMakeFiles/vdb-copy.dir/type_matcher.c.o.d -o CMakeFiles/vdb-copy.dir/type_matcher.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/type_matcher.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/txt2kdb.dir/txt2kdb.c.o -o ../../../bin/txt2kdb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX 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-ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o -MF CMakeFiles/bam-load.dir/mem-bank.cpp.o.d -o CMakeFiles/bam-load.dir/mem-bank.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/mem-bank.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o -MF CMakeFiles/copycat.dir/cctar.c.o.d -o CMakeFiles/copycat.dir/cctar.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/cctar.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 78%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g 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-I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -MF CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o.d -o CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-command-line.cpp [ 79%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o cd 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CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-json-parse.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f txt2kdb.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv txt2kdb txt2kdb.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3.0.9 txt2kdb.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3 txt2kdb make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 79%] Built target txt2kdb make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/DependInfo.cmake "--color=" [ 79%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o -MF CMakeFiles/copycat.dir/ccsra.c.o.d -o CMakeFiles/copycat.dir/ccsra.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccsra.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 79%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -MF CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o.d -o CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-sdl-response.cpp [ 79%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsubchunk.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsubchunk.c.o -MF CMakeFiles/copycat.dir/ccsubchunk.c.o.d -o CMakeFiles/copycat.dir/ccsubchunk.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccsubchunk.c [ 79%] Linking CXX executable ../../../bin/general-loader cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-loader.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/general-loader.dir/general-loader.cpp.o" "CMakeFiles/general-loader.dir/protocol-parser.cpp.o" "CMakeFiles/general-loader.dir/database-loader.cpp.o" "CMakeFiles/general-loader.dir/main.cpp.o" -o ../../../bin/general-loader ../../../ilib/libgeneral-writer.a ../../../ilib/libloader.a -lkapp ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 80%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o -MF CMakeFiles/vdb-copy.dir/redactval.c.o.d -o CMakeFiles/vdb-copy.dir/redactval.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/redactval.c [ 80%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o -MF CMakeFiles/copycat.dir/ccfile.c.o.d -o CMakeFiles/copycat.dir/ccfile.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/ccfile.c [ 80%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f general-loader.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv general-loader general-loader.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3.0.9 general-loader.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3 general-loader [ 80%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o -MF CMakeFiles/vdb-copy.dir/config_values.c.o.d -o CMakeFiles/vdb-copy.dir/config_values.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/config_values.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 80%] Built target general-loader make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/DependInfo.cmake "--color=" [ 80%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o -MF CMakeFiles/copycat.dir/kff/ffext.c.o.d -o CMakeFiles/copycat.dir/kff/ffext.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffext.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 80%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -MF CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o.d -o CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-accession.cpp [ 80%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o -MF CMakeFiles/vdb-copy.dir/vdb-copy.c.o.d -o CMakeFiles/vdb-copy.dir/vdb-copy.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/vdb-copy.c [ 81%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o -MF CMakeFiles/copycat.dir/kff/ffkey.c.o.d -o CMakeFiles/copycat.dir/kff/ffkey.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffkey.c [ 81%] Linking CXX executable ../../../test-bin/Test_Drivertool_BuildVersion cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_BuildVersion.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o" -o ../../../test-bin/Test_Drivertool_BuildVersion [ 81%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o -MF CMakeFiles/copycat.dir/kff/ffmagic.c.o.d -o CMakeFiles/copycat.dir/kff/ffmagic.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffmagic.c make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target Test_Drivertool_BuildVersion make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/DependInfo.cmake "--color=" [ 81%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -MF CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o.d -o CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-uuid.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/test-run-source.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/test-run-source.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/test-run-source.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/test-run-source.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-run-source.cpp [ 81%] Linking C executable ../../../bin/copycat cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cmake -E cmake_link_script CMakeFiles/copycat.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/copycat.dir/copycat.c.o CMakeFiles/copycat.dir/ccfileformat.c.o CMakeFiles/copycat.dir/cccat.c.o CMakeFiles/copycat.dir/cctree.c.o "CMakeFiles/copycat.dir/cctree-dump.c.o" CMakeFiles/copycat.dir/cctar.c.o CMakeFiles/copycat.dir/ccsra.c.o CMakeFiles/copycat.dir/ccsubchunk.c.o CMakeFiles/copycat.dir/ccfile.c.o CMakeFiles/copycat.dir/kff/fileformat.c.o CMakeFiles/copycat.dir/kff/ffext.c.o CMakeFiles/copycat.dir/kff/ffkey.c.o CMakeFiles/copycat.dir/kff/ffmagic.c.o -o ../../../bin/copycat /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libmagic.so [ 81%] Linking C executable ../../../bin/vdb-copy cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-copy.dir/link.txt --verbose=1 [ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o -MF CMakeFiles/sratools.dir/uuid.cpp.o.d -o CMakeFiles/sratools.dir/uuid.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/uuid.cpp /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-copy.dir/context.c.o" "CMakeFiles/vdb-copy.dir/helper.c.o" "CMakeFiles/vdb-copy.dir/coldefs.c.o" "CMakeFiles/vdb-copy.dir/get_platform.c.o" "CMakeFiles/vdb-copy.dir/copy_meta.c.o" "CMakeFiles/vdb-copy.dir/type_matcher.c.o" "CMakeFiles/vdb-copy.dir/redactval.c.o" "CMakeFiles/vdb-copy.dir/config_values.c.o" "CMakeFiles/vdb-copy.dir/vdb-copy.c.o" -o ../../../bin/vdb-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 81%] Linking CXX executable ../../../test-bin/Test_Drivertool_CommandLine cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_CommandLine.dir/link.txt --verbose=1 [ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o" -o ../../../test-bin/Test_Drivertool_CommandLine cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o -MF CMakeFiles/sratools.dir/accession.cpp.o.d -o CMakeFiles/sratools.dir/accession.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/accession.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-copy.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-copy vdb-copy.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f copycat.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3.0.9 vdb-copy.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv copycat copycat.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3 vdb-copy cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3.0.9 copycat.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy/vdb-copy.kfg /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/ncbi/vdb-copy.kfg cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3 copycat make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o -MF CMakeFiles/bam-load.dir/low-match-count.cpp.o.d -o CMakeFiles/bam-load.dir/low-match-count.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/bam-loader/low-match-count.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target copycat make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/depend [ 81%] Built target vdb-copy make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/DependInfo.cmake "--color=" make -f test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/build.make test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/DependInfo.cmake "--color=" [ 81%] Built target Test_Drivertool_CommandLine make -f test/external/prefetch/CMakeFiles/Build-prefetch.dir/build.make test/external/prefetch/CMakeFiles/Build-prefetch.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch/CMakeFiles/Build-prefetch.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/build.make test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/kdbmeta/CMakeFiles/Build-kdbmeta.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/prefetch/CMakeFiles/Build-prefetch.dir/build.make test/external/prefetch/CMakeFiles/Build-prefetch.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/prefetch/CMakeFiles/Build-prefetch.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/test-tool-args.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/test-tool-args.cpp.o -MF CMakeFiles/Test_Drivertool_ToolArgs.dir/test-tool-args.cpp.o.d -o CMakeFiles/Test_Drivertool_ToolArgs.dir/test-tool-args.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/test-tool-args.cpp [ 81%] Built target Build-kdbmeta make -f test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/build.make test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/depend [ 81%] Built target Build-prefetch make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/DependInfo.cmake "--color=" make -f test/external/srapath/CMakeFiles/Build-srapath.dir/build.make test/external/srapath/CMakeFiles/Build-srapath.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/srapath /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/srapath /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/srapath/CMakeFiles/Build-srapath.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/build.make test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/srapath/CMakeFiles/Build-srapath.dir/build.make test/external/srapath/CMakeFiles/Build-srapath.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/srapath/CMakeFiles/Build-srapath.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/test-quality.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/prefetch/CMakeFiles/SlowTest_Prefetch.dir/test-quality.cpp.o -MF CMakeFiles/SlowTest_Prefetch.dir/test-quality.cpp.o.d -o CMakeFiles/SlowTest_Prefetch.dir/test-quality.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/prefetch/test-quality.cpp [ 81%] Built target Build-srapath make -f test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/build.make test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/build.make test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/sra-pileup/CMakeFiles/Build-sra-pileup.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target Build-sra-pileup make -f test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/build.make test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/build.make test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/sra-stat/CMakeFiles/Build-sra-stat.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -MF CMakeFiles/sratools.dir/service.cpp.o.d -o CMakeFiles/sratools.dir/service.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/service.cpp [ 81%] Built target Build-sra-stat [ 81%] Linking CXX executable ../../../test-bin/Test_Drivertool_Accession make -f test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/build.make test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_Accession.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/DependInfo.cmake "--color=" /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o" -o ../../../test-bin/Test_Drivertool_Accession [ 82%] Linking CXX executable ../../../test-bin/SlowTest_Prefetch cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_Prefetch.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/build.make test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/SlowTest_Prefetch.dir/test-quality.cpp.o" -o ../../../test-bin/SlowTest_Prefetch /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 82%] Building CXX object test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/testAssemblyStatistics.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/sra-stat/CMakeFiles/testAssemblyStatistics.dir/testAssemblyStatistics.cpp.o -MF CMakeFiles/testAssemblyStatistics.dir/testAssemblyStatistics.cpp.o.d -o CMakeFiles/testAssemblyStatistics.dir/testAssemblyStatistics.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-stat/testAssemblyStatistics.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/DependInfo.cmake "--color=" [ 82%] Built target Test_Drivertool_Accession make -f test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/build.make test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/DependInfo.cmake "--color=" [ 82%] Built target SlowTest_Prefetch make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/build.make test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 82%] Building CXX object test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -MF CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o.d -o CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config/test-vdb-config-model.cpp [ 82%] Building CXX object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/test-view-spec.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/test-view-spec.cpp.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/test-view-spec.cpp.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/test-view-spec.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump/test-view-spec.cpp [ 82%] Building CXX object test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -MF CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o.d -o CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump/makedb.cpp Note: ngs_test_lib_load.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_compiled_test-ngs-java [ 82%] Generating CMakeFiles/test-ngs-java.dir/java_class_filelist cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake [ 83%] Creating Java archive test-ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar @java_class_filelist [ 83%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o [ 83%] Linking CXX executable ../../../test-bin/Test_Drivertool_UUID cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -MF CMakeFiles/sratools.dir/json-parse.cpp.o.d -o CMakeFiles/sratools.dir/json-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/json-parse.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_UUID.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o" -o ../../../test-bin/Test_Drivertool_UUID cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=test-ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.29/Modules/UseJava/Symlinks.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target test-ngs-java make -f test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/build.make test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/build.make test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target Test_Drivertool_UUID make -f test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/build.make test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/depend [ 83%] Building CXX object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/test-view-alias.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-alias.dir/test-view-alias.cpp.o -MF CMakeFiles/Test_Vdb_dump_view-alias.dir/test-view-alias.cpp.o.d -o CMakeFiles/Test_Vdb_dump_view-alias.dir/test-view-alias.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump/test-view-alias.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/build.make test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 83%] Linking CXX executable ../../../test-bin/vdb-dump-makedb cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump-makedb.dir/link.txt --verbose=1 [ 83%] Building CXX object test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/test-vdb-validate.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-validate -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/vdb-validate/CMakeFiles/Test_VdbValidate_Unit.dir/test-vdb-validate.cpp.o -MF CMakeFiles/Test_VdbValidate_Unit.dir/test-vdb-validate.cpp.o.d -o CMakeFiles/Test_VdbValidate_Unit.dir/test-vdb-validate.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-validate/test-vdb-validate.cpp In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/main.cpp:32: In member function 'void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = const char*]', inlined from 'static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = const char*]' at /usr/include/c++/13/bits/alloc_traits.h:517:23, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:390:19, inlined from 'std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:369:15, inlined from 'std::vector<_Tp, _Alloc>::~vector() [with _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:738:7, inlined from 'Arguments::Arguments(int, char**, std::initializer_list&&)' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/parameters.hpp:137:9: /usr/include/c++/13/bits/new_allocator.h:172:33: warning: 'void operator delete(void*, std::size_t)' called on pointer '' with nonzero offset [1, 17179869168] [-Wfree-nonheap-object] 172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = const char*]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = const char*]' at /usr/include/c++/13/bits/alloc_traits.h:482:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:381:33, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:378:7, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = char**; _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1692:25, inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = char**; = void; _Tp = const char*; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:711:23, inlined from 'Arguments::Arguments(int, char**, std::initializer_list&&)' at /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/parameters.hpp:77:65: /usr/include/c++/13/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o" -o ../../../test-bin/vdb-dump-makedb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 83%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o -MF CMakeFiles/sratools.dir/SDL-response.cpp.o.d -o CMakeFiles/sratools.dir/SDL-response.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/SDL-response.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target vdb-dump-makedb make -f test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/build.make test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/build.make test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/vdb-validate/CMakeFiles/Build-vdb-validate.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target Build-vdb-validate make -f test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/build.make test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/build.make test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 84%] Building CXX object test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/test-sra-info.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/sra-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-info -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/sra-info/CMakeFiles/Test_SraInfo_Unit.dir/test-sra-info.cpp.o -MF CMakeFiles/Test_SraInfo_Unit.dir/test-sra-info.cpp.o.d -o CMakeFiles/Test_SraInfo_Unit.dir/test-sra-info.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/test-sra-info.cpp [ 84%] Linking CXX executable ../../../test-bin/Test_Vdb_dump_view-alias cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Vdb_dump_view-alias.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Vdb_dump_view-alias.dir/test-view-alias.cpp.o" -o ../../../test-bin/Test_Vdb_dump_view-alias /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 84%] Linking CXX executable ../../../test-bin/testAssemblyStatistics cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-stat && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAssemblyStatistics.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/testAssemblyStatistics.dir/testAssemblyStatistics.cpp.o -o ../../../test-bin/testAssemblyStatistics /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 84%] Linking CXX executable ../../../test-bin/Test_Drivertool_JsonParsing cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_JsonParsing.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o" -o ../../../test-bin/Test_Drivertool_JsonParsing [ 84%] Built target Test_Vdb_dump_view-alias make -f test/external/sra-info/CMakeFiles/Build-sra-info.dir/build.make test/external/sra-info/CMakeFiles/Build-sra-info.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info/CMakeFiles/Build-sra-info.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sra-info/CMakeFiles/Build-sra-info.dir/build.make test/external/sra-info/CMakeFiles/Build-sra-info.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/sra-info/CMakeFiles/Build-sra-info.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target Build-sra-info make -f test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/build.make test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/build.make test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o -MF CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o.d -o CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/tool-args.cpp [ 85%] Built target Test_Drivertool_JsonParsing [ 85%] Building CXX object test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/sam-platform.cpp.o make -f test/loaders/kar/CMakeFiles/Build-kar.dir/build.make test/loaders/kar/CMakeFiles/Build-kar.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/bam-load/CMakeFiles/Test_BamLoader_platform.dir/sam-platform.cpp.o -MF CMakeFiles/Test_BamLoader_platform.dir/sam-platform.cpp.o.d -o CMakeFiles/Test_BamLoader_platform.dir/sam-platform.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load/sam-platform.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/kar /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/kar/CMakeFiles/Build-kar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/kar/CMakeFiles/Build-kar.dir/build.make test/loaders/kar/CMakeFiles/Build-kar.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/loaders/kar/CMakeFiles/Build-kar.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target testAssemblyStatistics make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/DependInfo.cmake "--color=" [ 85%] Built target Build-kar make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/DependInfo.cmake "--color=" make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building C object test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -MF CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o.d -o CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/qfiletest.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF CMakeFiles/sratools.dir/tool-args.cpp.o.d -o CMakeFiles/sratools.dir/tool-args.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/tool-args.cpp [ 85%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -MF CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o.d -o CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/test-loaderfile.cpp [ 85%] Linking C executable ../../../test-bin/Test_KAPP_qfile cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_KAPP_qfile.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -o ../../../test-bin/Test_KAPP_qfile ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Test_KAPP_qfile make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADER.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -MF CMakeFiles/Test_LOADER.dir/loadertest.cpp.o.d -o CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/loadertest.cpp [ 85%] Linking CXX executable ../../../test-bin/Test_BamLoader_platform cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_BamLoader_platform.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_BamLoader_platform.dir/sam-platform.cpp.o" -o ../../../test-bin/Test_BamLoader_platform /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/loadertest.cpp:307:117: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 307 | REQUIRE_RC ( KLoaderMeta_Write ( node, LoaderName.c_str(), __DATE__, FormatterName.c_str(), KAppVersion() ) ); | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/loadertest.cpp:321:80: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 321 | REQUIRE_EQ ( string ( __DATE__), GetMetadata ( "SOFTWARE/loader", "date" ) ); | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/loadertest.cpp:350:143: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 350 | REQUIRE_RC ( KLoaderMeta_WriteWithVersion ( node, LoaderName.c_str(), __DATE__, LoaderVersion, FormatterName.c_str(), KAppVersion() ) ); | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader/loadertest.cpp:364:80: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | REQUIRE_EQ ( string ( __DATE__), GetMetadata ( "SOFTWARE/loader", "date" ) ); | ^ [ 85%] Linking CXX executable ../../../bin/sam-factory cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-factory && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-factory.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sam-factory.dir/sam-factory.cpp.o" -o ../../../bin/sam-factory /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Test_BamLoader_platform make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/Test_Align_samextract.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/../ncbi-vdb/interfaces/ext -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -MF CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o.d -o CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align/test-samextract.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target sam-factory make -f test/internal/align-cache/CMakeFiles/Build-align-cache.dir/build.make test/internal/align-cache/CMakeFiles/Build-align-cache.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align-cache /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align-cache /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align-cache/CMakeFiles/Build-align-cache.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align-cache/CMakeFiles/Build-align-cache.dir/build.make test/internal/align-cache/CMakeFiles/Build-align-cache.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/align-cache/CMakeFiles/Build-align-cache.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Build-align-cache make -f test/internal/copycat/CMakeFiles/Build-copycat.dir/build.make test/internal/copycat/CMakeFiles/Build-copycat.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat/CMakeFiles/Build-copycat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/copycat/CMakeFiles/Build-copycat.dir/build.make test/internal/copycat/CMakeFiles/Build-copycat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/copycat/CMakeFiles/Build-copycat.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Build-copycat make -f test/internal/copycat/CMakeFiles/Test_KFF.dir/build.make test/internal/copycat/CMakeFiles/Test_KFF.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat/CMakeFiles/Test_KFF.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/copycat/CMakeFiles/Test_KFF.dir/build.make test/internal/copycat/CMakeFiles/Test_KFF.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object test/internal/copycat/CMakeFiles/Test_KFF.dir/kfftest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/internal/copycat/CMakeFiles/Test_KFF.dir/kfftest.cpp.o -MF CMakeFiles/Test_KFF.dir/kfftest.cpp.o.d -o CMakeFiles/Test_KFF.dir/kfftest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat/kfftest.cpp [ 85%] Building CXX object tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/input.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/input.cpp.o -MF CMakeFiles/qa-stats.dir/input.cpp.o.d -o CMakeFiles/qa-stats.dir/input.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/input.cpp [ 85%] Building C object tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/sqlite3.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-analyze && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/test-tools/sam-analyze/CMakeFiles/sam-analyze.dir/sqlite3.c.o -MF CMakeFiles/sam-analyze.dir/sqlite3.c.o.d -o CMakeFiles/sam-analyze.dir/sqlite3.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/sam-analyze/sqlite3.c [ 85%] Linking CXX executable ../../test-bin/test-vdb cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/vdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-vdb.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-vdb.dir/test-vdb.cpp.o" -o ../../test-bin/test-vdb -lkapp /usr/lib/x86_64-linux-gnu/libkapp.a ../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 85%] Linking CXX executable ../../../test-bin/Test_VdbValidate_Unit cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_VdbValidate_Unit.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_VdbValidate_Unit.dir/test-vdb-validate.cpp.o" -o ../../../test-bin/Test_VdbValidate_Unit /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target test-vdb [ 85%] Linking CXX executable ../../../test-bin/Test_LOADERFILE make -f test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/build.make test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADERFILE.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/build.make test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/make-read-filter/CMakeFiles/Build-make-read-filter.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o" -o ../../../test-bin/Test_LOADERFILE ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 85%] Built target Build-make-read-filter make -f test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/build.make test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/read-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/read-filter-redact /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/build.make test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/read-filter-redact/CMakeFiles/Build-read-filter-redact.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Build-read-filter-redact make -f test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/build.make test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/build.make test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/vdb-copy/CMakeFiles/Build-vdb-copy.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF CMakeFiles/sratools.dir/build-version.cpp.o.d -o CMakeFiles/sratools.dir/build-version.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/build-version.cpp [ 85%] Built target Build-vdb-copy make -f test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/build.make test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/build.make test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/internal/vdb-diff/CMakeFiles/Build-vdb-diff.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Test_VdbValidate_Unit [ 85%] Built target Build-vdb-diff make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/depend [ 85%] Building C object test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffext.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffext.c.o -MF CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffext.c.o.d -o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffext.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffext.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-c++ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/DependInfo.cmake "--color=" [ 85%] Building C object test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffkey.c.o [ 85%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffkey.c.o -MF CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffkey.c.o.d -o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffkey.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffkey.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o -MF CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o.d -o CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/command-line.cpp [ 85%] Built target Test_LOADERFILE make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build [ 85%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-c++\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIC -rdynamic -MD -MT ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -MF CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o.d -o CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/bin/jar\ -cf\ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-doc.jar\ . [ 85%] Linking CXX executable ../../../test-bin/Test_Drivertool_FilePath cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_FilePath.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o" -o ../../../test-bin/Test_Drivertool_FilePath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 86%] Building C object test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/fileformat.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/fileformat.c.o -MF CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/fileformat.c.o.d -o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/fileformat.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/fileformat.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 86%] Building C object test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffmagic.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/internal/copycat/CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffmagic.c.o -MF CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffmagic.c.o.d -o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffmagic.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/copycat/kff/ffmagic.c [ 86%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/.. -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o -MF CMakeFiles/test-general-loader.dir/testsource.cpp.o.d -o CMakeFiles/test-general-loader.dir/testsource.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp [ 86%] Built target ngs-doc-jar make -f ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java && bash -c /usr/bin/jar\ -cf\ /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java [ 86%] Built target Test_Drivertool_FilePath make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/depend [ 86%] Linking CXX executable ../../../test-bin/Test_LOADER make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADER.dir/link.txt --verbose=1 [ 86%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -o ../../../test-bin/Test_LOADER ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/file-path.posix.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-c++.dir/link.txt --verbose=1 [ 88%] Building Java objects for ngs-examples.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake /usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar -d /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources /usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs-c++.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3.0.9 libncbi-ngs-c++.a.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/run-source.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/run-source.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/run-source.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/run-source.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/run-source.cpp [ 88%] Built target ncbi-ngs-c++ [ 88%] Linking CXX executable ../../../test-bin/Test_KFF make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/copycat && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_KFF.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/gw-dumper.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_KFF.dir/kfftest.cpp.o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffext.c.o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffkey.c.o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/fileformat.c.o CMakeFiles/Test_KFF.dir/__/__/__/tools/internal/copycat/kff/ffmagic.c.o -o ../../../test-bin/Test_KFF /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lmagic make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target Test_LOADER make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/depend [ 88%] Building CXX object libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test/CMakeFiles/test-general-writer.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -MF CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o.d -o CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/gw-dumper.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -MF CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o.d -o CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test/test-general-writer.cpp [ 88%] Linking CXX executable ../../../test-bin/Test_Drivertool_SDLResponse make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_SDLResponse.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target Test_KFF [ 88%] Built target ngs-src-jar /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o" -o ../../../test-bin/Test_Drivertool_SDLResponse make -f tools/external/vdb-config/CMakeFiles/vdb-config.dir/build.make tools/external/vdb-config/CMakeFiles/vdb-config.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/CMakeFiles/vdb-config.dir/DependInfo.cmake "--color=" [ 88%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/command-line.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/CMakeFiles/vdb-config.dir/build.make tools/external/vdb-config/CMakeFiles/vdb-config.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o -MF CMakeFiles/vdb-config.dir/configure.cpp.o.d -o CMakeFiles/vdb-config.dir/configure.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/configure.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp: In constructor 'TestSource::Buffer::Buffer(const std::string&, uint32_t, uint32_t, bool)': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/testsource.cpp:52:13: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 8 equals destination size [-Wstringop-truncation] 52 | strncpy ( m_header . dad . signature, p_signature . c_str(), sizeof m_header . dad . signature ); | ^ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target Test_Drivertool_SDLResponse make -f tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build.make tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/DependInfo.cmake "--color=" [ 88%] Building C object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-view-spec.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-view-spec.c.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-view-spec.c.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-view-spec.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-view-spec.c [ 89%] Linking CXX executable ../../../test-bin/test-vdb-config-model cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-vdb-config-model.dir/link.txt --verbose=1 [ 89%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o -MF CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/build-version.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build.make tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o" -o ../../../test-bin/test-vdb-config-model /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 89%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o -MF CMakeFiles/latf-load.dir/spot-assembler.c.o.d -o CMakeFiles/latf-load.dir/spot-assembler.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/spot-assembler.c [ 89%] Building C object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-helper.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-helper.c.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-helper.c.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-helper.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-helper.c [ 89%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -MF CMakeFiles/sratools.dir/proc.posix.cpp.o.d -o CMakeFiles/sratools.dir/proc.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/proc.posix.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 89%] Built target test-vdb-config-model make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 89%] Linking CXX static library ../../lib/libngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ngs-c++.dir/cmake_clean_target.cmake [ 90%] Building C object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-context.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-context.c.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-context.c.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-context.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-context.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++.dir/link.txt --verbose=1 [ 90%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o /usr/bin/ar qc ../../lib/libngs-c++.a "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dcd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o -MF CMakeFiles/latf-load.dir/common-writer.c.o.d -o CMakeFiles/latf-load.dir/common-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/common-writer.c ir/jni_ErrorMsg.c.o" [ 90%] Linking CXX executable ../../../test-bin/Test_Align_samextract cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Align_samextract.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o" -o ../../../test-bin/Test_Align_samextract -lsam-extract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/ranlib ../../lib/libngs-c++.a [ 90%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o -MF CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o.d -o CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/file-path.posix.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && rm -f libngs-c++.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && mv libngs-c++.a libngs-c++.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3.0.9 libngs-c++.a.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3 libngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a libngs-c++-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 90%] Built target ngs-c++ make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/DependInfo.cmake "--color=" [ 90%] Built target Test_Align_samextract make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test/test-general-writer.cpp: In function 'void ncbi::runTest(int, const char**, const char*, const char*)': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test/test-general-writer.cpp:271:13: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 271 | delete gw; | ^~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test/test-general-writer.cpp:217:24: note: 'gw' was declared here 217 | GeneralWriter *gw; | ^~ make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 90%] Building C object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-coldefs.c.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-coldefs.c.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c [ 90%] Linking CXX shared library ../../lib/libngs-c++.so cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++-shared.dir/link.txt --verbose=1 [ 90%] Linking CXX static library ../../lib/libncbi-ngs.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ncbi-ngs.dir/cmake_clean_target.cmake /usr/bin/c++ -fPIC -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libngs-c++.so.3 -o ../../lib/libngs-c++.so.3.0.9 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"../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs.dir/link.txt --verbose=1 [ 91%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/SDL-response.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/SDL-response.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/SDL-response.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/SDL-response.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/SDL-response.cpp /usr/bin/ar qc ../../lib/libncbi-ngs.a "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" [ 92%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o -MF CMakeFiles/latf-load.dir/sequence-writer.c.o.d -o CMakeFiles/latf-load.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/sequence-writer.c /usr/bin/ranlib ../../lib/libncbi-ngs.a [ 92%] Building C object test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-str.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT test/external/vdb-dump/CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-str.c.o -MF CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-str.c.o.d -o CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-str.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-dump/vdb-dump-str.c cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs.a libncbi-ngs.a.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3.0.9 libncbi-ngs.a.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3 libncbi-ngs.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a libncbi-ngs-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libngs-c++.so.3.0.9 ../../lib/libngs-c++.so.3 ../../lib/libngs-c++.so [ 92%] Linking CXX executable ../../../test-bin/test-general-writer [ 92%] Built target ncbi-ngs cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-writer.dir/link.txt --verbose=1 make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/DependInfo.cmake "--color=" [ 92%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o -MF CMakeFiles/latf-load.dir/common-reader.c.o.d -o CMakeFiles/latf-load.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/common-reader.c /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o" -o ../../../test-bin/test-general-writer ../../../ilib/libgeneral-writer.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Linking CXX shared library ../../lib/libncbi-ngs.so [ 93%] Built target ngs-c++-shared [ 93%] Generating CMakeFiles/ngs-examples.dir/java_class_filelist cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-shared.dir/link.txt --verbose=1 make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/depend cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/DependInfo.cmake "--color=" /usr/bin/c++ -fPIC -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libncbi-ngs.so.3 -o ../../lib/libncbi-ngs.so.3.0.9 "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" /usr/lib/x86_64-linux-gnu/libkapp.a ../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 93%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o -MF CMakeFiles/latf-load.dir/fastq-reader.c.o.d -o CMakeFiles/latf-load.dir/fastq-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/fastq-reader.c [ 93%] Linking CXX executable ../../../bin/sratools make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 [ 93%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c [ 93%] Creating Java archive ngs-examples.jar cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-examples.jar @java_class_filelist /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/sratools.dir/sratools.cpp.o CMakeFiles/sratools.dir/config.cpp.o "CMakeFiles/sratools.dir/command-line.cpp.o" "CMakeFiles/sratools.dir/run-source.cpp.o" CMakeFiles/sratools.dir/proc.cpp.o CMakeFiles/sratools.dir/uuid.cpp.o CMakeFiles/sratools.dir/accession.cpp.o CMakeFiles/sratools.dir/service.cpp.o "CMakeFiles/sratools.dir/json-parse.cpp.o" "CMakeFiles/sratools.dir/SDL-response.cpp.o" "CMakeFiles/sratools.dir/tool-args.cpp.o" "CMakeFiles/sratools.dir/build-version.cpp.o" "CMakeFiles/sratools.dir/file-path.posix.cpp.o" CMakeFiles/sratools.dir/proc.posix.cpp.o -o ../../../bin/sratools /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 93%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o -MF CMakeFiles/FragTest.dir/FragTest.cpp.o.d -o CMakeFiles/FragTest.dir/FragTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/FragTest.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Linking CXX executable ../../../test-bin/Test_Vdb_dump_view-spec cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Vdb_dump_view-spec.dir/link.txt --verbose=1 [ 93%] Built target test-general-writer make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/DependInfo.cmake "--color=" /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Vdb_dump_view-spec.dir/test-view-spec.cpp.o" "CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-view-spec.c.o" "CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-helper.c.o" "CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-context.c.o" "CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-coldefs.c.o" "CMakeFiles/Test_Vdb_dump_view-spec.dir/__/__/__/tools/external/vdb-dump/vdb-dump-str.c.o" -o ../../../test-bin/Test_Vdb_dump_view-spec /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -Wno-misleading-indentation -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-lex.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c [ 93%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o -MF CMakeFiles/AlignTest.dir/AlignTest.cpp.o.d -o CMakeFiles/AlignTest.dir/AlignTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libncbi-ngs.so.3.0.9 ../../lib/libncbi-ngs.so.3 ../../lib/libncbi-ngs.so cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sratools.3.0.9 [ 93%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sratools sratools.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.9 sratools.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3 sratools cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o -MF CMakeFiles/latf-load.dir/id2name.c.o.d -o CMakeFiles/latf-load.dir/id2name.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/id2name.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target sratools make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target ncbi-ngs-shared make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target Test_Vdb_dump_view-spec make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/DependInfo.cmake "--color=" [ 93%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -MF CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o.d -o CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp [ 94%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o -MF CMakeFiles/PileupTest.dir/PileupTest.cpp.o.d -o CMakeFiles/PileupTest.dir/PileupTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Linking CXX executable ../../../test-bin/Test_Drivertool_ToolArgs cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_ToolArgs.dir/link.txt --verbose=1 [ 94%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o -MF CMakeFiles/latf-load.dir/fastq-loader.c.o.d -o CMakeFiles/latf-load.dir/fastq-loader.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/fastq-loader.c /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_ToolArgs.dir/test-tool-args.cpp.o" "CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o" "CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o" "CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o" "CMakeFiles/Test_Drivertool_ToolArgs.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o" -o ../../../test-bin/Test_Drivertool_ToolArgs /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.29/Modules/UseJava/Symlinks.cmake [ 94%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o -MF CMakeFiles/RefTest.dir/RefTest.cpp.o.d -o CMakeFiles/RefTest.dir/RefTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/RefTest.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target ngs-examples make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o [ 94%] Linking CXX executable ../../../test-bin/FragTest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragTest.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -MF CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o.d -o CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o -MF CMakeFiles/latf-load.dir/loader-imp.c.o.d -o CMakeFiles/latf-load.dir/loader-imp.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/loader-imp.c /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/FragTest.dir/FragTest.cpp.o -o ../../../test-bin/FragTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 94%] Built target Test_Drivertool_ToolArgs make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/loader-imp.c: In function 'WriteLoaderSignature': /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/fastq-loader/loader-imp.c:180:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 180 | rc = KLoaderMeta_Write(node, progName, __DATE__, "FASTQ", KAppVersion()); | ^~~~~~~~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o -MF CMakeFiles/test-ngs.dir/ngstest.cpp.o.d -o CMakeFiles/test-ngs.dir/ngstest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest.cpp [ 94%] Linking CXX executable ../../../test-bin/AlignTest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignTest.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignTest.dir/AlignTest.cpp.o -o ../../../test-bin/AlignTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target FragTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/DependInfo.cmake "--color=" make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build [ 94%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/file-path.posix.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Linking CXX executable ../../../test-bin/RefTest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/RefTest.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/RefTest.dir/RefTest.cpp.o -o ../../../test-bin/RefTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o [ 94%] Linking C executable ../../../bin/latf-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -MF CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o.d -o CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -MF CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o.d -o CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_sra.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/latf-load.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/latf-load.dir/spot-assembler.c.o" "CMakeFiles/latf-load.dir/common-writer.c.o" "CMakeFiles/latf-load.dir/sequence-writer.c.o" "CMakeFiles/latf-load.dir/common-reader.c.o" "CMakeFiles/latf-load.dir/fastq-reader.c.o" "CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o" "CMakeFiles/latf-load.dir/zz_fastq-lex.c.o" "CMakeFiles/latf-load.dir/id2name.c.o" "CMakeFiles/latf-load.dir/fastq-loader.c.o" "CMakeFiles/latf-load.dir/loader-imp.c.o" -o ../../../bin/latf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target AlignTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Linking CXX executable ../../../test-bin/DumpReferenceFASTA cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/DumpReferenceFASTA.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -o ../../../test-bin/DumpReferenceFASTA ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -MF CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o.d -o CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f latf-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv latf-load latf-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3.0.9 latf-load.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3 latf-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Linking CXX executable ../../../test-bin/AlignSliceTest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignSliceTest.dir/link.txt --verbose=1 [ 94%] Built target latf-load make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/DependInfo.cmake "--color=" /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -o ../../../test-bin/AlignSliceTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target RefTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/DependInfo.cmake "--color=" [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o [ 94%] Linking CXX executable ../../../test-bin/test-ngs cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -MF CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o.d -o CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_readcollection.cpp /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs.dir/ngstest.cpp.o" -o ../../../test-bin/test-ngs -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Linking CXX executable ../../../test-bin/PileupTest cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/PileupTest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -MF CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o.d -o CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/PileupTest.dir/PileupTest.cpp.o -o ../../../test-bin/PileupTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 94%] Built target DumpReferenceFASTA make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/DependInfo.cmake "--color=" [ 94%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -MF CMakeFiles/vdb-config.dir/util.cpp.o.d -o CMakeFiles/vdb-config.dir/util.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/util.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -MF CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o.d -o CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/DependInfo.cmake "--color=" [ 95%] Built target AlignSliceTest make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -MF CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o.d -o CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_reference.cpp [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -MF CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o.d -o CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_fragmentblob.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target PileupTest make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -MF CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o.d -o CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_referenceblob.cpp [ 95%] Linking CXX executable ../../bin/gw-dumper cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/gw-dumper.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o" -o ../../bin/gw-dumper ../../ilib/libgeneral-writer.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceWindow_Slice_Filtered::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:591:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 591 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:669:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 669 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound_StartInWindow::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:696:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 696 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:719:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 719 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound_StartInWindow::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:740:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 740 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target gw-dumper make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3SelectNew': make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] 115649 | return pNew; | ^~~~ [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -MF CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o.d -o CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/ngstest_byteblob.cpp /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here 115609 | Select standin; | ^~~~~~~ [ 95%] Building CXX object tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/output.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++17 -rdynamic -MD -MT tools/test-tools/qa-stats/CMakeFiles/qa-stats.dir/output.cpp.o -MF CMakeFiles/qa-stats.dir/output.cpp.o.d -o CMakeFiles/qa-stats.dir/output.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats/output.cpp [ 95%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/json-parse.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/json-parse.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/json-parse.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/json-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/json-parse.cpp [ 95%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/build-version.cpp [ 95%] Linking CXX executable ../../../bin/qa-stats cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/qa-stats && /usr/bin/cmake -E cmake_link_script CMakeFiles/qa-stats.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/qa-stats.dir/main.cpp.o" "CMakeFiles/qa-stats.dir/input.cpp.o" "CMakeFiles/qa-stats.dir/output.cpp.o" -o ../../../bin/qa-stats make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target qa-stats make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -MF CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o.d -o CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/SRAtest.cpp [ 95%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o -MF CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o.d -o CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/driver-tool/tool-args.cpp make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/depend [ 95%] Linking CXX executable ../../../../test-bin/test-general-loader make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-loader.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o" "CMakeFiles/test-general-loader.dir/testsource.cpp.o" -o ../../../../test-bin/test-general-loader ../../../../ilib/libgeneral-writer.a -lkapp -lktst ../../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o -MF CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o.d -o CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/SRADBtest.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-general-loader make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o -MF CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o.d -o CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/CSRA1test.cpp [ 95%] Linking CXX executable ../../../test-bin/test-byteblob cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-byteblob.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o" -o ../../../test-bin/test-byteblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 95%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -MF CMakeFiles/vdb-config.dir/vdb-config.c.o.d -o CMakeFiles/vdb-config.dir/vdb-config.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/vdb-config.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-byteblob make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o -MF CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o.d -o CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/CSRA1PileupTest.cpp make -f libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Linking CXX executable ../../../test-bin/Test_Drivertool_RunSource [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_RunSource.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -fPIE -rdynamic -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o -MF CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o.d -o CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/test-ngs-vdb.cpp /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_RunSource.dir/test-run-source.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/run-source.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/command-line.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/SDL-response.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/file-path.posix.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/json-parse.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/build-version.cpp.o" "CMakeFiles/Test_Drivertool_RunSource.dir/__/__/__/tools/external/driver-tool/tool-args.cpp.o" -o ../../../test-bin/Test_Drivertool_RunSource /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 95%] Linking CXX executable ../../../test-bin/Test_SraInfo_Unit cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sra-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_SraInfo_Unit.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_SraInfo_Unit.dir/test-sra-info.cpp.o" -o ../../../test-bin/Test_SraInfo_Unit /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target Test_Drivertool_RunSource make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -MF CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o.d -o CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp [ 95%] Built target Test_SraInfo_Unit make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake "--color=" [ 96%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o -MF CMakeFiles/vdb-config.dir/interactive2.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive2.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/interactive2.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o -MF CMakeFiles/ref-variation.dir/common.cpp.o.d -o CMakeFiles/ref-variation.dir/common.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/common.cpp [ 96%] Linking CXX executable ../../../test-bin/test-fragmentblob cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-fragmentblob.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o" -o ../../../test-bin/test-fragmentblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -MF CMakeFiles/ref-variation.dir/helper.cpp.o.d -o CMakeFiles/ref-variation.dir/helper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/helper.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-fragmentblob make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/var-expand.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -MF CMakeFiles/var-expand.dir/common.cpp.o.d -o CMakeFiles/var-expand.dir/common.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/common.cpp [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -MF CMakeFiles/var-expand.dir/helper.cpp.o.d -o CMakeFiles/var-expand.dir/helper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/helper.cpp [ 96%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o -MF CMakeFiles/ngs-pileup.dir/main.cpp.o.d -o CMakeFiles/ngs-pileup.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ngs-pileup/main.cpp [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -MF CMakeFiles/ref-variation.dir/ref-variation.cpp.o.d -o CMakeFiles/ref-variation.dir/ref-variation.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/ref-variation.cpp [ 96%] Linking CXX executable ../../../test-bin/test-referenceblob cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-referenceblob.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o" -o ../../../test-bin/test-referenceblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 96%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o CMakeFiles/var-expand.dir/var-expand.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/var-expand.cpp [ 96%] Linking CXX executable ../../../bin/ngs-pileup cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-pileup.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o" "CMakeFiles/ngs-pileup.dir/main.cpp.o" -o ../../../bin/ngs-pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-referenceblob make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/CMakeFiles/sra-search.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o -MF CMakeFiles/sra-search.dir/main.cpp.o.d -o CMakeFiles/sra-search.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/main.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f ngs-pileup.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv ngs-pileup ngs-pileup.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3.0.9 ngs-pileup.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3 ngs-pileup make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target ngs-pileup make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -MF CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/test-sra-search.cpp [ 96%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -MF CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o.d -o CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/vdb-config/vdb-config-model.cpp [ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1_pileup cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_pileup.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o" -o ../../../test-bin/test-ngs_csra1_pileup -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-ngs_csra1_pileup make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp [ 96%] Linking CXX executable ../../../bin/var-expand cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/var-expand.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/var-expand.dir/common.cpp.o" "CMakeFiles/var-expand.dir/helper.cpp.o" "CMakeFiles/var-expand.dir/var-expand.cpp.o" -o ../../../bin/var-expand ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f var-expand.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv var-expand var-expand.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3.0.9 var-expand.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3 var-expand make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target var-expand make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/test-searchblock.cpp [ 96%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o -MF CMakeFiles/sra-search.dir/searchblock.cpp.o.d -o CMakeFiles/sra-search.dir/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/searchblock.cpp [ 97%] Linking CXX executable ../../../test-bin/test-ngs_reference cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_reference.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o" -o ../../../test-bin/test-ngs_reference -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 97%] Linking CXX executable ../../../bin/vdb-config cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-config.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-config.dir/configure.cpp.o" "CMakeFiles/vdb-config.dir/util.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config.c.o" "CMakeFiles/vdb-config.dir/interactive2.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o" -o ../../../bin/vdb-config ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1pileup++ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1pileup++.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o" -o ../../../test-bin/test-ngs_csra1pileup++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 97%] Linking CXX executable ../../../bin/ref-variation cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/ref-variation.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/ref-variation.dir/common.cpp.o" "CMakeFiles/ref-variation.dir/helper.cpp.o" "CMakeFiles/ref-variation.dir/ref-variation.cpp.o" -o ../../../bin/ref-variation ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1_refwin cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_refwin.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o" -o ../../../test-bin/test-ngs_csra1_refwin -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-config.3.0.9 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_csra1pileup++ make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/pileup-stats /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Building CXX object tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -MF CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o.d -o CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp [ 97%] Built target test-ngs_reference make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/testy-the-bear /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build [ 97%] Linking CXX executable ../../../test-bin/test-ngs_sra_c++ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra_c++.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o" -o ../../../test-bin/test-ngs_sra_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-config vdb-config.3.0.9 [ 97%] Building CXX object test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/ngs/testy-the-bear\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -MF CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o.d -o CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3.0.9 vdb-config.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3 vdb-config cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E copy /usr/include/ncbi-vdb/kfg/ncbi/default.kfg /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/ncbi/default.kfg make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb.dir/link.txt --verbose=1 [ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1_readcollection cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_readcollection.dir/link.txt --verbose=1 [ 97%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o [ 97%] Built target vdb-config /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o" -o ../../../test-bin/test-ngs_sradb -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/DependInfo.cmake "--color=" /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o" -o ../../../test-bin/test-ngs_csra1_readcollection -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f ref-variation.3.0.9 [ 97%] Building CXX object test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv ref-variation ref-variation.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -MF CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o.d -o CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3.0.9 ref-variation.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3 ref-variation make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target ref-variation make -f test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/ngs-pileup/CMakeFiles/Build-ngs-pileup.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target Build-ngs-pileup make -f test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/build.make test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/DependInfo.cmake "--color=" [ 97%] Built target test-ngs_csra1_refwin make -f test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/build.make test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/build.make test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/vdb-config/CMakeFiles/Build-vdb-config.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/build.make test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/loaders/fastq-loader/CMakeFiles/Build-latf-load.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_sra_c++ [ 97%] Built target Build-vdb-config make -f test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/build.make test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/depend [ 97%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/searchblock.cpp [ 97%] Built target Build-latf-load make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/build.make test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Building CXX object test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/test-id2name.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/fastq-loader/CMakeFiles/SlowTest_FastqLoader_id2name.dir/test-id2name.cpp.o -MF CMakeFiles/SlowTest_FastqLoader_id2name.dir/test-id2name.cpp.o.d -o CMakeFiles/SlowTest_FastqLoader_id2name.dir/test-id2name.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/test-id2name.cpp [ 97%] Building CXX object test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/wb-test-fastq.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/wb-test-fastq.cpp.o -MF CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/wb-test-fastq.cpp.o.d -o CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/wb-test-fastq.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/wb-test-fastq.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_sradb [ 97%] Built target test-ngs_csra1_readcollection make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/depend [ 97%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/blobmatchiterator.cpp make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/DependInfo.cmake "--color=" make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/build.make test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/build [ 98%] Building CXX object test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/wb-test-fastq-parse.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqParse.dir/wb-test-fastq-parse.cpp.o -MF CMakeFiles/Test_FastqLoader_WbFastqParse.dir/wb-test-fastq-parse.cpp.o.d -o CMakeFiles/Test_FastqLoader_WbFastqParse.dir/wb-test-fastq-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/wb-test-fastq-parse.cpp [ 98%] Building CXX object test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/test-fastq-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/loaders/fastq-loader/CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/test-fastq-loader.cpp.o -MF CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/test-fastq-loader.cpp.o.d -o CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/test-fastq-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/test-fastq-loader.cpp [ 98%] Linking CXX executable ../../../../test-bin/testy-the-bear cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/cmake -E cmake_link_script CMakeFiles/testy-the-bear.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o" -o ../../../../test-bin/testy-the-bear /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a ../../../../lib/libncbi-ngs-c++.a ../../../../lib/libncbi-ngs.a ../../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 98%] Linking CXX executable ../../../../test-bin/test-searchblock cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-searchblock.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o" "CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o" -o ../../../../test-bin/test-searchblock ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a [ 98%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -MF CMakeFiles/sra-search.dir/referencematchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/referencematchiterator.cpp [ 98%] Built target testy-the-bear make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 98%] Building CXX object test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/../ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ncbi/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -MF CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o.d -o CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align/pileup_estimator.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target test-searchblock [ 98%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o CMakeFiles/sra-search.dir/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/vdb-search.cpp [ 98%] Linking CXX executable ../../../test-bin/test-ngs-vdb cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs-vdb.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o" -o ../../../test-bin/test-ngs-vdb ../../../ilib/libtk-version.a ../../../ilib/libngs-vdb.a -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 98%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/vdb-search.cpp [ 98%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/searchblock.cpp [ 98%] Linking CXX executable ../../../bin/pileup-stats cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pileup-stats.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o" -o ../../../bin/pileup-stats ../../../ilib/libgeneral-writer.a ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 98%] Linking CXX executable ../../../test-bin/test-ngs_sradb_c++ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb_c++.dir/link.txt --verbose=1 [ 98%] Built target test-ngs-vdb /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o" -o ../../../test-bin/test-ngs_sradb_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 98%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/blobmatchiterator.cpp cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f pileup-stats.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv pileup-stats pileup-stats.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3.0.9 pileup-stats.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3 pileup-stats make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target pileup-stats [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/vdb-search.cpp [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-ngs_sradb_c++ [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/referencematchiterator.cpp [ 99%] Linking CXX executable ../../../test-bin/SlowTest_FastqLoader_id2name cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_FastqLoader_id2name.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/SlowTest_FastqLoader_id2name.dir/test-id2name.cpp.o" -o ../../../test-bin/SlowTest_FastqLoader_id2name ../../../ilib/libfastqloader.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target SlowTest_FastqLoader_id2name [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/searchblock.cpp [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/blobmatchiterator.cpp [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp [ 99%] Linking CXX executable ../../../bin/sra-search cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-search.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-search.dir/main.cpp.o" "CMakeFiles/sra-search.dir/searchblock.cpp.o" "CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/referencematchiterator.cpp.o" "CMakeFiles/sra-search.dir/vdb-search.cpp.o" -o ../../../bin/sra-search ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -Wl,-Bstatic -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 99%] Linking CXX executable ../../../test-bin/test-ngs_sra cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra.dir/link.txt --verbose=1 [ 99%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c++11 -rdynamic -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/referencematchiterator.cpp /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o" -o ../../../test-bin/test-ngs_sra -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-search.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv sra-search sra-search.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3.0.9 sra-search.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3 sra-search make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target sra-search make -f tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/DependInfo.cmake "--color=" [ 99%] Linking CXX executable ../../../test-bin/test-ngs_csra1 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'tools/external/sra-search/test/CMakeFiles/Build-sra-search.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o" -o ../../../test-bin/test-ngs_csra1 -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 99%] Built target Build-sra-search make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-ngs_sra [ 99%] Linking CXX executable ../../../../test-bin/test-sra-search cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a [ 99%] Linking CXX executable ../../../test-bin/Test_Ngs_Pileup cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Ngs_Pileup.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o" -o ../../../test-bin/Test_Ngs_Pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-ngs_csra1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-sra-search make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target Test_Ngs_Pileup [ 99%] Linking CXX executable ../../../../test-bin/test-sra-search-slow cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search-slow.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search-slow ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-sra-search-slow [ 99%] Linking CXX executable ../../../test-bin/SlowTest_Align_estimator cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_Align_estimator.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -o ../../../test-bin/SlowTest_Align_estimator ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 99%] Linking CXX executable ../../../test-bin/Test_FastqLoader_WbFastqLoader cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_FastqLoader_WbFastqLoader.dir/test-fastq-loader.cpp.o" -o ../../../test-bin/Test_FastqLoader_WbFastqLoader ../../../ilib/libfastqloader.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 99%] Linking CXX executable ../../../test-bin/Test_FastqLoader_WbFastqParse cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_FastqLoader_WbFastqParse.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_FastqLoader_WbFastqParse.dir/wb-test-fastq-parse.cpp.o" -o ../../../test-bin/Test_FastqLoader_WbFastqParse ../../../ilib/libfastqloader.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 99%] Built target SlowTest_Align_estimator make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target Test_FastqLoader_WbFastqLoader make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target Test_FastqLoader_WbFastqParse [ 99%] Linking C static library ../../ilib/libvdb-sqlite.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -P CMakeFiles/vdb-sqlite.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sqlite.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libvdb-sqlite.a "CMakeFiles/vdb-sqlite.dir/sqlite3.c.o" "CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o" /usr/bin/ranlib ../../ilib/libvdb-sqlite.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target vdb-sqlite make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/DependInfo.cmake "--color=" make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/fastconv.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Building C object tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o -MF CMakeFiles/vdb-sql.dir/vdb_shell.c.o.d -o CMakeFiles/vdb-sql.dir/vdb_shell.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-sql/vdb_shell.c [ 99%] Building C object tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/inc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -std=c11 -rdynamic -MD -MT tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o -MF CMakeFiles/fastconv.dir/fastconv.c.o.d -o CMakeFiles/fastconv.dir/fastconv.c.o -c /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-sql/fastconv.c [ 99%] Linking CXX executable ../../../test-bin/Test_FastqLoader_WbFastq_dflt cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_FastqLoader_WbFastq_dflt.dir/wb-test-fastq.cpp.o" -o ../../../test-bin/Test_FastqLoader_WbFastq_dflt ../../../ilib/libfastqloader.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target Test_FastqLoader_WbFastq_dflt [ 99%] Linking C executable ../../../bin/fastconv cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastconv.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now CMakeFiles/fastconv.dir/fastconv.c.o -o ../../../bin/fastconv /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastconv.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv fastconv fastconv.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3.0.9 fastconv.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3 fastconv make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target fastconv [ 99%] Linking CXX executable ../../../test-bin/test-ngs_csra1_c++ cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_c++.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o" -o ../../../test-bin/test-ngs_csra1_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-ngs_csra1_c++ [100%] Linking C executable ../../../bin/vdb-sql cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sql.dir/link.txt --verbose=1 /usr/bin/cc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-sql.dir/vdb_shell.c.o" -o ../../../bin/vdb-sql ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-sql.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-sql vdb-sql.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3.0.9 vdb-sql.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3 vdb-sql make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [100%] Built target vdb-sql [100%] Linking CXX executable ../../../bin/bam-load cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-load.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/bam-load.dir/bam-loader.c.o" "CMakeFiles/bam-load.dir/bam.c.o" "CMakeFiles/bam-load.dir/sam.c.o" "CMakeFiles/bam-load.dir/alignment-writer.c.o" "CMakeFiles/bam-load.dir/reference-writer.c.o" "CMakeFiles/bam-load.dir/sequence-writer.c.o" "CMakeFiles/bam-load.dir/loader-imp.c.o" "CMakeFiles/bam-load.dir/mem-bank.cpp.o" "CMakeFiles/bam-load.dir/low-match-count.cpp.o" -o ../../../bin/bam-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lz cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && rm -f bam-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && mv bam-load bam-load.3.0.9 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3.0.9 bam-load.3 cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3 bam-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [100%] Built target bam-load make -f test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/build.make test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/depend make -f test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/build.make test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/depend make -f test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/build.make test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/depend make -f test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/build.make test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sam-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.9+dfsg /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/build.make test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/sam-dump/CMakeFiles/Build-sam-dump.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/build.make test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/build.make test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/build make -f test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/build.make test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/loaders/bam-load/CMakeFiles/Build-bam-load.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/external/fasterq-dump/CMakeFiles/Build-fasterq-dump.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'test/loaders/sra-sort/CMakeFiles/Build-sra-sort.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [100%] Built target Build-sam-dump [100%] Built target Build-sra-sort [100%] Built target Build-bam-load [100%] Built target Build-fasterq-dump [100%] Linking CXX executable ../../../bin/sam-analyze cd /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sam-analyze && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-analyze.dir/link.txt --verbose=1 /usr/bin/c++ -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -Wl,-z,relro -Wl,-z,now "CMakeFiles/sam-analyze.dir/main.cpp.o" "CMakeFiles/sam-analyze.dir/sqlite3.c.o" -o ../../../bin/sam-analyze /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' [100%] Built target sam-analyze make[2]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' cd obj-x86_64-linux-gnu && \ ctest --force-new-ctest-process --verbose -j1 -LE online UpdateCTestConfiguration from :/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/sra-sdk-3.0.9+dfsg/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 9 Start 9: Test_NGS_Python_install 9: Test command: /usr/bin/python3 "/build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-python/setup.py" "-q" "install" "--user" 9: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/ngs/ngs-python 9: Environment variables: 9: PYTHONUSERBASE=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/tmp/python 9: Test timeout computed to be: 1500 9: /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 9: !! 9: 9: ******************************************************************************** 9: Please avoid running ``setup.py`` directly. 9: Instead, use pypa/build, pypa/installer or other 9: standards-based tools. 9: 9: See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 9: ******************************************************************************** 9: 9: !! 9: self.initialize_options() 9: /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. 9: !! 9: 9: ******************************************************************************** 9: Please avoid running ``setup.py`` and ``easy_install``. 9: Instead, use pypa/build, pypa/installer or other 9: standards-based tools. 9: 9: See https://github.com/pypa/setuptools/issues/917 for details. 9: ******************************************************************************** 9: 9: !! 9: self.initialize_options() 9: zip_safe flag not set; analyzing archive contents... 1/187 Test #9: Test_NGS_Python_install ........................... Passed 1.56 sec test 15 Start 15: Ngs_MakeDB 15: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/ngs-makedb 15: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test/data 15: Test timeout computed to be: 1500 15: Running 1 test case... 15: SparseFragmentBlobs (0 s) 15: 15: *** No errors detected (0 s total) 2/187 Test #15: Ngs_MakeDB ........................................ Passed 0.13 sec test 16 Start 16: Test_Ngs 16: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-ngs 16: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/ngs-vdb/test 16: Test timeout computed to be: 1500 16: 16: *** No errors detected (0 s total) 3/187 Test #16: Test_Ngs .......................................... Passed 0.01 sec test 32 Start 32: GeneralWriterTest 32: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-writer 32: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/libs/general-writer/test 32: Test timeout computed to be: 1500 32: CreateGw Success 32: --------------------------------- 32: addTable Success 32: --------------------------------- 32: addColumn Success 32: --------------------------------- 32: dbAddDatabase Success 32: --------------------------------- 32: dbAddTable Success 32: --------------------------------- 32: write Success 32: --------------------------------- 32: setDBMetadataNode Success 32: --------------------------------- 32: setTblMetadataNode Success 32: --------------------------------- 32: setColMetadataNode Success 32: --------------------------------- 32: setProgMsg Success 32: --------------------------------- 32: Attempting add table after endStream 32: state violation adding table 32: addTable correctly failed 32: endStream Success 32: --------------------------------- 4/187 Test #32: GeneralWriterTest ................................. Passed 0.04 sec test 33 Start 33: Ref-Variation-1.0 33: Test command: /usr/bin/sh "./have-access.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "ref-variation" 33: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/test 33: Test timeout computed to be: 1500 33: ./have-access.sh: 6: vdb-config: not found 33: no access to repository, skipping ref-variation test... 5/187 Test #33: Ref-Variation-1.0 ................................. Passed 0.00 sec test 34 Start 34: Var-Expand-1.0 34: Test command: /usr/bin/sh "./have-access.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "var-expand" 34: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/ref-variation/test 34: Test timeout computed to be: 1500 34: ./have-access.sh: 6: vdb-config: not found 34: no access to repository, skipping var-expand test... 6/187 Test #34: Var-Expand-1.0 .................................... Passed 0.00 sec test 35 Start 35: SearchBlockWhiteBox 35: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-searchblock 35: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test 35: Test timeout computed to be: 1500 35: Running 8 test cases... 35: FgrepDumb (0 s) 35: SearchFgrepBoyerMoore (0 s) 35: SearchFgrepAho (0 s) 35: SearchAgrepDP (0 s) 35: SearchNucStrstr_NoExpr_NoCoords (0 s) 35: SearchNucStrstr_NoExpr_Coords_NotSupported (0 s) 35: SearchNucStrstr_Expr_Coords (0 s) 35: SearchSmithWaterman_Coords_NotSupported (0 s) 35: 35: *** No errors detected (0 s total) 7/187 Test #35: SearchBlockWhiteBox ............................... Passed 0.01 sec test 38 Start 38: SraSearch-1.0-h 38: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "1.0-h" "--args" "-h" 38: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 38: Test timeout computed to be: 1500 38: running test case 1.0-h... passed 8/187 Test #38: SraSearch-1.0-h ................................... Passed 0.11 sec test 39 Start 39: SraSearch-1.1-help 39: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "1.1-help" "--args" "--help" 39: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 39: Test timeout computed to be: 1500 39: running test case 1.1-help... passed 9/187 Test #39: SraSearch-1.1-help ................................ Passed 0.06 sec test 40 Start 40: SraSearch-1.2-V 40: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/execandgrep.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search -V" "3.0.9" 40: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 40: Test timeout computed to be: 1500 40: sra-search : 3.0.9 10/187 Test #40: SraSearch-1.2-V ................................... Passed 0.01 sec test 41 Start 41: SraSearch-1.3-version 41: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/execandgrep.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search --version" "3.0.9" 41: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 41: Test timeout computed to be: 1500 41: sra-search : 3.0.9 11/187 Test #41: SraSearch-1.3-version ............................. Passed 0.01 sec test 42 Start 42: SraSearch-2.0-no-args 42: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "2.0-no-args" "--rc" "3" 42: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 42: Test timeout computed to be: 1500 42: running test case 2.0-no-args... passed 12/187 Test #42: SraSearch-2.0-no-args ............................. Passed 0.37 sec test 43 Start 43: SraSearch-2.1-no-run 43: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "2.1-no-run" "--rc" "3" "--args" "AGCT" 43: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 43: Test timeout computed to be: 1500 43: running test case 2.1-no-run... passed 13/187 Test #43: SraSearch-2.1-no-run .............................. Passed 0.48 sec test 44 Start 44: SraSearch-2.2-missing-algorithm 44: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "2.2-missing-algorithm" "--rc" "3" "--args" "AGCT SRR000001 -a" 44: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 44: Test timeout computed to be: 1500 44: running test case 2.2-missing-algorithm... passed 14/187 Test #44: SraSearch-2.2-missing-algorithm ................... Passed 0.44 sec test 45 Start 45: SraSearch-2.3-bad-algorithm 45: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "2.3-bad-algorithm" "--rc" "3" "--args" "--algorithm bad AGCT SRR000001" 45: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 45: Test timeout computed to be: 1500 45: running test case 2.3-bad-algorithm... passed 15/187 Test #45: SraSearch-2.3-bad-algorithm ....................... Passed 0.87 sec test 61 Start 61: SraSearch-5.1-run-not-nucstrstr-with-expression 61: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "5.1-run-not-nucstrstr-with-expression" "--args" "AAAAAAACCCCCCCAAAAAAACCCCCCC\|\|AGCTAGCTAGCT --algorithm FgrepStandard --expression SRR000001" "--rc" "3" 61: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 61: Test timeout computed to be: 1500 61: running test case 5.1-run-not-nucstrstr-with-expression... passed 16/187 Test #61: SraSearch-5.1-run-not-nucstrstr-with-expression ... Passed 0.07 sec test 62 Start 62: SraSearch-6.0.1-imperfect-match-no-arg 62: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.0.1-imperfect-match-no-arg" "--args" "AGCTAGCTAGCT SRR000001 -S" "--rc" "3" 62: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 62: Test timeout computed to be: 1500 62: running test case 6.0.1-imperfect-match-no-arg... passed 17/187 Test #62: SraSearch-6.0.1-imperfect-match-no-arg ............ Passed 0.72 sec test 63 Start 63: SraSearch-6.0.2-imperfect-match-bad-arg 63: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.0.2-imperfect-match-bad-arg" "--args" "AGCTAGCTAGCT SRR000001 -S qq" "--rc" "3" 63: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 63: Test timeout computed to be: 1500 63: running test case 6.0.2-imperfect-match-bad-arg... passed 18/187 Test #63: SraSearch-6.0.2-imperfect-match-bad-arg ........... Passed 0.27 sec test 64 Start 64: SraSearch-6.0.3-imperfect-match-default 64: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.0.3-imperfect-match-default" "--args" "AGCTAGCTAGCT -S 90 SRR000001" "--rc" "3" 64: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 64: Test timeout computed to be: 1500 64: running test case 6.0.3-imperfect-match-default... passed 19/187 Test #64: SraSearch-6.0.3-imperfect-match-default ........... Passed 0.12 sec test 65 Start 65: SraSearch-6.1-imperfect-match-fgrep-standard 65: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.1-imperfect-match-fgrep-standard" "--args" "AGCTAGCTAGCT --score 90 -a FgrepStandard SRR000001" "--rc" "3" 65: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 65: Test timeout computed to be: 1500 65: running test case 6.1-imperfect-match-fgrep-standard... passed 20/187 Test #65: SraSearch-6.1-imperfect-match-fgrep-standard ...... Passed 0.06 sec test 66 Start 66: SraSearch-6.2-imperfect-match-fgrep-boyer-moore 66: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.2-imperfect-match-fgrep-boyer-moore" "--args" "AGCTAGCTAGCT --score 90 --algorithm FgrepBoyerMoore SRR000001" "--rc" "3" 66: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 66: Test timeout computed to be: 1500 66: running test case 6.2-imperfect-match-fgrep-boyer-moore... passed 21/187 Test #66: SraSearch-6.2-imperfect-match-fgrep-boyer-moore ... Passed 0.15 sec test 67 Start 67: SraSearch-6.3-imperfect-match-fgrep-aho 67: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.3-imperfect-match-fgrep-aho" "--args" "AGCTAGCTAGCT --score 90 --algorithm FgrepAho SRR000001" "--rc" "3" 67: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 67: Test timeout computed to be: 1500 67: running test case 6.3-imperfect-match-fgrep-aho... passed 22/187 Test #67: SraSearch-6.3-imperfect-match-fgrep-aho ........... Passed 0.10 sec test 72 Start 72: SraSearch-6.8-imperfect-match-nucstrstr 72: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "6.8-imperfect-match-nucstrstr" "--args" "AGCTAGCTAGCT --score 90 --algorithm NucStrstr SRR000001" "--rc" "3" 72: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 72: Test timeout computed to be: 1500 72: running test case 6.8-imperfect-match-nucstrstr... passed 23/187 Test #72: SraSearch-6.8-imperfect-match-nucstrstr ........... Passed 0.14 sec test 74 Start 74: SraSearch-7.0.1-threads-no-arg 74: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "7.0.1-threads-no-arg" "--rc" "3" "--args" "AGCTAGCTAGCT SRR600094 SRR600095 -T" 74: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 74: Test timeout computed to be: 1500 74: running test case 7.0.1-threads-no-arg... passed 24/187 Test #74: SraSearch-7.0.1-threads-no-arg .................... Passed 0.09 sec test 75 Start 75: SraSearch-7.0.2-threads-bad-arg 75: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "7.0.2-threads-bad-arg" "--rc" "3" "--args" "AGCTAGCTAGCT SRR600094 SRR600095 --threads -1" 75: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 75: Test timeout computed to be: 1500 75: running test case 7.0.2-threads-bad-arg... passed 25/187 Test #75: SraSearch-7.0.2-threads-bad-arg ................... Passed 0.05 sec test 80 Start 80: SlowTest_SraSearch-8.0-nothing-found 80: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "8.0-nothing-found" "--rc" "3" "--args" "TTTTTTTTAAAAAAACCCC -T 1 SRR000001" 80: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 80: Test timeout computed to be: 1500 80: running test case 8.0-nothing-found... passed 26/187 Test #80: SlowTest_SraSearch-8.0-nothing-found .............. Passed 1.08 sec test 84 Start 84: SraSearch-9.3-reference-expression 84: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-search" "9.3-reference-expression" "--args" "ACGTAGGGTCC SRR600094 --reference --expression" "--rc" "3" 84: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/external/sra-search/test 84: Test timeout computed to be: 1500 84: running test case 9.3-reference-expression... passed 27/187 Test #84: SraSearch-9.3-reference-expression ................ Passed 0.07 sec test 86 Start 86: GeneralLoaderWhiteBox 86: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-loader 86: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 86: Test timeout computed to be: 1500 86: Unpacked protocol: Running 62 test cases... 86: EmptyInput (0 s) 86: ShortInput (0 s) 86: BadSignature (0 s) 86: BadEndianness (0 s) 86: ReverseEndianness (0 s) 86: LaterVersion (0 s) 86: BadSchemaFileName (0 s) 86: BadSchemaFileName_Long (0 s) 86: BadSchemaName (0 s) 86: BadSchemaName_Long (0 s) 86: BadTableName (0 s) 86: BadTableName_Long (0 s) 86: DuplicateTableId (0 s) 86: BadColumnName (0 s) 86: BadTableId (0 s) 86: DuplicateColumnName (0 s) 86: DuplicateColumnId (0 s) 86: NoOpenStreamEvent (0 s) 86: NoCloseStreamEvent (0 s) 86: NoColumns (0 s) 86: SoftwareName (0 s) 86: SoftwareName_BadVersion (0 s) 86: DBAddDatabase (0 s) 86: DBAddSubDatabase (0 s) 86: DBAddTable (0 s) 86: DBAddTableToSubDb (0 s) 86: DBMetadataNode (0 s) 86: SubDBMetadataNode (0 s) 86: TblMetadataNode (0 s) 86: ColMetadataNode (0 s) 86: NoData (0 s) 86: Chunk_BadColumnId (0 s) 86: WriteNoCommit (0 s) 86: CommitBadTableId (0 s) 86: OneColumnOneCellOneChunk (0 s) 86: OneColumnOneCellOneChunk_Long (0 s) 86: OneColumnOneCellManyChunks (0 s) 86: IntegerCompression_MinimumCompression (0 s) 86: IntegerCompression_MaximumCompression (0 s) 86: IntegerCompression_MultipleValues (0 s) 86: OneColumnDefaultNoWrite (0 s) 86: OneColumnDefaultNoWrite_Long (0 s) 86: MoveAhead (0 s) 86: OneColumnDefaultOverwite (0 s) 86: OneColumnChangeDefault (0 s) 86: OneColumnDataAndDefaultsMixed (0 s) 86: TwoColumnsFullRow (0 s) 86: TwoColumnsIncompleteRow (0 s) 86: TwoColumnsPartialRowWithDefaults (0 s) 86: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 86: EmptyDefault_String (0 s) 86: EmptyDefault_Int (0 s) 86: MultipleTables_Multiple_Columns_MultipleRows (0 s) 86: AdditionalSchemaIncludePaths_Single (0 s) 86: AdditionalSchemaIncludePaths_Multiple (0 s) 86: AdditionalSchemaFiles_Single (0 s) 86: AdditionalSchemaFiles_Multiple (0 s) 86: ErrorMessage (0 s) 86: ErrorMessage_Long (0 s) 86: LogMessage (0 s) 86: ProgressMessage (0 s) 86: TargetOverride (0 s) 86: 86: *** No errors detected (1 s total) 86: Packed protocol: Running 62 test cases... 86: EmptyInput (0 s) 86: ShortInput (0 s) 86: BadSignature (0 s) 86: BadEndianness (0 s) 86: ReverseEndianness (0 s) 86: LaterVersion (0 s) 86: BadSchemaFileName (0 s) 86: BadSchemaFileName_Long (0 s) 86: BadSchemaName (0 s) 86: BadSchemaName_Long (0 s) 86: BadTableName (0 s) 86: BadTableName_Long (0 s) 86: DuplicateTableId (0 s) 86: BadColumnName (0 s) 86: BadTableId (0 s) 86: DuplicateColumnName (0 s) 86: DuplicateColumnId (0 s) 86: NoOpenStreamEvent (0 s) 86: NoCloseStreamEvent (0 s) 86: NoColumns (0 s) 86: SoftwareName (0 s) 86: SoftwareName_BadVersion (0 s) 86: DBAddDatabase (0 s) 86: DBAddSubDatabase (0 s) 86: DBAddTable (0 s) 86: DBAddTableToSubDb (0 s) 86: DBMetadataNode (0 s) 86: SubDBMetadataNode (0 s) 86: TblMetadataNode (0 s) 86: ColMetadataNode (0 s) 86: NoData (0 s) 86: Chunk_BadColumnId (0 s) 86: WriteNoCommit (0 s) 86: CommitBadTableId (0 s) 86: OneColumnOneCellOneChunk (0 s) 86: OneColumnOneCellOneChunk_Long (0 s) 86: OneColumnOneCellManyChunks (0 s) 86: IntegerCompression_MinimumCompression (0 s) 86: IntegerCompression_MaximumCompression (0 s) 86: IntegerCompression_MultipleValues (0 s) 86: OneColumnDefaultNoWrite (0 s) 86: OneColumnDefaultNoWrite_Long (0 s) 86: MoveAhead (0 s) 86: OneColumnDefaultOverwite (0 s) 86: OneColumnChangeDefault (0 s) 86: OneColumnDataAndDefaultsMixed (0 s) 86: TwoColumnsFullRow (0 s) 86: TwoColumnsIncompleteRow (0 s) 86: TwoColumnsPartialRowWithDefaults (0 s) 86: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 86: EmptyDefault_String (0 s) 86: EmptyDefault_Int (0 s) 86: MultipleTables_Multiple_Columns_MultipleRows (0 s) 86: AdditionalSchemaIncludePaths_Single (0 s) 86: AdditionalSchemaIncludePaths_Multiple (0 s) 86: AdditionalSchemaFiles_Single (0 s) 86: AdditionalSchemaFiles_Multiple (0 s) 86: ErrorMessage (0 s) 86: ErrorMessage_Long (0 s) 86: LogMessage (0 s) 86: ProgressMessage (0 s) 86: TargetOverride (0 s) 86: 86: *** No errors detected (1 s total) 28/187 Test #86: GeneralLoaderWhiteBox ............................. Passed 2.39 sec test 87 Start 87: GWDumper 87: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-gw-dumper 87: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test 87: Test timeout computed to be: 1500 29/187 Test #87: GWDumper .......................................... Passed 0.00 sec test 88 Start 88: makeinputs 88: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/makeinputs 88: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 88: Test timeout computed to be: 1500 30/187 Test #88: makeinputs ........................................ Passed 0.01 sec test 89 Start 89: GeneralLoader-1.0-Basic-Unpacked 89: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "1" "0" "-I/usr/include/ncbi-vdb" 89: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 89: Test timeout computed to be: 1500 89: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 1 0 -I/usr/include/ncbi-vdb 89: running test case 1 89: cat input/1.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1/load.stderr 89: Load succeeded, dumping and matching stdout 89: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1/dump.stderr 31/187 Test #89: GeneralLoader-1.0-Basic-Unpacked .................. Passed 0.65 sec test 90 Start 90: GeneralLoader-1.1-Basic-Packed 90: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "1packed" "0" "-I/usr/include/ncbi-vdb" 90: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 90: Test timeout computed to be: 1500 90: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 1packed 0 -I/usr/include/ncbi-vdb 90: running test case 1packed 90: cat input/1packed.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stderr 90: Load succeeded, dumping and matching stdout 90: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1packed/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stderr 32/187 Test #90: GeneralLoader-1.1-Basic-Packed .................... Passed 0.91 sec test 91 Start 91: GeneralLoader-1.2-TargetDbOverride 91: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb --target actual/1override/db" 91: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 91: Test timeout computed to be: 1500 91: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb --target actual/1override/db 91: running test case 1override 91: cat input/1override.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb --target actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 91: Load succeeded, dumping and matching stdout 91: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 33/187 Test #91: GeneralLoader-1.2-TargetDbOverride ................ Passed 0.43 sec test 92 Start 92: GeneralLoader-1.3-TargetDbOverrideShorthand 92: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb -T actual/1override/db" 92: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 92: Test timeout computed to be: 1500 92: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb -T actual/1override/db 92: running test case 1override 92: cat input/1override.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -T actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 92: Load succeeded, dumping and matching stdout 92: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 34/187 Test #92: GeneralLoader-1.3-TargetDbOverrideShorthand ....... Passed 0.50 sec test 93 Start 93: GeneralLoader-2.0-ErrorMessageEvent-Unpacked 93: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "2" "3" "-I/usr/include/ncbi-vdb -L=err" 93: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 93: Test timeout computed to be: 1500 93: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 2 3 -I/usr/include/ncbi-vdb -L=err 93: running test case 2 93: cat input/2.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/2/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/2/load.stderr 93: Load failed as expected, matching stderr 35/187 Test #93: GeneralLoader-2.0-ErrorMessageEvent-Unpacked ...... Passed 0.52 sec test 94 Start 94: GeneralLoader-2.1-ErrorMessageEvent-Packed 94: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "2packed" "3" "-I/usr/include/ncbi-vdb -L=err" 94: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 94: Test timeout computed to be: 1500 94: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 2packed 3 -I/usr/include/ncbi-vdb -L=err 94: running test case 2packed 94: cat input/2packed.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stderr 94: Load failed as expected, matching stderr 36/187 Test #94: GeneralLoader-2.1-ErrorMessageEvent-Packed ........ Passed 0.31 sec test 95 Start 95: GeneralLoader-3.0-EmptyDefaultValues-Unpacked 95: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 95: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 95: Test timeout computed to be: 1500 95: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 95: running test case 3 95: cat input/3.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 95: Load succeeded, dumping and matching stdout 95: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 37/187 Test #95: GeneralLoader-3.0-EmptyDefaultValues-Unpacked ..... Passed 0.47 sec test 96 Start 96: GeneralLoader-3.1-EmptyDefaultValues-Packed 96: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 96: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 96: Test timeout computed to be: 1500 96: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 96: running test case 3 96: cat input/3.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 96: Load succeeded, dumping and matching stdout 96: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 38/187 Test #96: GeneralLoader-3.1-EmptyDefaultValues-Packed ....... Passed 0.48 sec test 97 Start 97: GeneralLoader-4.0-MoveAheadEvent-Unpacked 97: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "4" "0" "-I/usr/include/ncbi-vdb" 97: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 97: Test timeout computed to be: 1500 97: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 4 0 -I/usr/include/ncbi-vdb 97: running test case 4 97: cat input/4.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4/load.stderr 97: Load succeeded, dumping and matching stdout 97: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4/dump.stderr 39/187 Test #97: GeneralLoader-4.0-MoveAheadEvent-Unpacked ......... Passed 1.21 sec test 98 Start 98: GeneralLoader-4.1-MoveAheadEvent-Packed 98: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "4packed" "0" "-I/usr/include/ncbi-vdb" 98: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 98: Test timeout computed to be: 1500 98: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 4packed 0 -I/usr/include/ncbi-vdb 98: running test case 4packed 98: cat input/4packed.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stderr 98: Load succeeded, dumping and matching stdout 98: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4packed/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stderr 40/187 Test #98: GeneralLoader-4.1-MoveAheadEvent-Packed ........... Passed 0.45 sec test 99 Start 99: GeneralLoader-5.0-IntegerConversion 99: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "5packed" "0" "-I/usr/include/ncbi-vdb" 99: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 99: Test timeout computed to be: 1500 99: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 5packed 0 -I/usr/include/ncbi-vdb 99: running test case 5packed 99: cat input/5packed.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stderr 99: Load succeeded, dumping and matching stdout 99: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/5packed/db 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stderr 41/187 Test #99: GeneralLoader-5.0-IntegerConversion ............... Passed 0.56 sec test 100 Start 100: GeneralLoader-6.0-SoftwareName-Unpacked 100: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "6" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 100: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 100: Test timeout computed to be: 1500 100: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 6 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 100: running test case 6 100: cat input/6.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6/load.stderr 100: Load succeeded, dumping and matching stdout 100: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6/db SOFTWARE/formatter 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6/dump.stderr 42/187 Test #100: GeneralLoader-6.0-SoftwareName-Unpacked ........... Passed 0.30 sec test 101 Start 101: GeneralLoader-6.1-SoftwareName-Packed 101: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test" "6packed" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 101: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 101: Test timeout computed to be: 1500 101: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test 6packed 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 101: running test case 6packed 101: cat input/6packed.gl | /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stderr 101: Load succeeded, dumping and matching stdout 101: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6packed/db SOFTWARE/formatter 1>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stderr 43/187 Test #101: GeneralLoader-6.1-SoftwareName-Packed ............. Passed 0.36 sec test 102 Start 102: bio-end-makeinputs 102: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/bio-end-makeinputs 102: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 102: Test timeout computed to be: 1500 44/187 Test #102: bio-end-makeinputs ................................ Passed 0.00 sec test 103 Start 103: BioEnd-Excl-1 103: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" "-L=debug" 103: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 103: Test timeout computed to be: 1500 103: running test bio-end:excl-1 45/187 Test #103: BioEnd-Excl-1 ..................................... Passed 0.22 sec test 104 Start 104: BioEnd-Excl-2 104: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-2" "0" "n" "-I/usr/include/ncbi-vdb" 104: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 104: Test timeout computed to be: 1500 104: running test bio-end:excl-2 46/187 Test #104: BioEnd-Excl-2 ..................................... Passed 0.25 sec test 105 Start 105: BioEnd-Excl-3 105: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-3" "0" "n" "-I/usr/include/ncbi-vdb" 105: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 105: Test timeout computed to be: 1500 105: running test bio-end:excl-3 47/187 Test #105: BioEnd-Excl-3 ..................................... Passed 0.24 sec test 106 Start 106: BioEnd-Excl-4 106: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-4" "0" "n" "-I/usr/include/ncbi-vdb" 106: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 106: Test timeout computed to be: 1500 106: running test bio-end:excl-4 48/187 Test #106: BioEnd-Excl-4 ..................................... Passed 0.25 sec test 107 Start 107: BioEnd-Incl-1 107: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "incl-1" "0" "n" "-I/usr/include/ncbi-vdb" 107: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 107: Test timeout computed to be: 1500 107: running test bio-end:incl-1 49/187 Test #107: BioEnd-Incl-1 ..................................... Passed 0.30 sec test 108 Start 108: IdxText-CI-1 108: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" 108: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 108: Test timeout computed to be: 1500 108: running test bio-end:excl-1 50/187 Test #108: IdxText-CI-1 ...................................... Passed 0.24 sec test 109 Start 109: idx-text-makeinputs 109: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-makeinputs 109: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 109: Test timeout computed to be: 1500 51/187 Test #109: idx-text-makeinputs ............................... Passed 0.01 sec test 110 Start 110: IdxText-ci-1 110: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-1" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 110: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 110: Test timeout computed to be: 1500 110: running test idx-text:ci-1 52/187 Test #110: IdxText-ci-1 ...................................... Passed 0.27 sec test 111 Start 111: IdxText-ci-2 111: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-2" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 111: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 111: Test timeout computed to be: 1500 111: running test idx-text:ci-2 53/187 Test #111: IdxText-ci-2 ...................................... Passed 0.45 sec test 112 Start 112: IdxText-ci-3 112: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-3" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 112: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 112: Test timeout computed to be: 1500 112: running test idx-text:ci-3 54/187 Test #112: IdxText-ci-3 ...................................... Passed 0.23 sec test 113 Start 113: IdxText-ci-4 113: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-4" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 113: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 113: Test timeout computed to be: 1500 113: running test idx-text:ci-4 55/187 Test #113: IdxText-ci-4 ...................................... Passed 0.25 sec test 114 Start 114: IdxText-ci-5 114: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-5" "0" "n" "-I/usr/include/ncbi-vdb" 114: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 114: Test timeout computed to be: 1500 114: running test idx-text:ci-5 56/187 Test #114: IdxText-ci-5 ...................................... Passed 0.18 sec test 115 Start 115: IdxText-cs-1 115: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-1" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 115: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 115: Test timeout computed to be: 1500 115: running test idx-text:cs-1 57/187 Test #115: IdxText-cs-1 ...................................... Passed 0.23 sec test 116 Start 116: IdxText-cs-2 116: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-2" "0" "y" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 116: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 116: Test timeout computed to be: 1500 116: running test idx-text:cs-2 58/187 Test #116: IdxText-cs-2 ...................................... Passed 0.23 sec test 117 Start 117: IdxText-cs-3 117: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-3" "0" "n" "-I/usr/include/ncbi-vdb" 117: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/loaders/general-loader/test/vschema 117: Test timeout computed to be: 1500 117: running test idx-text:cs-3 59/187 Test #117: IdxText-cs-3 ...................................... Passed 0.15 sec test 118 Start 118: PileupStats-Version 118: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -V | grep --quiet `head -n 1 /build/reproducible-path/sra-sdk-3.0.9+dfsg/shared/toolkit.vers`" 118: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 118: Test timeout computed to be: 1500 60/187 Test #118: PileupStats-Version ............................... Passed 0.01 sec test 119 Start 119: PileupStats-Help 119: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -h | grep --quiet Usage" 119: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 119: Test timeout computed to be: 1500 61/187 Test #119: PileupStats-Help .................................. Passed 0.01 sec test 120 Start 120: PileupStats-NoArgs 120: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats; if [ $? == 0 ] ; then exit 1; fi;" 120: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 120: Test timeout computed to be: 1500 120: 120: Usage: 120: pileup-stats [options] 120: 120: Options: 120: -o|--output-file file for output 120: (default pipe to stdout) 120: -r|--remote-db name of remote database to create 120: (default .pileup_stat) 120: -x|--depth-cutoff cutoff for depth <= value (default 1) 120: -e|--event-cutoff cutoff for number of events > value (default 1) 120: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 120: -a|--align-category the types of alignments to pile up: 120: { primary, secondary, all } (default primary) 120: --buffer-size bytes size of output pipe buffer - default 32K bytes 120: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 120: -h|--help output brief explanation of the program 120: -v|--verbose increase the verbosity of the program. 120: -V|--version display the version of the program then quit. 120: use multiple times for more verbosity. 120: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 120: 120: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 120: 120: /usr/bin/sh: 1: [: 3: unexpected operator 62/187 Test #120: PileupStats-NoArgs ................................ Passed 0.01 sec test 121 Start 121: PileupStats-IgnoreArgs-L 121: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -L 1; if [ $? == 0 ] ; then exit 1; fi;" 121: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 121: Test timeout computed to be: 1500 121: 121: Usage: 121: pileup-stats [options] 121: 121: Options: 121: -o|--output-file file for output 121: (default pipe to stdout) 121: -r|--remote-db name of remote database to create 121: (default .pileup_stat) 121: -x|--depth-cutoff cutoff for depth <= value (default 1) 121: -e|--event-cutoff cutoff for number of events > value (default 1) 121: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 121: -a|--align-category the types of alignments to pile up: 121: { primary, secondary, all } (default primary) 121: --buffer-size bytes size of output pipe buffer - default 32K bytes 121: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 121: -h|--help output brief explanation of the program 121: -v|--verbose increase the verbosity of the program. 121: -V|--version display the version of the program then quit. 121: use multiple times for more verbosity. 121: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 121: 121: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 121: 121: /usr/bin/sh: 1: [: 3: unexpected operator 63/187 Test #121: PileupStats-IgnoreArgs-L .......................... Passed 0.01 sec test 122 Start 122: PileupStats-IgnoreArgs-z 122: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -z ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 122: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 122: Test timeout computed to be: 1500 122: 122: Usage: 122: pileup-stats [options] 122: 122: Options: 122: -o|--output-file file for output 122: (default pipe to stdout) 122: -r|--remote-db name of remote database to create 122: (default .pileup_stat) 122: -x|--depth-cutoff cutoff for depth <= value (default 1) 122: -e|--event-cutoff cutoff for number of events > value (default 1) 122: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 122: -a|--align-category the types of alignments to pile up: 122: { primary, secondary, all } (default primary) 122: --buffer-size bytes size of output pipe buffer - default 32K bytes 122: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 122: -h|--help output brief explanation of the program 122: -v|--verbose increase the verbosity of the program. 122: -V|--version display the version of the program then quit. 122: use multiple times for more verbosity. 122: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 122: 122: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 122: 122: /usr/bin/sh: 1: [: 3: unexpected operator 64/187 Test #122: PileupStats-IgnoreArgs-z .......................... Passed 0.01 sec test 123 Start 123: PileupStats-IgnoreArgs-loglevel 123: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --log-level 1; if [ $? == 0 ] ; then exit 1; fi;" 123: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 123: Test timeout computed to be: 1500 123: 123: Usage: 123: pileup-stats [options] 123: 123: Options: 123: -o|--output-file file for output 123: (default pipe to stdout) 123: -r|--remote-db name of remote database to create 123: (default .pileup_stat) 123: -x|--depth-cutoff cutoff for depth <= value (default 1) 123: -e|--event-cutoff cutoff for number of events > value (default 1) 123: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 123: -a|--align-category the types of alignments to pile up: 123: { primary, secondary, all } (default primary) 123: --buffer-size bytes size of output pipe buffer - default 32K bytes 123: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 123: -h|--help output brief explanation of the program 123: -v|--verbose increase the verbosity of the program. 123: -V|--version display the version of the program then quit. 123: use multiple times for more verbosity. 123: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 123: 123: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 123: 123: /usr/bin/sh: 1: [: 3: unexpected operator 65/187 Test #123: PileupStats-IgnoreArgs-loglevel ................... Passed 0.01 sec test 124 Start 124: PileupStats-IgnoreArgs-xmllog 124: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 124: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 124: Test timeout computed to be: 1500 124: 124: Usage: 124: pileup-stats [options] 124: 124: Options: 124: -o|--output-file file for output 124: (default pipe to stdout) 124: -r|--remote-db name of remote database to create 124: (default .pileup_stat) 124: -x|--depth-cutoff cutoff for depth <= value (default 1) 124: -e|--event-cutoff cutoff for number of events > value (default 1) 124: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 124: -a|--align-category the types of alignments to pile up: 124: { primary, secondary, all } (default primary) 124: --buffer-size bytes size of output pipe buffer - default 32K bytes 124: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 124: -h|--help output brief explanation of the program 124: -v|--verbose increase the verbosity of the program. 124: -V|--version display the version of the program then quit. 124: use multiple times for more verbosity. 124: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 124: 124: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 124: 124: /usr/bin/sh: 1: [: 3: unexpected operator 66/187 Test #124: PileupStats-IgnoreArgs-xmllog ..................... Passed 0.01 sec test 125 Start 125: PileupStats-IgnoreArgs-xmllogfd 125: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log-fd ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 125: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 125: Test timeout computed to be: 1500 125: 125: Usage: 125: pileup-stats [options] 125: 125: Options: 125: -o|--output-file file for output 125: (default pipe to stdout) 125: -r|--remote-db name of remote database to create 125: (default .pileup_stat) 125: -x|--depth-cutoff cutoff for depth <= value (default 1) 125: -e|--event-cutoff cutoff for number of events > value (default 1) 125: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 125: -a|--align-category the types of alignments to pile up: 125: { primary, secondary, all } (default primary) 125: --buffer-size bytes size of output pipe buffer - default 32K bytes 125: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 125: -h|--help output brief explanation of the program 125: -v|--verbose increase the verbosity of the program. 125: -V|--version display the version of the program then quit. 125: use multiple times for more verbosity. 125: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 125: 125: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.9 125: 125: /usr/bin/sh: 1: [: 3: unexpected operator 67/187 Test #125: PileupStats-IgnoreArgs-xmllogfd ................... Passed 0.01 sec test 126 Start 126: test-vdb 126: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb 126: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/vdb 126: Test timeout computed to be: 1500 126: Running 38 test cases... 126: Error_RcToString (0 s) 126: Error_RcToString_English (0 s) 126: Manager_Construction (0 s) 126: RC 1426393646 thrown by ./libs/inc/vdb.hpp:239 126: Manager_Schema_Bad (0 s) 126: Manager_Schema_Good (0 s) 126: Manager_Schema_Include (0 s) 126: Manager_SchemaFromFile (0 s) 126: Manager_SchemaFromFile_Bad (0 s) 126: RC 2615477144 thrown by ./libs/inc/vdb.hpp:621 126: Manager_Database_Bad (0 s) 126: Manager_OpenDatabase_Good (0 s) 126: RC 1273301772 thrown by ./libs/inc/vdb.hpp:628 126: Manager_OpenTable_Bad (0 s) 126: Manager_OpenTable_Good (0 s) 126: Manager_PathType_Table (0 s) 126: Manager_PathType_Database (0 s) 126: Manager_PathType_Invalid (1 s) 126: RC 807538648 thrown by ./libs/inc/vdb.hpp:551 126: Database_Table_Bad (0 s) 126: Database_Table_Good (0 s) 126: Database_hasTable_Yes (0 s) 126: Database_hasTable_No (0 s) 126: Table_Default (0 s) 126: Table_Assign (0 s) 126: RC 1367638680 thrown by ./libs/inc/vdb.hpp:437 126: Table_ReadCursor1_BadColumn (0 s) 126: Table_ReadCursor1 (0 s) 126: RC 1367638680 thrown by ./libs/inc/vdb.hpp:470 126: Table_ReadCursor2_BadColumn (0 s) 126: Table_ReadCursor2 (0 s) 126: Table_PhysicaColumns (0 s) 126: Cursor_Columns (0 s) 126: Cursor_RowRange (0 s) 126: Cursor_ReadOne (0 s) 126: Cursor_ReadN (0 s) 126: Cursor_ForEach (0 s) 126: Cursor_ForEachWithFilter (0 s) 126: Cursor_IsStaticColumn_True (0 s) 126: Cursor_IsStaticColumn_False (0 s) 126: RawData_asVector_badCast (0 s) 126: RawData_asVector (0 s) 126: RawData_value_badCast (0 s) 126: RawData_value (0 s) 126: 126: *** No errors detected (2 s total) 68/187 Test #126: test-vdb .......................................... Passed 2.57 sec test 127 Start 127: Test_NgsJava_lib_load 127: Test command: /usr/bin/java "-cp" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java/junit-4.11.jar" "-Dvdb.System.loadLibrary=1" "-Dvdb.log=FINEST" "org.junit.runner.JUnitCore" "gov.nih.nlm.ncbi.ngs.ngs_test_lib_load" 127: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/ngs/ngs-java 127: Test timeout computed to be: 1500 127: JUnit version 4.11 127: ......... 127: Time: 0.087 127: 127: OK (9 tests) 127: 69/187 Test #127: Test_NgsJava_lib_load ............................. Passed 0.36 sec test 131 Start 131: Test_Align_Info 131: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/align-info "-h" 131: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/align-info 131: Test timeout computed to be: 1500 131: Usage: 131: align-info [options] 131: 131: Summary: 131: Print database alignment information 131: 131: Parameters: 131: db-path Path to the database 131: 131: Options: 131: -a|--all print all information 131: -r|--ref print refseq information [default] 131: -b|--bam print bam header (if present) 131: -Q|--qual print quality statistics (if present) 131: -H|--headers print headers for output blocks 131: --ngc path to ngc file 131: 131: -h|--help Output brief explanation for the program. 131: -V|--version Display the version of the program then 131: quit. 131: -L|--log-level Logging level as number or enum string. One 131: of (fatal|sys|int|err|warn|info|debug) or 131: (0-6) Current/default is warn. 131: -v|--verbose Increase the verbosity of the program 131: status messages. Use multiple times for more 131: verbosity. Negates quiet. 131: -q|--quiet Turn off all status messages for the 131: program. Negated by verbose. 131: --option-file Read more options and parameters from the 131: file. 131: 131: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/align-info : 3.0.9 131: 70/187 Test #131: Test_Align_Info ................................... Passed 0.01 sec test 132 Start 132: Test_Drivertool_BuildVersion 132: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_BuildVersion 132: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 132: Test timeout computed to be: 1500 132: Test_Version passed. 71/187 Test #132: Test_Drivertool_BuildVersion ...................... Passed 0.00 sec test 133 Start 133: Test_Drivertool_FilePath 133: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_FilePath 133: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 133: Test timeout computed to be: 1500 133: Running 27 test cases... 133: DefaultConstruct (0 s) 133: Construct_Cstring (0 s) 133: Construct_String (0 s) 133: CopyConstruct_Empty (0 s) 133: CopyConstruct (0 s) 133: Assign_Empty (0 s) 133: Assign (0 s) 133: Copy (0 s) 133: Split (0 s) 133: BaseName (0 s) 133: Append (0 s) 133: RemoveSuffix_0 (0 s) 133: RemoveSuffix (0 s) 133: RemoveSuffix_Ext (0 s) 133: RemoveSuffix_Oversized (0 s) 133: SimpleName (0 s) 133: CWD (0 s) 133: Exists (0 s) 133: CWD_Append (0 s) 133: Exists_Static (0 s) 133: Readable (0 s) 133: IsSame_Directory (0 s) 133: NotIsSame_Directory (0 s) 133: IsSame_File (0 s) 133: NotIsSame_File (0 s) 133: Current_Executable (0 s) 133: Executable_Yes (0 s) 133: 133: *** No errors detected (0 s total) 72/187 Test #133: Test_Drivertool_FilePath .......................... Passed 0.01 sec test 134 Start 134: Test_Drivertool_CommandLine 134: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_CommandLine 134: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 134: Test timeout computed to be: 1500 134: Test_CommandLine passed. 73/187 Test #134: Test_Drivertool_CommandLine ....................... Passed 0.00 sec test 135 Start 135: Test_Drivertool_JsonParsing 135: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_JsonParsing 135: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 135: Test timeout computed to be: 1500 74/187 Test #135: Test_Drivertool_JsonParsing ....................... Passed 0.02 sec test 136 Start 136: Test_Drivertool_SDLResponse 136: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_SDLResponse 136: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 136: Test timeout computed to be: 1500 75/187 Test #136: Test_Drivertool_SDLResponse ....................... Passed 0.01 sec test 137 Start 137: Test_Drivertool_Accession 137: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_Accession 137: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 137: Test timeout computed to be: 1500 76/187 Test #137: Test_Drivertool_Accession ......................... Passed 0.00 sec test 138 Start 138: Test_Drivertool_UUID 138: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_UUID 138: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 138: Test timeout computed to be: 1500 77/187 Test #138: Test_Drivertool_UUID .............................. Passed 0.83 sec test 139 Start 139: Test_Drivertool_RunSource 139: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_RunSource 139: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 139: Test timeout computed to be: 1500 139: Running 18 test cases... 139: CopmmandLine_GetToolPath (0 s) 139: CommandLine_Defaults (0 s) 139: UnknownTool (0 s) 139: URL_parameter (0 s) 139: ConstructNoSDL (0 s) 139: ConstructSDL_false (0 s) 139: ConstructSDL_true (0 s) 139: ConstructSDL_badSDL (0 s) 139: ConstructSDL_noResults (0 s) 139: ConstructSDL_oneResult (0 s) 139: ConstructSDL_multipleFiles (0 s) 139: ConstructSDL_multipleLocations (0 s) 139: Query SRR000001: Error 400 no data 139: ConstructSDL_status_400 (0 s) 139: ConstructSDL_status_404 (0 s) 139: No usable source for SRR000001 was found. 139: SRR000001 might be available in a different cloud provider or region. 139: ConstructSDL_pileupIgnored (0 s) 139: No usable source for SRR000001 was found. 139: SRR000001 might be available in a different cloud provider or region. 139: ConstructSDL_noObject_Ignored (0 s) 139: No usable source for SRR000001 was found. 139: SRR000001 might be available in a different cloud provider or region. 139: ConstructSDL_noQuality_Ignored (0 s) 139: No usable source for SRR000001 was found. 139: SRR000001 might be available in a different cloud provider or region. 139: ConstructSDL_Encrypted_NoNGC_Skipped (0 s) 139: 139: *** No errors detected (0 s total) 78/187 Test #139: Test_Drivertool_RunSource ......................... Passed 0.01 sec test 140 Start 140: Test_Drivertool_ToolArgs 140: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_ToolArgs 140: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/driver-tool 140: Test timeout computed to be: 1500 140: Running 1 test case... 140: ParseArgs (0 s) 140: 140: *** No errors detected (0 s total) 79/187 Test #140: Test_Drivertool_ToolArgs .......................... Passed 0.01 sec test 141 Start 141: Test_FasterqDump_Help 141: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump "-h" 141: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump 141: Test timeout computed to be: 1500 141: 141: Usage: 141: fasterq-dump [options] 141: fasterq-dump [options] 141: 141: Options: 141: -F|--format format (special, fastq, default=fastq) 141: -o|--outfile output-file 141: -O|--outdir output-dir 141: -b|--bufsize size of file-buffer dflt=1MB 141: -c|--curcache size of cursor-cache dflt=10MB 141: -m|--mem memory limit for sorting dflt=100MB 141: -t|--temp where to put temp. files dflt=curr dir 141: -e|--threads how many thread dflt=6 141: -p|--progress show progress 141: -x|--details print details 141: -s|--split-spot split spots into reads 141: -S|--split-files write reads into different files 141: -3|--split-3 writes single reads in special file 141: --concatenate-reads writes whole spots into one file 141: -Z|--stdout print output to stdout 141: -f|--force force to overwrite existing file(s) 141: --skip-technical skip technical reads 141: --include-technical include technical reads 141: -M|--min-read-len filter by sequence-len 141: --table which seq-table to use in case of pacbio 141: -B|--bases filter by bases 141: -A|--append append to output-file 141: --fasta produce FASTA output 141: --fasta-unsorted produce FASTA output, unsorted 141: --fasta-ref-tbl produce FASTA output from REFERENCE tbl 141: --fasta-concat-all concatenate all rows and produce FASTA 141: --internal-ref extract only internal REFERENCEs 141: --external-ref extract only external REFERENCEs 141: --ref-name extract only these REFERENCEs 141: --ref-report enumerate references 141: --use-name print name instead of seq-id 141: --seq-defline custom defline for sequence: $ac=accession, 141: $sn=spot-name, $sg=spot-group, $si=spot-id, 141: $ri=read-id, $rl=read-length 141: --qual-defline custom defline for qualities: same as 141: seq-defline 141: -U|--only-unaligned process only unaligned reads 141: -a|--only-aligned process only aligned reads 141: --disk-limit explicitly set disk-limit 141: --disk-limit-tmp explicitly set disk-limit for temp. files 141: --size-check switch to control: on=perform size-check 141: (default), off=do not perform size-check, 141: only=perform size-check only 141: --ngc PATH to ngc file 141: 141: -h|--help Output brief explanation for the program. 141: -V|--version Display the version of the program then 141: quit. 141: -L|--log-level Logging level as number or enum string. One 141: of (fatal|sys|int|err|warn|info|debug) or 141: (0-6) Current/default is warn. 141: -v|--verbose Increase the verbosity of the program 141: status messages. Use multiple times for more 141: verbosity. Negates quiet. 141: -q|--quiet Turn off all status messages for the 141: program. Negated by verbose. 141: --option-file Read more options and parameters from the 141: file. 141: for more information visit: 141: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump 141: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump 141: 141: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump : 3.0.9 141: 80/187 Test #141: Test_FasterqDump_Help ............................. Passed 0.01 sec test 142 Start 142: Test_FasterqDump_NotZeroWithoutParameters 142: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump 142: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump 142: Test timeout computed to be: 1500 142: 142: Usage: 142: fasterq-dump [options] 142: fasterq-dump [options] 142: 142: Options: 142: -F|--format format (special, fastq, default=fastq) 142: -o|--outfile output-file 142: -O|--outdir output-dir 142: -b|--bufsize size of file-buffer dflt=1MB 142: -c|--curcache size of cursor-cache dflt=10MB 142: -m|--mem memory limit for sorting dflt=100MB 142: -t|--temp where to put temp. files dflt=curr dir 142: -e|--threads how many thread dflt=6 142: -p|--progress show progress 142: -x|--details print details 142: -s|--split-spot split spots into reads 142: -S|--split-files write reads into different files 142: -3|--split-3 writes single reads in special file 142: --concatenate-reads writes whole spots into one file 142: -Z|--stdout print output to stdout 142: -f|--force force to overwrite existing file(s) 142: --skip-technical skip technical reads 142: --include-technical include technical reads 142: -M|--min-read-len filter by sequence-len 142: --table which seq-table to use in case of pacbio 142: -B|--bases filter by bases 142: -A|--append append to output-file 142: --fasta produce FASTA output 142: --fasta-unsorted produce FASTA output, unsorted 142: --fasta-ref-tbl produce FASTA output from REFERENCE tbl 142: --fasta-concat-all concatenate all rows and produce FASTA 142: --internal-ref extract only internal REFERENCEs 142: --external-ref extract only external REFERENCEs 142: --ref-name extract only these REFERENCEs 142: --ref-report enumerate references 142: --use-name print name instead of seq-id 142: --seq-defline custom defline for sequence: $ac=accession, 142: $sn=spot-name, $sg=spot-group, $si=spot-id, 142: $ri=read-id, $rl=read-length 142: --qual-defline custom defline for qualities: same as 142: seq-defline 142: -U|--only-unaligned process only unaligned reads 142: -a|--only-aligned process only aligned reads 142: --disk-limit explicitly set disk-limit 142: --disk-limit-tmp explicitly set disk-limit for temp. files 142: --size-check switch to control: on=perform size-check 142: (default), off=do not perform size-check, 142: only=perform size-check only 142: --ngc PATH to ngc file 142: 142: -h|--help Output brief explanation for the program. 142: -V|--version Display the version of the program then 142: quit. 142: -L|--log-level Logging level as number or enum string. One 142: of (fatal|sys|int|err|warn|info|debug) or 142: (0-6) Current/default is warn. 142: -v|--verbose Increase the verbosity of the program 142: status messages. Use multiple times for more 142: verbosity. Negates quiet. 142: -q|--quiet Turn off all status messages for the 142: program. Negated by verbose. 142: --option-file Read more options and parameters from the 142: file. 142: for more information visit: 142: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump 142: https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump 142: 142: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump : 3.0.9 142: 81/187 Test #142: Test_FasterqDump_NotZeroWithoutParameters ......... Passed 0.01 sec test 143 Start 143: Test_FasterDump_Fasta_unsorted_flat_tbl_read_id 143: Test command: /usr/bin/bash "test_for_read_id_flat.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 143: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump 143: Test timeout computed to be: 1500 143: spots read : 10 143: reads read : 20 143: reads written : 20 143: READ_ID1: 10 143: READ_ID2: 10 143: success testing read-id for --fasta-unsorted mode on flat table 82/187 Test #143: Test_FasterDump_Fasta_unsorted_flat_tbl_read_id ... Passed 0.39 sec test 144 Start 144: Test_FasterDump_Fasta_unsorted_cSRA_read_id 144: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump" "bash" "-c" "echo 'vdb/schema/paths = "/usr/include/ncbi-vdb"' > tmp.kfg; ./test_for_read_id_cSRA.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 144: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump 144: Test timeout computed to be: 1500 144: spots read : 10 144: reads read : 20 144: reads written : 20 144: READ_ID1: 10 144: READ_ID2: 10 144: success testing read-id for --fasta-unsorted mode on cSRA table 83/187 Test #144: Test_FasterDump_Fasta_unsorted_cSRA_read_id ....... Passed 0.90 sec test 145 Start 145: Test_Tiny_cSRA 145: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump" "bash" "-c" "echo 'vdb/schema/paths = "/usr/include/ncbi-vdb"' > tmp.kfg; ./tiny_csra.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 145: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/fasterq-dump 145: Test timeout computed to be: 1500 145: 145: testing /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump on tiny cSRA-accession 145: spots read : 3 145: reads read : 3 145: reads written : 3 84/187 Test #145: Test_Tiny_cSRA .................................... Passed 1.82 sec test 159 Start 159: SamDumpTestSetup 159: Test command: /usr/bin/bash "-c" "echo 'vdb/schema/paths = "/usr/include/ncbi-vdb" /LIBS/GUID="8test002-6ab7-41b2-bfd0-sam-dump-test"' > tmp.kfg" 159: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump 159: Test timeout computed to be: 1500 85/187 Test #159: SamDumpTestSetup .................................. Passed 0.00 sec test 160 Start 160: Test_sam_dump_verify_omit 160: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump" "./verify_omit_qual.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 160: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump 160: Test timeout computed to be: 1500 86/187 Test #160: Test_sam_dump_verify_omit ......................... Passed 2.20 sec test 161 Start 161: Test_sam_dump_star_quality 161: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump" "./print_star_on_missing_qual.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 161: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sam-dump 161: Test timeout computed to be: 1500 87/187 Test #161: Test_sam_dump_star_quality ........................ Passed 1.36 sec test 162 Start 162: Test_Srapath_Check_exit_code 162: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=../.." "/usr/bin/python3" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/srapath" 162: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/srapath 162: Test timeout computed to be: 1500 162: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/srapath] 88/187 Test #162: Test_Srapath_Check_exit_code ...................... Passed 0.08 sec test 164 Start 164: Test_SraPileup_Check_exit_code 164: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=.." "/usr/bin/python3" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-pileup" 164: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-pileup 164: Test timeout computed to be: 1500 164: WARNING[TEST1] help message is in 'STDOUT' 164: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-pileup] 89/187 Test #164: Test_SraPileup_Check_exit_code .................... Passed 0.13 sec test 168 Start 168: Test_VDB_Config_model 168: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config/model.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model" 168: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config 168: Test timeout computed to be: 1500 168: testing /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model 168: Running 11 test cases... 168: get_config_changed (0 s) 168: prefetch_download_to_cache (0 s) 168: user_accept_aws_charges (0 s) 168: user_accept_gcp_charges (0 s) 168: ./test/external/vdb-config/test-vdb-config-model.cpp:92: fatal error in "temp_cache_location": critical check string ( "path" ) == m . get_temp_cache_location() failed [path != /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config/path] 168: temp_cache_location (0 s) 168: gcp_credential_file_location (0 s) 168: aws_credential_file_location (0 s) 168: aws_profile (0 s) 168: noCommit (0 s) 168: Commit (0 s) 168: Reload (0 s) 168: 168: *** 1 failure detected in test suite "VdbConfStridesModelTestSuite" 168: VDB Copy model test is finished 90/187 Test #168: Test_VDB_Config_model ............................. Passed 0.16 sec test 169 Start 169: Test_VDB_Config 169: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config/test-vdb-config.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 169: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-config 169: Test timeout computed to be: 1500 169: Testing /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-config... 169: VDB config test is finished 91/187 Test #169: Test_VDB_Config ................................... Passed 0.09 sec test 170 Start 170: Test_Vdb_dump_Check_exit_code 170: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=.." "/usr/bin/python3" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" 170: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump 170: Test timeout computed to be: 1500 170: WARNING[TEST1] help message is in 'STDOUT' 170: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump] 92/187 Test #170: Test_Vdb_dump_Check_exit_code ..................... Passed 0.13 sec test 171 Start 171: Test_Vdb_dump_view-spec 171: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Vdb_dump_view-spec 171: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-dump 171: Test timeout computed to be: 1500 171: Running 21 test cases... 171: NullSelf (0 s) 171: NullSpec (0 s) 171: EmptySpec (0 s) 171: NullError (0 s) 171: ZeroSizeError (0 s) 171: MissingLeftAngle (0 s) 171: EmptyAngles (0 s) 171: OneParam (0 s) 171: ManyParams (0 s) 171: MissingComma (0 s) 171: MissingParam (0 s) 171: ExtraChars (0 s) 171: NestedViews (0 s) 171: ViewSpecOpen_NullSelf (0 s) 171: ViewSpecOpen_NullParam_Db (0 s) 171: ViewSpecOpen_NullParam_Schema (0 s) 171: ViewSpecOpen_NullParam_View (0 s) 171: ViewSpecOpen_WrongNumberOfParams (0 s) 171: ViewSpecOpen_ParamNotTable (0 s) 171: MakeCursor (0 s) 171: NestedView (0 s) 171: 171: *** No errors detected (0 s total) 93/187 Test #171: Test_Vdb_dump_view-spec ........................... Passed 0.08 sec test 174 Start 174: Test_VdbValidate_Unit 174: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_VdbValidate_Unit 174: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/vdb-validate 174: Test timeout computed to be: 1500 174: Running 3 test cases... 174: is_sorted_empty (0 s) 174: is_sorted_sorted (0 s) 174: is_sorted_unsorted (0 s) 174: 174: *** No errors detected (0 s total) 94/187 Test #174: Test_VdbValidate_Unit ............................. Passed 0.01 sec test 178 Start 178: Test_Sra_Info_Help 178: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info "-h" ">actual/Test_Sra_Info_Help.stdout" 178: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 178: Test timeout computed to be: 1500 178: 178: Usage: 178: sra-info [options] 178: 178: Options: 178: -P|--platform print platform(s) 178: -Q|--quality are quality scores stored or generated 178: -A|--is-aligned is data aligned 178: -C|--schema print schema version and dependencies 178: -S|--spot-layout print spot layout(s). Uses CONSENSUS table 178: if present, SEQUENCE table otherwise 178: -f|--format output format: 178: csv ..... comma separated values on one line 178: xml ..... xml-style 178: json .... json-style 178: tab ..... tab-separated values on one line 178: csv and tab formats can be used just with a single query 178: --schema does npt support csv and tab 178: -l|--limit limit output to elements, e.g. most 178: popular spot layouts; must be positive 178: -D|--detail detail level, <0> the least detailed 178: output; must be or greater 178: -R|--rows report spot layouts for the first rows 178: of the table 178: -h|--help Output brief explanation for the program. 178: -V|--version Display the version of the program then 178: quit. 178: -L|--log-level Logging level as number or enum string. One 178: of (fatal|sys|int|err|warn|info|debug) or 178: (0-6) Current/default is warn. 178: -v|--verbose Increase the verbosity of the program 178: status messages. Use multiple times for more 178: verbosity. Negates quiet. 178: -q|--quiet Turn off all status messages for the 178: program. Negated by verbose. 178: --option-file Read more options and parameters from the 178: file. 178: 178: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info : 3.0.9 178: 95/187 Test #178: Test_Sra_Info_Help ................................ Passed 0.01 sec test 179 Start 179: Test_Sra_Info_NoParam 179: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info 179: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 179: Test timeout computed to be: 1500 179: 179: Usage: 179: sra-info [options] 179: 179: 179: Use option --help for more information. 179: 96/187 Test #179: Test_Sra_Info_NoParam ............................. Passed 0.06 sec test 180 Start 180: Test_Sra_Info_MultipleParams 180: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info "SRR000123" "SRR0001234" 180: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 180: Test timeout computed to be: 1500 180: 180: Usage: 180: sra-info [options] 180: 180: 180: Use option --help for more information. 180: 97/187 Test #180: Test_Sra_Info_MultipleParams ...................... Passed 0.06 sec test 181 Start 181: Test_Sra_Info_Limit_Negative 181: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info "--spot-layout" "DRR032985" "--limit" "-1" 181: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 181: Test timeout computed to be: 1500 181: 181: 181: invalid value for --limit(not a positive number) 98/187 Test #181: Test_Sra_Info_Limit_Negative ...................... Passed 0.06 sec test 182 Start 182: Test_Sra_Info_Limit_Zero 182: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info "--spot-layout" "DRR032985" "--limit" "0" 182: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 182: Test timeout computed to be: 1500 182: 182: 182: invalid value for --limit(not a positive number) 99/187 Test #182: Test_Sra_Info_Limit_Zero .......................... Passed 0.06 sec test 188 Start 188: Test_Sra_Info_Platform_Format_CSV 188: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f csv" "." "4.1" 188: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 188: Test timeout computed to be: 1500 188: running 4.1 188: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f csv 1>./actual/4.1/stdout 2>./actual/4.1/stderr 100/187 Test #188: Test_Sra_Info_Platform_Format_CSV ................. Passed 0.22 sec test 189 Start 189: Test_Sra_Info_Platform_Format_XML 189: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f xml" "." "4.2" 189: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 189: Test timeout computed to be: 1500 189: running 4.2 189: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f xml 1>./actual/4.2/stdout 2>./actual/4.2/stderr 101/187 Test #189: Test_Sra_Info_Platform_Format_XML ................. Passed 0.28 sec test 190 Start 190: Test_Sra_Info_Platform_Format_Json 190: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f json" "." "4.3" 190: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 190: Test timeout computed to be: 1500 190: running 4.3 190: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f json 1>./actual/4.3/stdout 2>./actual/4.3/stderr 102/187 Test #190: Test_Sra_Info_Platform_Format_Json ................ Passed 0.24 sec test 191 Start 191: Test_Sra_Info_Platform_Format_Tab 191: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f tab" "." "4.4" 191: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 191: Test timeout computed to be: 1500 191: running 4.4 191: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -P ./input/MultiPlatform.sra -f tab 1>./actual/4.4/stdout 2>./actual/4.4/stderr 103/187 Test #191: Test_Sra_Info_Platform_Format_Tab ................. Passed 0.24 sec test 192 Start 192: Test_Sra_Info_IsAligned_No 192: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -A SRR000123" "." "5.1" 192: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 192: Test timeout computed to be: 1500 192: running 5.1 192: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info -A SRR000123 1>./actual/5.1/stdout 2>./actual/5.1/stderr 104/187 Test #192: Test_Sra_Info_IsAligned_No ........................ Passed 1.37 sec test 194 Start 194: Test_Sra_Info_Quality_Physical 194: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --quality ./input/MultiPlatform.sra" "." "6.1" 194: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 194: Test timeout computed to be: 1500 194: running 6.1 194: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --quality ./input/MultiPlatform.sra 1>./actual/6.1/stdout 2>./actual/6.1/stderr 105/187 Test #194: Test_Sra_Info_Quality_Physical .................... Passed 0.25 sec test 208 Start 208: Test_Sra_Info_Schema_Default 208: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra" "." "9.0" 208: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 208: Test timeout computed to be: 1500 208: running 9.0 208: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra 1>./actual/9.0/stdout 2>./actual/9.0/stderr 106/187 Test #208: Test_Sra_Info_Schema_Default ...................... Passed 0.49 sec test 209 Start 209: Test_Sra_Info_Schema_Json 209: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra -fjson" "." "9.1" 209: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 209: Test timeout computed to be: 1500 209: running 9.1 209: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra -fjson 1>./actual/9.1/stdout 2>./actual/9.1/stderr 107/187 Test #209: Test_Sra_Info_Schema_Json ......................... Passed 0.22 sec test 210 Start 210: Test_Sra_Info_Schema_Xml 210: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra -fxml" "." "9.2" 210: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 210: Test timeout computed to be: 1500 210: running 9.2 210: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info --schema input/MultiPlatform.sra -fxml 1>./actual/9.2/stdout 2>./actual/9.2/stderr 108/187 Test #210: Test_Sra_Info_Schema_Xml .......................... Passed 0.22 sec test 211 Start 211: Test_Sra_Info_ACPQS_Default 211: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS" "." "10.0" 211: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 211: Test timeout computed to be: 1500 211: running 10.0 211: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS 1>./actual/10.0/stdout 2>./actual/10.0/stderr 109/187 Test #211: Test_Sra_Info_ACPQS_Default ....................... Passed 0.57 sec test 212 Start 212: Test_Sra_Info_ACPQS_Json 212: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS -fjson" "." "10.1" 212: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 212: Test timeout computed to be: 1500 212: running 10.1 212: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS -fjson 1>./actual/10.1/stdout 2>./actual/10.1/stderr 110/187 Test #212: Test_Sra_Info_ACPQS_Json .......................... Passed 0.62 sec test 213 Start 213: Test_Sra_Info_ACPQS_Xml 213: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS -fxml" "." "10.2" 213: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/external/sra-info 213: Test timeout computed to be: 1500 213: running 10.2 213: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/sra-info input/MultiPlatform.sra -ACPQS -fxml 1>./actual/10.2/stdout 2>./actual/10.2/stderr 111/187 Test #213: Test_Sra_Info_ACPQS_Xml ........................... Passed 0.52 sec test 214 Start 214: BamTestSetup 214: Test command: /usr/bin/bash "-c" "echo 'vdb/schema/paths = "/usr/include/ncbi-vdb" /LIBS/GUID="8test002-6ab7-41b2-bfd0-bamfload"' > tmp.kfg" 214: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load 214: Test timeout computed to be: 1500 112/187 Test #214: BamTestSetup ...................................... Passed 0.01 sec test 215 Start 215: Test_BamLoader_1 215: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load" "bash" "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/bam-load -o out.sra test.sam" 215: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load 215: Test timeout computed to be: 1500 113/187 Test #215: Test_BamLoader_1 .................................. Passed 0.44 sec test 216 Start 216: Test_BamLoader_MinBatchSize 216: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load" "bash" "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/bam-load -o out.sra --min-batch-size 999999 test.sam" 216: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load 216: Test timeout computed to be: 1500 114/187 Test #216: Test_BamLoader_MinBatchSize ....................... Passed 0.46 sec test 217 Start 217: Test_BamLoader_MinBatchSize_Bad 217: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load" "bash" "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/bam-load -o out.sra --min-batch-size notanumber test.sam" 217: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load 217: Test timeout computed to be: 1500 217: min-batch-size: bad value 217: Usage: 217: bam-load [options] 217: 217: Summary: 217: Load a BAM formatted data file 217: 217: Example: 217: bam-load -o /tmp/SRZ123456 -k analysis.bam.cfg 123456.bam 217: 217: 217: Use option --help for more information. 217: 217: 2024-05-29T09:33:15 bam-load.3.0.9 err: param incorrect while accessing argument list within application support module - load failed 115/187 Test #217: Test_BamLoader_MinBatchSize_Bad ................... Passed 0.06 sec test 218 Start 218: Test_BamLoader_platform 218: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_BamLoader_platform 218: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/bam-load 218: Test timeout computed to be: 1500 116/187 Test #218: Test_BamLoader_platform ........................... Passed 0.00 sec test 219 Start 219: LatfTestSetup 219: Test command: /usr/bin/bash "-c" "echo 'vdb/schema/paths = "/usr/include/ncbi-vdb" /LIBS/GUID="8test002-6ab7-41b2-bfd0-latfload"' > tmp.kfg" 219: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 219: Test timeout computed to be: 1500 117/187 Test #219: LatfTestSetup ..................................... Passed 0.00 sec test 220 Start 220: SlowTest_FastqLoader_id2name 220: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/SlowTest_FastqLoader_id2name 220: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 220: Test timeout computed to be: 1500 220: Running 12 test cases... 220: Init_NullSelf (0 s) 220: Whack_NullSelf (0 s) 220: Init_Whack (0 s) 220: Add_NullSelf (0 s) 220: Add_NullName (0 s) 220: Get_NullSelf (0 s) 220: Get_NullRes (0 s) 220: Get_Empty (0 s) 220: Get_Found (0 s) 220: Get_NotFound (0 s) 220: AddMultiple_Get (0 s) 220: AddRealloc (0 s) 220: 220: *** No errors detected (0 s total) 118/187 Test #220: SlowTest_FastqLoader_id2name ...................... Passed 0.01 sec test 221 Start 221: Test_FastqLoader_WbFastq_dflt 221: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_FastqLoader_WbFastq_dflt 221: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 221: Test timeout computed to be: 1500 221: Running 103 test cases... 221: EmptyFile (0 s) 221: EndLines (0 s) 221: SyntaxError1 (0 s) 221: SyntaxError2 (0 s) 221: RecoveryFromErrorAtTopLevel (0 s) 221: RecoveryFromErrorInHeader (0 s) 221: RecoveryFromErrorInRead (0 s) 221: RecoveryFromErrorInQuality (0 s) 221: ErrorLineNumber (0 s) 221: Tag1 (0 s) 221: Tag2_1 (0 s) 221: Tag2_2 (0 s) 221: Tag3 (0 s) 221: Tag4 (0 s) 221: Tag5 (0 s) 221: Tag6 (0 s) 221: Tag7 (0 s) 221: Tag8 (0 s) 221: Tag9 (0 s) 221: Tag10 (0 s) 221: Tag11 (0 s) 221: Tag12 (0 s) 221: Tag13 (0 s) 221: Tag14 (0 s) 221: Tag15 (0 s) 221: NotRejected (0 s) 221: SequenceNoAlignment (0 s) 221: TestSequenceGetReadLength (0 s) 221: TestSequenceGetReadLength_MultiLine (0 s) 221: TestSequenceGetRead (0 s) 221: TestSequenceGetRead_MultiLine (0 s) 221: TestSequenceGetRead2 (0 s) 221: TestSequenceGetRead2_StopOutOfRange (0 s) 221: TestSequenceGetRead2_StartOutOfRange (0 s) 221: TestSequenceGetRead2_MultiLine_InsideFirstLine (0 s) 221: TestSequenceGetRead2_MultiLine_InsideSecondLine (0 s) 221: TestSequenceGetRead2_MultiLine_AcrossEOL (0 s) 221: TestSequenceGetRead2_MultiLine_StopOutOfRange (0 s) 221: TestSequenceGetRead2_MultiLine_StartOutOfRange (0 s) 221: SequenceGetQuality33 (0 s) 221: SequenceGetQuality64 (0 s) 221: SequenceGetQualityLogOdds (0 s) 221: SequenceBaseSpace (0 s) 221: SequenceColorSpace (0 s) 221: SequenceGetOrientationIsReverse (0 s) 221: ReadNumber (0 s) 221: ReadNumberMissing (0 s) 221: ReadNumberDefault (0 s) 221: ReadNumberOverride (0 s) 221: RunSpotRead (0 s) 221: RunSpotRead_withTail (0 s) 221: RunSpotNothing (0 s) 221: SequenceGetSpotNameIllumina (0 s) 221: SequenceGetSpotGroupIllumina (0 s) 221: SequenceGetSpotGroupIllumina_Ignored (0 s) 221: SequenceGetSpotGroup_Empty (0 s) 221: SequenceGetSpotGroup_Zero (0 s) 221: SequenceGetSpotGroupBarcode (0 s) 221: SequenceGetSpotGroupBarcode_WithPluses (0 s) 221: SequenceGetSpotGroupUnderscore (0 s) 221: HashStyleBarcodeAndReadNumbersAndJunk (0 s) 221: SequenceWasPaired1 (0 s) 221: SequenceWasPaired2 (0 s) 221: SequenceWasPaired3 (0 s) 221: SequenceWasPaired4 (0 s) 221: SequenceWasPaired5 (0 s) 221: SequenceGetSpotNameOneLine (0 s) 221: SequenceGetNameNumeric (0 s) 221: GtStartsQualityOnly (0 s) 221: OneLineRead (0 s) 221: ForcePhredOffset (0 s) 221: IlluminaCasava_1_8 (0 s) 221: IlluminaCasava_1_8_SpotGroupNumber (0 s) 221: IlluminaCasava_1_8_SpotGroup_MoreMadness (0 s) 221: IlluminaCasava_1_8_EmptyTag (0 s) 221: Illumina_NegativeCoords (0 s) 221: Illumina_Underscore (0 s) 221: Illumina_IdentifierAtFront (0 s) 221: Illumina_SpaceAndIdentifierAtFront (0 s) 221: SRR1778155 (0 s) 221: SRA192487 (0 s) 221: NoEolAtEof (0 s) 221: GtStartsReadOnly (0 s) 221: Quality33TooLow (0 s) 221: Quality64TooLow (0 s) 221: QualityLogoddsTooLow (0 s) 221: DecimalQualityRejected (0 s) 221: PacbioRaw (0 s) 221: PacbioCcs (0 s) 221: PacbioNoReadNumbers (0 s) 221: PacbioWsCcs (0 s) 221: PacbioError (0 s) 221: NotPairedRead_Error (0 s) 221: NoFragmentInfo_Error (0 s) 221: NoColonAtTheEnd_Error (0 s) 221: MissingRead (0 s) 221: UnexpectedEOLreported (0 s) 221: AnotherUnexpectedEOLreported (0 s) 221: FastqDumpOutput (0 s) 221: Barcodes_Plus (0 s) 221: Barcodes_Underscore (0 s) 221: FastqMultiLineSequenceFasta (0 s) 221: FastqMultiLineSequenceFastq (0 s) 221: 221: *** No errors detected (0 s total) 119/187 Test #221: Test_FastqLoader_WbFastq_dflt ..................... Passed 0.05 sec test 222 Start 222: Test_FastqLoader_WbFastqParse 222: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_FastqLoader_WbFastqParse 222: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 222: Test timeout computed to be: 1500 222: Running 17 test cases... 222: EmptyInput (0 s) 222: TagLine1 (0 s) 222: SequenceQuality (0 s) 222: QualityOnly (0 s) 222: NoEOL_InQuality (0 s) 222: CRnoLF (0 s) 222: CommaSeparatedQuality3 (0 s) 222: WsBeforeEol (0 s) 222: SkipToEol (0 s) 222: InlineBaseSequence (0 s) 222: BufferBreakInTag (0 s) 222: BufferBreakInMultilineRead (0 s) 222: BufferBreakInMultilineQuality (0 s) 222: ReadNumberNotSeparated (0 s) 222: ReadNumberNotSeparated_Variation (0 s) 222: BarcodesReadNumbersJunkOhMy (0 s) 222: Aviti (0 s) 222: 222: *** No errors detected (0 s total) 120/187 Test #222: Test_FastqLoader_WbFastqParse ..................... Passed 0.01 sec test 223 Start 223: Test_FastqLoader_WbFastqLoader 223: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_FastqLoader_WbFastqLoader 223: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 223: Environment variables: 223: NCBI_SETTINGS=/ 223: VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 223: Test timeout computed to be: 1500 223: Running 14 test cases... 223: CommonWriterOneFile (0 s) 223: 2024-05-29T09:33:15 Test_FastqLoader_WbFastqLoader.1.0.0 err: data inconsistent while reading file within application support module - Duplicate read name 'HWUSI-EAS499:1:3:9:1822' 223: CommonWriterDuplicateReadnames_Error (0 s) 223: 2024-05-29T09:33:16 Test_FastqLoader_WbFastqLoader.1.0.0 warn: Spot 'HWUSI-EAS499:1:3:9:1822' has already been assigned a spot id 223: CommonWriterDuplicateReadnames_Allowed (0 s) 223: 2024-05-29T09:33:16 Test_FastqLoader_WbFastqLoader.1.0.0 err: data inconsistent while reading file within application support module - Duplicate read name 'HWUSI-EAS499:1:3:9:1822' 223: CommonWriterDuplicateReadnames_SameFragment (0 s) 223: CommonWriterDuplicateReadnames_DiffFragment (0 s) 223: 2024-05-29T09:33:17 Test_FastqLoader_WbFastqLoader.1.0.0 warn: data inconsistent while reading file within application support module - Spot 'HWUSI-EAS499:1:3:9:1822', which was first seen with mate info, now has no mate info 223: 2024-05-29T09:33:17 Test_FastqLoader_WbFastqLoader.1.0.0 err: data invalid while closing table - Too many bad records: records: 2, bad records: 1, bad records percentage: 0.50, allowed percentage: 0.00 223: CommonWriterDuplicateReadnames_MatedThenUnmated (0 s) 223: 2024-05-29T09:33:17 Test_FastqLoader_WbFastqLoader.1.0.0 warn: data inconsistent while reading file within application support module - Spot 'HWUSI-EAS499:1:3:9:1822', which was first seen without mate info, now has mate info 223: 2024-05-29T09:33:17 Test_FastqLoader_WbFastqLoader.1.0.0 err: data invalid while closing table - Too many bad records: records: 2, bad records: 1, bad records percentage: 0.50, allowed percentage: 0.00 223: CommonWriterDuplicateReadnames_UnmatedThenMated (0 s) 223: NoSpotAssemply (0 s) 223: NoSpotAssemply_case2 (0 s) 223: Interleaved_OneRead (0 s) 223: Interleaved_MultipleReads (0 s) 223: Interleaved_NoMatch (0 s) 223: Interleaved_1_longer (0 s) 223: Interleaved_2_longer (0 s) 223: 223: *** No errors detected (4 s total) 121/187 Test #223: Test_FastqLoader_WbFastqLoader .................... Passed 4.16 sec test 224 Start 224: Test_FastqLoader_1.1 224: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.1.fastq --quality PHRED_33" "." "1.1" "0" 224: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 224: Test timeout computed to be: 1500 224: running 1.1 224: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.1.fastq --quality PHRED_33 -o ./actual/1.1/obj 1>./actual/1.1/load.stdout 2>./actual/1.1/load.stderr 122/187 Test #224: Test_FastqLoader_1.1 .............................. Passed 0.66 sec test 225 Start 225: Test_FastqLoader_1.2 225: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.2.fastq --quality PHRED_64" "." "1.2" "0" 225: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 225: Test timeout computed to be: 1500 225: running 1.2 225: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.2.fastq --quality PHRED_64 -o ./actual/1.2/obj 1>./actual/1.2/load.stdout 2>./actual/1.2/load.stderr 123/187 Test #225: Test_FastqLoader_1.2 .............................. Passed 0.59 sec test 226 Start 226: Test_FastqLoader_1.3 226: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.3.fastq --quality PHRED_33" "." "1.3" "3" 226: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 226: Test timeout computed to be: 1500 226: running 1.3 226: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.3.fastq --quality PHRED_33 -o ./actual/1.3/obj 1>./actual/1.3/load.stdout 2>./actual/1.3/load.stderr 124/187 Test #226: Test_FastqLoader_1.3 .............................. Passed 0.32 sec test 227 Start 227: Test_FastqLoader_1.4 227: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.4.fastq --quality LOGODDS" "." "1.4" "0" 227: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 227: Test timeout computed to be: 1500 227: running 1.4 227: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/1.4.fastq --quality LOGODDS -o ./actual/1.4/obj 1>./actual/1.4/load.stdout 2>./actual/1.4/load.stderr 125/187 Test #227: Test_FastqLoader_1.4 .............................. Passed 0.79 sec test 228 Start 228: Test_FastqLoader_2.1 228: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.1.fastq --quality PHRED_33" "." "2.1" "0" 228: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 228: Test timeout computed to be: 1500 228: running 2.1 228: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.1.fastq --quality PHRED_33 -o ./actual/2.1/obj 1>./actual/2.1/load.stdout 2>./actual/2.1/load.stderr 126/187 Test #228: Test_FastqLoader_2.1 .............................. Passed 0.69 sec test 229 Start 229: Test_FastqLoader_2.5 229: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.5.fastq --quality PHRED_33" "." "2.5" "0" 229: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 229: Test timeout computed to be: 1500 229: running 2.5 229: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.5.fastq --quality PHRED_33 -o ./actual/2.5/obj 1>./actual/2.5/load.stdout 2>./actual/2.5/load.stderr 127/187 Test #229: Test_FastqLoader_2.5 .............................. Passed 0.64 sec test 230 Start 230: Test_FastqLoader_2.6 230: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.6.fastq --quality PHRED_33" "." "2.6" "0" 230: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 230: Test timeout computed to be: 1500 230: running 2.6 230: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.6.fastq --quality PHRED_33 -o ./actual/2.6/obj 1>./actual/2.6/load.stdout 2>./actual/2.6/load.stderr 128/187 Test #230: Test_FastqLoader_2.6 .............................. Passed 0.67 sec test 231 Start 231: Test_FastqLoader_2.7 231: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.7.fastq --quality PHRED_33" "." "2.7" "3" 231: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 231: Test timeout computed to be: 1500 231: running 2.7 231: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.7.fastq --quality PHRED_33 -o ./actual/2.7/obj 1>./actual/2.7/load.stdout 2>./actual/2.7/load.stderr 129/187 Test #231: Test_FastqLoader_2.7 .............................. Passed 0.43 sec test 232 Start 232: Test_FastqLoader_2.7.1 232: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/2.7.fastq --quality PHRED_33 --allow_duplicates" "." "2.7.1" "0" 232: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 232: Test timeout computed to be: 1500 232: running 2.7.1 232: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/2.7.fastq --quality PHRED_33 --allow_duplicates -o ./actual/2.7.1/obj 1>./actual/2.7.1/load.stdout 2>./actual/2.7.1/load.stderr 130/187 Test #232: Test_FastqLoader_2.7.1 ............................ Passed 0.70 sec test 233 Start 233: Test_FastqLoader_2.8.1 233: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.8.1.fastq --quality PHRED_33" "." "2.8.1" "0" 233: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 233: Test timeout computed to be: 1500 233: running 2.8.1 233: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.8.1.fastq --quality PHRED_33 -o ./actual/2.8.1/obj 1>./actual/2.8.1/load.stdout 2>./actual/2.8.1/load.stderr 131/187 Test #233: Test_FastqLoader_2.8.1 ............................ Passed 0.76 sec test 234 Start 234: Test_FastqLoader_2.9 234: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.9.fastq --quality PHRED_33" "." "2.9" "3" 234: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 234: Test timeout computed to be: 1500 234: running 2.9 234: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.9.fastq --quality PHRED_33 -o ./actual/2.9/obj 1>./actual/2.9/load.stdout 2>./actual/2.9/load.stderr 132/187 Test #234: Test_FastqLoader_2.9 .............................. Passed 0.56 sec test 235 Start 235: Test_FastqLoader_2.9.1 235: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.9.1.fastq --quality PHRED_33" "." "2.9.1" "3" 235: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 235: Test timeout computed to be: 1500 235: running 2.9.1 235: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/2.9.1.fastq --quality PHRED_33 -o ./actual/2.9.1/obj 1>./actual/2.9.1/load.stdout 2>./actual/2.9.1/load.stderr 133/187 Test #235: Test_FastqLoader_2.9.1 ............................ Passed 0.70 sec test 236 Start 236: Test_FastqLoader_3.1 236: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/3.1a.fastq input/3.1b.fastq --quality PHRED_33" "." "3.1" "0" 236: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 236: Test timeout computed to be: 1500 236: running 3.1 236: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/3.1a.fastq input/3.1b.fastq --quality PHRED_33 -o ./actual/3.1/obj 1>./actual/3.1/load.stdout 2>./actual/3.1/load.stderr 134/187 Test #236: Test_FastqLoader_3.1 .............................. Passed 0.65 sec test 237 Start 237: Test_FastqLoader_4.1 237: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "bash" "-c" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load ./input/4.fastq --tmpfs ./actual -v -o actual/4.1.obj --quality PHRED_33 2>&1 | grep "Path for scratch files: ./actual/key2id"" 237: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 237: Test timeout computed to be: 1500 237: 2024-05-29T09:33:28 latf-load.3.0.9: Path for scratch files: ./actual/key2id.3357499.1 135/187 Test #237: Test_FastqLoader_4.1 .............................. Passed 0.33 sec test 238 Start 238: Test_FastqLoader_4.2 238: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq --qual-quant 1:10,10:20,20:30,30:- --quality PHRED_33" "." "4.2" "0" 238: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 238: Test timeout computed to be: 1500 238: running 4.2 238: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq --qual-quant 1:10,10:20,20:30,30:- --quality PHRED_33 -o ./actual/4.2/obj 1>./actual/4.2/load.stdout 2>./actual/4.2/load.stderr 136/187 Test #238: Test_FastqLoader_4.2 .............................. Passed 0.58 sec test 239 Start 239: Test_FastqLoader_4.3.1 239: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq --cache-size BIG --quality PHRED_33" "." "4.3.1" "3" 239: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 239: Test timeout computed to be: 1500 239: running 4.3.1 239: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq --cache-size BIG --quality PHRED_33 -o ./actual/4.3.1/obj 1>./actual/4.3.1/load.stdout 2>./actual/4.3.1/load.stderr 137/187 Test #239: Test_FastqLoader_4.3.1 ............................ Passed 0.16 sec test 240 Start 240: Test_FastqLoader_4.5 240: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/4.5.fastq --max-err-count 2 --quality PHRED_33" "." "4.5" "3" 240: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 240: Test timeout computed to be: 1500 240: running 4.5 240: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/4.5.fastq --max-err-count 2 --quality PHRED_33 -o ./actual/4.5/obj 1>./actual/4.5/load.stdout 2>./actual/4.5/load.stderr 138/187 Test #240: Test_FastqLoader_4.5 .............................. Passed 0.58 sec test 241 Start 241: Test_FastqLoader_4.5.2 241: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/4.5.2.fastq --platform ILLUMINA --quality PHRED_33 --max-err-count 2" "." "4.5.2" "3" 241: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 241: Test timeout computed to be: 1500 241: running 4.5.2 241: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/4.5.2.fastq --platform ILLUMINA --quality PHRED_33 --max-err-count 2 -o ./actual/4.5.2/obj 1>./actual/4.5.2/load.stdout 2>./actual/4.5.2/load.stderr 139/187 Test #241: Test_FastqLoader_4.5.2 ............................ Passed 0.38 sec test 242 Start 242: Test_FastqLoader_4.6 242: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq -p LS454 --quality PHRED_33" "." "4.6" "0" 242: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 242: Test timeout computed to be: 1500 242: running 4.6 242: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq -p LS454 --quality PHRED_33 -o ./actual/4.6/obj 1>./actual/4.6/load.stdout 2>./actual/4.6/load.stderr 140/187 Test #242: Test_FastqLoader_4.6 .............................. Passed 0.69 sec test 243 Start 243: Test_FastqLoader_4.6.1 243: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq -p SOMETHINGELSE --quality PHRED_33" "." "4.6.1" "3" 243: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 243: Test timeout computed to be: 1500 243: running 4.6.1 243: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.fastq -p SOMETHINGELSE --quality PHRED_33 -o ./actual/4.6.1/obj 1>./actual/4.6.1/load.stdout 2>./actual/4.6.1/load.stderr 141/187 Test #243: Test_FastqLoader_4.6.1 ............................ Passed 0.10 sec test 244 Start 244: Test_FastqLoader_4.7 244: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/not_there --quality PHRED_33" "." "4.7" "3" 244: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 244: Test timeout computed to be: 1500 244: running 4.7 244: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/not_there --quality PHRED_33 -o ./actual/4.7/obj 1>./actual/4.7/load.stdout 2>./actual/4.7/load.stderr 142/187 Test #244: Test_FastqLoader_4.7 .............................. Passed 0.73 sec test 245 Start 245: Test_FastqLoader_4.8 245: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.8.fastq --quality PHRED_33 --no-readnames" "." "4.8" "0" 245: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 245: Test timeout computed to be: 1500 245: running 4.8 245: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/4.8.fastq --quality PHRED_33 --no-readnames -o ./actual/4.8/obj 1>./actual/4.8/load.stdout 2>./actual/4.8/load.stderr 143/187 Test #245: Test_FastqLoader_4.8 .............................. Passed 0.75 sec test 246 Start 246: Test_FastqLoader_5.0 246: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/5.0.fastq.gz --quality PHRED_33" "." "5.0" "0" 246: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 246: Test timeout computed to be: 1500 246: running 5.0 246: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/5.0.fastq.gz --quality PHRED_33 -o ./actual/5.0/obj 1>./actual/5.0/load.stdout 2>./actual/5.0/load.stderr 144/187 Test #246: Test_FastqLoader_5.0 .............................. Passed 0.58 sec test 247 Start 247: Test_FastqLoader_6.0 247: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/6.0.fastq --quality PHRED_33" "." "6.0" "0" 247: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 247: Test timeout computed to be: 1500 247: running 6.0 247: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/6.0.fastq --quality PHRED_33 -o ./actual/6.0/obj 1>./actual/6.0/load.stdout 2>./actual/6.0/load.stderr 145/187 Test #247: Test_FastqLoader_6.0 .............................. Passed 0.81 sec test 248 Start 248: Test_FastqLoader_7.1 248: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.1.fastq --platform=PACBIO --quality PHRED_33" "." "7.1" "0" 248: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 248: Test timeout computed to be: 1500 248: running 7.1 248: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.1.fastq --platform=PACBIO --quality PHRED_33 -o ./actual/7.1/obj 1>./actual/7.1/load.stdout 2>./actual/7.1/load.stderr 146/187 Test #248: Test_FastqLoader_7.1 .............................. Passed 0.65 sec test 249 Start 249: Test_FastqLoader_7.2 249: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.2.fastq --platform=PACBIO --quality PHRED_33" "." "7.2" "0" 249: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 249: Test timeout computed to be: 1500 249: running 7.2 249: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.2.fastq --platform=PACBIO --quality PHRED_33 -o ./actual/7.2/obj 1>./actual/7.2/load.stdout 2>./actual/7.2/load.stderr 147/187 Test #249: Test_FastqLoader_7.2 .............................. Passed 0.66 sec test 250 Start 250: Test_FastqLoader_7.3 250: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.3.fastq --platform=PACBIO --quality PHRED_33" "." "7.3" "0" 250: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 250: Test timeout computed to be: 1500 250: running 7.3 250: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/7.3.fastq --platform=PACBIO --quality PHRED_33 -o ./actual/7.3/obj 1>./actual/7.3/load.stdout 2>./actual/7.3/load.stderr 148/187 Test #250: Test_FastqLoader_7.3 .............................. Passed 0.69 sec test 251 Start 251: Test_FastqLoader_8.0 251: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/8.0.fastq --quality PHRED_33" "." "8.0" "0" 251: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 251: Test timeout computed to be: 1500 251: running 8.0 251: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/8.0.fastq --quality PHRED_33 -o ./actual/8.0/obj 1>./actual/8.0/load.stdout 2>./actual/8.0/load.stderr 149/187 Test #251: Test_FastqLoader_8.0 .............................. Passed 1.21 sec test 252 Start 252: Test_FastqLoader_8.1 252: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/8.1.fastq --quality PHRED_33" "." "8.1" "3" 252: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 252: Test timeout computed to be: 1500 252: running 8.1 252: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/8.1.fastq --quality PHRED_33 -o ./actual/8.1/obj 1>./actual/8.1/load.stdout 2>./actual/8.1/load.stderr 150/187 Test #252: Test_FastqLoader_8.1 .............................. Passed 0.78 sec test 253 Start 253: Test_FastqLoader_9.0 253: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/9.0.fastq --quality PHRED_33" "." "9.0" "0" 253: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 253: Test timeout computed to be: 1500 253: running 9.0 253: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/9.0.fastq --quality PHRED_33 -o ./actual/9.0/obj 1>./actual/9.0/load.stdout 2>./actual/9.0/load.stderr 151/187 Test #253: Test_FastqLoader_9.0 .............................. Passed 0.65 sec test 254 Start 254: Test_FastqLoader_10.0 254: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/10.0.fastq --quality PHRED_33" "." "10.0" "0" 254: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 254: Test timeout computed to be: 1500 254: running 10.0 254: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/10.0.fastq --quality PHRED_33 -o ./actual/10.0/obj 1>./actual/10.0/load.stdout 2>./actual/10.0/load.stderr 152/187 Test #254: Test_FastqLoader_10.0 ............................. Passed 0.67 sec test 255 Start 255: Test_FastqLoader_11.0 255: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/11.0.1.fasta input/11.0.2.fasta --quality PHRED_33" "." "11.0" "0" 255: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 255: Test timeout computed to be: 1500 255: running 11.0 255: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/11.0.1.fasta input/11.0.2.fasta --quality PHRED_33 -o ./actual/11.0/obj 1>./actual/11.0/load.stdout 2>./actual/11.0/load.stderr 153/187 Test #255: Test_FastqLoader_11.0 ............................. Passed 1.02 sec test 256 Start 256: Test_FastqLoader_11.1 256: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/11.1.1.fastq input/11.1.2.fastq --quality PHRED_33" "." "11.1" "0" 256: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 256: Test timeout computed to be: 1500 256: running 11.1 256: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/11.1.1.fastq input/11.1.2.fastq --quality PHRED_33 -o ./actual/11.1/obj 1>./actual/11.1/load.stdout 2>./actual/11.1/load.stderr 154/187 Test #256: Test_FastqLoader_11.1 ............................. Passed 0.66 sec test 257 Start 257: Test_FastqLoader_12.0 257: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.0.fastq --quality PHRED_33 --ignore-illumina-tags" "." "12.0" "0" 257: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 257: Test timeout computed to be: 1500 257: running 12.0 257: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.0.fastq --quality PHRED_33 --ignore-illumina-tags -o ./actual/12.0/obj 1>./actual/12.0/load.stdout 2>./actual/12.0/load.stderr 155/187 Test #257: Test_FastqLoader_12.0 ............................. Passed 0.60 sec test 258 Start 258: Test_FastqLoader_12.1 258: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.1.fastq --quality PHRED_33" "." "12.1" "0" 258: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 258: Test timeout computed to be: 1500 258: running 12.1 258: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.1.fastq --quality PHRED_33 -o ./actual/12.1/obj 1>./actual/12.1/load.stdout 2>./actual/12.1/load.stderr 156/187 Test #258: Test_FastqLoader_12.1 ............................. Passed 0.64 sec test 259 Start 259: Test_FastqLoader_12.2 259: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.2.fastq --quality PHRED_33" "." "12.2" "0" 259: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 259: Test timeout computed to be: 1500 259: running 12.2 259: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/12.2.fastq --quality PHRED_33 -o ./actual/12.2/obj 1>./actual/12.2/load.stdout 2>./actual/12.2/load.stderr 157/187 Test #259: Test_FastqLoader_12.2 ............................. Passed 0.60 sec test 260 Start 260: Test_FastqLoader_13.0 260: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/13.0.fastq --quality PHRED_33" "." "13.0" "0" 260: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 260: Test timeout computed to be: 1500 260: running 13.0 260: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/13.0.fastq --quality PHRED_33 -o ./actual/13.0/obj 1>./actual/13.0/load.stdout 2>./actual/13.0/load.stderr 158/187 Test #260: Test_FastqLoader_13.0 ............................. Passed 0.58 sec test 261 Start 261: Test_FastqLoader_13.1 261: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/13.1.fastq --quality PHRED_33" "." "13.1" "0" 261: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 261: Test timeout computed to be: 1500 261: running 13.1 261: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/13.1.fastq --quality PHRED_33 -o ./actual/13.1/obj 1>./actual/13.1/load.stdout 2>./actual/13.1/load.stderr 159/187 Test #261: Test_FastqLoader_13.1 ............................. Passed 0.66 sec test 262 Start 262: Test_FastqLoader_14.0 262: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/14.0.fasta --quality PHRED_33" "." "14.0" "0" 262: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 262: Test timeout computed to be: 1500 262: running 14.0 262: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/14.0.fasta --quality PHRED_33 -o ./actual/14.0/obj 1>./actual/14.0/load.stdout 2>./actual/14.0/load.stderr 160/187 Test #262: Test_FastqLoader_14.0 ............................. Passed 0.81 sec test 263 Start 263: Test_FastqLoader_15.0 263: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump -x READ_SEG" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load ./input/15.0.fastq --quality PHRED_33" "." "15.0" "0" 263: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 263: Test timeout computed to be: 1500 263: running 15.0 263: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load ./input/15.0.fastq --quality PHRED_33 -o ./actual/15.0/obj 1>./actual/15.0/load.stdout 2>./actual/15.0/load.stderr 161/187 Test #263: Test_FastqLoader_15.0 ............................. Passed 0.86 sec test 264 Start 264: Test_FastqLoader_16.0 264: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/16.0.fasta --quality PHRED_33 --platform=PACBIO" "." "16.0" "0" 264: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 264: Test timeout computed to be: 1500 264: running 16.0 264: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/16.0.fasta --quality PHRED_33 --platform=PACBIO -o ./actual/16.0/obj 1>./actual/16.0/load.stdout 2>./actual/16.0/load.stderr 162/187 Test #264: Test_FastqLoader_16.0 ............................. Passed 0.62 sec test 265 Start 265: Test_FastqLoader_16.1 265: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/16.1.fastq --quality PHRED_33 --platform=PACBIO" "." "16.1" "0" 265: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 265: Test timeout computed to be: 1500 265: running 16.1 265: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load input/16.1.fastq --quality PHRED_33 --platform=PACBIO -o ./actual/16.1/obj 1>./actual/16.1/load.stdout 2>./actual/16.1/load.stderr 163/187 Test #265: Test_FastqLoader_16.1 ............................. Passed 1.34 sec test 266 Start 266: Test_FastqLoader_17.0 266: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/17.0.fastq --quality PHRED_33" "." "17.0" "3" 266: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 266: Test timeout computed to be: 1500 266: running 17.0 266: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/17.0.fastq --quality PHRED_33 -o ./actual/17.0/obj 1>./actual/17.0/load.stdout 2>./actual/17.0/load.stderr 164/187 Test #266: Test_FastqLoader_17.0 ............................. Passed 1.04 sec test 267 Start 267: Test_FastqLoader_18.0 267: Test command: /usr/bin/cmake "-E" "env" "NCBI_SETTINGS=/" "/usr/bin/cmake" "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader" "./runtestcase.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump " "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/18.0.fastq --quality PHRED_33" "." "18.0" "3" 267: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader 267: Test timeout computed to be: 1500 267: running 18.0 267: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/latf-load /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/fastq-loader/input/18.0.fastq --quality PHRED_33 -o ./actual/18.0/obj 1>./actual/18.0/load.stdout 2>./actual/18.0/load.stderr 165/187 Test #267: Test_FastqLoader_18.0 ............................. Passed 0.96 sec test 269 Start 269: Test_KAPP_qfile 269: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_KAPP_qfile 269: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader 269: Test timeout computed to be: 1500 269: start-position : 0 269: queue-size : 1024 269: block-size : 0 269: chunk-size : 1024 166/187 Test #269: Test_KAPP_qfile ................................... Passed 0.01 sec test 270 Start 270: Test_LOADERFILE 270: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADERFILE 270: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader 270: Test timeout computed to be: 1500 270: Running 5 test cases... 270: KQueueFile_ReadTimeout_FGsleeps (2 s) 270: KQueueFile_ReadTimeout_BGsleeps (3 s) 270: KQueueFile_WriteTimeout (2 s) 270: KLoaderFile_eolBeforeEof (0 s) 270: KLoaderFile_noEolBeforeEof (0 s) 270: 270: *** No errors detected (7 s total) 167/187 Test #270: Test_LOADERFILE ................................... Passed 7.01 sec test 271 Start 271: Test_LOADER 271: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADER 271: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/loader 271: Test timeout computed to be: 1500 271: Running 2 test cases... 271: LoaderMeta_Write (0 s) 271: LoaderMeta_WriteWithVersion (0 s) 271: 271: *** No errors detected (0 s total) 168/187 Test #271: Test_LOADER ....................................... Passed 0.07 sec test 272 Start 272: Test_sra_sort_meta_copy 272: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/sra-sort/sra_sort_meta_copy.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/usr/include/ncbi-vdb" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 272: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/loaders/sra-sort 272: Test timeout computed to be: 1500 272: Files before.xml and after.xml are identical 169/187 Test #272: Test_sra_sort_meta_copy ........................... Passed 6.48 sec test 273 Start 273: Test_Align_samextract 273: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Align_samextract 273: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align 273: Test timeout computed to be: 1500 273: Running 14 test cases... 273: Test_Qual_Decode (0 s) 273: Fast_Sequence (0 s) 273: Fast_u32toa (0 s) 273: Fast_i32toa (0 s) 273: Fast_strtoi64 (0 s) 273: Decode_Cigar (0 s) 273: Check_Cigar (0 s) 273: In_Range (0 s) 273: Is_MD5 (0 s) 273: Is_floworder (0 s) 273: header1 (0 s) 273: BAMfile (0 s) 273: Filter (0 s) 273: None of below files should hang: 273: fuzz/id000000,sig11,src000036,ophavoc,rep128 273: fuzz/id000000,src000000+000001,opsplice,rep16 273: fuzz/id000000,src000000,oparith8,pos3,val+10 273: fuzz/id000001,src000001,oparith16,pos10,val-6 273: fuzz/id000001,src000001,oparith8,pos10,val+9 273: fuzz/id000001,src000003,ophavoc,rep2 273: fuzz/id000002,src000000+000006,opsplice,rep64 273: fuzz/id000002,src000001,oparith8,pos10,val-31 273: fuzz/id000002,src000001,ophavoc,rep4 273: fuzz/id000003,src000001,ophavoc,rep2 273: fuzz/id000003,src000001,ophavoc,rep8 273: fuzz/id000003,src000007,ophavoc,rep2 273: fuzz/id000004,src000001,ophavoc,rep2 273: fuzz/id000004,src000001,ophavoc,rep32 273: fuzz/id000004,src000012,ophavoc,rep8 273: fuzz/id000005,src000001,ophavoc,rep2 273: fuzz/id000005,src000001,ophavoc,rep8 273: fuzz/id000005,src000013+000012,opsplice,rep4 273: fuzz/id000006,src000001,ophavoc,rep2 273: fuzz/id000006,src000001,ophavoc,rep4 273: fuzz/id000006,src000014,ophavoc,rep2 273: fuzz/id000007,src000002,opflip1,pos4 273: fuzz/id000007,src000023,ophavoc,rep4 273: fuzz/id000008,src000002,opflip1,pos8 273: fuzz/id000008,src000029,ophavoc,rep64 273: fuzz/id000009,src000002,opflip1,pos22 273: fuzz/id000009,src000031,ophavoc,rep2 273: fuzz/id000010,src000002,opflip1,pos25 273: fuzz/id000010,src000037+000017,opsplice,rep2 273: fuzz/id000011,src000002,opflip1,pos33 273: fuzz/id000011,src000046,ophavoc,rep2 273: fuzz/id000012,src000002,opflip4,pos20 273: fuzz/id000012,src000049,ophavoc,rep4 273: fuzz/id000013,src000002,opflip4,pos38 273: fuzz/id000013,src000048,ophavoc,rep2 273: fuzz/id000014,src000002,opflip4,pos76 273: fuzz/id000014,src000021+000026,opsplice,rep2 273: fuzz/id000015,src000002,opflip8,pos25 273: fuzz/id000015,src000056,ophavoc,rep2 273: fuzz/id000016,src000002,opint16,pos77,val-129 273: fuzz/id000016,src000002,opint8,pos14,val-1 273: fuzz/id000017,src000002,ophavoc,rep32 273: fuzz/id000017,src000002,opint16,pos77,val-129 273: fuzz/id000018,src000002,opint32,pos25,val+2147483647 273: fuzz/id000018,src000003,opint16,pos3,val-129 273: fuzz/id000019,src000002,opint32,pos33,valbe-128 273: fuzz/id000019,src000007,opflip16,pos33 273: fuzz/id000020,src000002,ophavoc,rep4 273: fuzz/id000020,src000007,opint16,pos117,val-129 273: fuzz/id000021,src000004,opint16,pos4,val+32767 273: fuzz/id000021,src000011,opflip4,pos76 273: fuzz/id000022,src000004,ophavoc,rep16 273: fuzz/id000022,src000011,opflip4,pos116 273: fuzz/id000023,src000011,opflip4,pos116 273: fuzz/id000023,src000018,opflip1,pos15 273: fuzz/id000024,src000011,opflip16,pos52 273: fuzz/id000024,src000018,opflip1,pos26 273: fuzz/id000025,src000018,opflip1,pos15 273: fuzz/id000025,src000018,opflip4,pos92 273: fuzz/id000026,src000018,opflip1,pos26 273: fuzz/id000026,src000018,opflip4,pos137 273: fuzz/id000027,src000018,opflip4,pos24 273: fuzz/id000028,src000018,opflip4,pos92 273: fuzz/id000029,src000018,opflip4,pos137 273: fuzz/id000030,src000018,opint16,pos138,val-129 273: fuzz/id000031,src000018,ophavoc,rep8 273: 273: Fuzz_Hangs (0 s) 273: 273: *** No errors detected (0 s total) 170/187 Test #273: Test_Align_samextract ............................. Passed 0.61 sec test 275 Start 275: Test_Align_Cache 275: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align-cache/runtest.sh "/usr/include/ncbi-vdb" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "align-cache" 275: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/align-cache 275: Test timeout computed to be: 1500 275: testing align-cache 171/187 Test #275: Test_Align_Cache .................................. Passed 0.46 sec test 276 Start 276: Test_KFF 276: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/Test_KFF 276: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat 276: Test timeout computed to be: 1500 276: Running 2 test cases... 276: ExtFileFormat (0 s) 276: MagicFileFormat (0 s) 276: 276: *** No errors detected (0 s total) 172/187 Test #276: Test_KFF .......................................... Passed 0.01 sec test 277 Start 277: Test_Copycat_Help 277: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/copycat "-h" 277: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat 277: Test timeout computed to be: 1500 277: 277: Usage: 277: copycat [options] src-file dst-file 277: copycat [options] src-file [src-file...] dst-dir 277: copycat [options] -o dst-dir src-file [src-file...] 277: 277: Summary: 277: Copies files and/or directories, creating a catalog of the copied files. 277: -x|--cache-dir location of output cached files 277: -f|--force force overwrite of existing files 277: -o|--output location of output 277: -e|--extract location of extracted files 277: -E|--extract-to-dir extracted directories match normal XML 277: -X|--xml-dir XML matches extracted files 277: --input-buffer system file reads are of blocks of this size 277: --output-buffer system file writes are of blocks of this 277: size 277: --no-bzip2 do not decompress files compressed with 277: bzip2 277: --no-md5 do not calculate md5 hashes 277: -h|--help Output brief explanation for the program. 277: -V|--version Display the version of the program then 277: quit. 277: -L|--log-level Logging level as number or enum string. One 277: of (fatal|sys|int|err|warn|info|debug) or 277: (0-6) Current/default is warn. 277: -v|--verbose Increase the verbosity of the program 277: status messages. Use multiple times for more 277: verbosity. Negates quiet. 277: -q|--quiet Turn off all status messages for the 277: program. Negated by verbose. 277: --option-file Read more options and parameters from the 277: file. 277: Use: 277: Copy and catalog: 277: Some quick examples: 277: copycat dir/file.tar other-dir/file.tar 277: copy file.tar from dir to other-dir and write the catalog to stdout 277: copycat dir/file.tar otherdir/ 277: the same 277: copycat "ncbi-file:dir/file.tar.nenc?encrypt&pwfile=pw other-dir.file.tar 277: copy and decrypt file.tar.nenc from dir to other-dir and catalog 277: copycat dir/file.tar "ncbi-file:other-dir/file.tar.nenc?encrypt&pwfile=pw 277: copy and encrypt file.tar from dir to other-dir/file.tar.nenc and catalog 277: copycat "ncbi-file:dir/file.tar.nenc?encrypt&pwfile=pw1 \ 277: "ncbi-file:other-dir/file.tar.nenc?encrypt&pwfile=pw2 277: copy the file as above while changing the encryption 277: 277: Use: 277: Copy source file[s] to a destination file or directory. 277: File names can either be typical path names or they can be URLs (IRLs) using 277: the standard "file" or extended "ncbi-file" schemes. 277: The catalog is XML output sent by default to stdout. 277: As UTF-8 is accepted in the paths they are IRLs for International Resource 277: Locators. 277: 277: If the specified destination does not exist, there could be an ambiguity 277: whether the destination is supposed to be a file or directory. If the 277: entered path ends in a '/' character or if there is more than one source 277: it is assumed to mean a directory and is created as such. If neither of 277: of those apply it is assumed to be a file. 277: 277: The sources or destination may also be special Unix devices: 277: /dev/stdin is supported as a source. 277: /dev/stdout and /dev/stderr is supported as a destination. 277: Other file descriptor devices can be used in the form: 277: /dev/fd/ 277: For example /dev/stdin is synonymous with /dev/fd/0 as a source. 277: If /dev/stdout or /dev/fd/1 is used as the destination then the XML 277: output is redirected to /dev/stderr (/dev/fd/2). 277: Device /dev/null as the destination is treated as a file with only one 277: source but as a directory if more than one source. Using this device 277: means no actual file will be copied but the cataloging will be done but 277: xml-base-node must be used. 277: 277: These special devices can be entered using the URL (IRL) schemes if 277: desired. This allows the use of 'query' decorators. 277: 277: If a query is added to the URL it will need to be enclosed within '"' 277: characters on a command line to prevent premature interpretation. 277: The query for the 'ncbi-file' extension to the 'file' scheme allows 277: encryption and decryption. The supported query is introduced by the 277: standard URI/IRI syntax of a '?' character with a '&' character 277: separating individual query-entries. 277: 277: The supported query entries are: 277: 'encrypt' or 'enc' to mean the input may be encrypted or the output 277: will be encrypted, 277: 'pwfile=' gives the path to file containing the password. 277: 'pwfd=' gives the numerical file descriptor from which to read 277: the password, 277: 277: In this program the encrypted input can apply to a file contained within 277: the source rather than just the source file itself. The tool is fully 277: compatible with all versions of NCBI encryption. 277: 277: If the output is to be encrypted only the newer FIPS compliant encryption 277: will be used and applies to the whole file. 277: 277: NOTE: Not all combinations of URL specifications will work at this point. 277: 277: NOTE: using the same file descriptor for multiple sources or overlapping with 277: stdin/stdout/stderr may cause undefined behavior including hanging the 277: the program. 277: 277: The '-x' option allows small files that are typed as eligible for 277: caching to be copied to the cache directory provided. the directory 277: will be created if necessary. 277: the intent is to capture top-level files, such that files are copied 277: into the flat cache directory without regard to where they were found 277: in the input hierarchy. in the case of name conflict, output files will 277: be renamed. 277: 277: To prevent internal decompression of bzipped files, use the option 277: '--no-bzip2' 277: 277: To prevent calculation of MD5 hashes, use the option 277: '--no-md5' 277: 277: 277: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/copycat : 3.0.9 277: 173/187 Test #277: Test_Copycat_Help ................................. Passed 0.02 sec test 278 Start 278: Test_Copycat_Bad_Name 278: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat/test-bad-name.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "copycat" 278: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat 278: Test timeout computed to be: 1500 278: testing copycat expected output for file name with % 278: copycat test file name with % succeeded 174/187 Test #278: Test_Copycat_Bad_Name ............................. Passed 0.08 sec test 279 Start 279: Test_Copycat_IdenticalCopy 279: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat/test-copy.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "copycat" 279: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat 279: Test timeout computed to be: 1500 279: testing copycat copy 279: copycat copy succeeded 175/187 Test #279: Test_Copycat_IdenticalCopy ........................ Passed 0.08 sec test 280 Start 280: Test_Copycat_FastqParser 280: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat/test-fastq.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "copycat" 280: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/copycat 280: Test timeout computed to be: 1500 280: testing copycat fastq parser 280: copycat fastq parser succeeded 176/187 Test #280: Test_Copycat_FastqParser .......................... Passed 0.24 sec test 281 Start 281: Test_MakeReadFilter 281: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/tmp" "/usr/bin/cmake" "-E" "env" "NCBI_SETTINGS=/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/tmp/tmp.mkfg" "/usr/bin/cmake" "-E" "env" "VDB_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" "./runtest.sh" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/usr/lib/x86_64-linux-gnu" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/tmp" "" 281: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/make-read-filter 281: Test timeout computed to be: 1500 281: /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin /usr/lib/x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/test-bin/tmp 177/187 Test #281: Test_MakeReadFilter ............................... Passed 0.76 sec test 282 Start 282: Test_Read_filter_redact_Check_exit_code 282: Test command: /usr/bin/python3 "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/read-filter-redact" 282: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/read-filter-redact 282: Test timeout computed to be: 1500 282: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/read-filter-redact] 178/187 Test #282: Test_Read_filter_redact_Check_exit_code ........... Passed 0.06 sec test 283 Start 283: Test_Read_filter_redact 283: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/read-filter-redact/runtests.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "read-filter-redact" 283: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/read-filter-redact 283: Test timeout computed to be: 1500 283: Testing read-filter-redact from /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin 179/187 Test #283: Test_Read_filter_redact ........................... Passed 0.74 sec test 284 Start 284: Test_VDB_Copy_Check_exit_code 284: Test command: /usr/bin/python3 "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-copy" 284: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/vdb-copy 284: Test timeout computed to be: 1500 284: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-copy] 180/187 Test #284: Test_VDB_Copy_Check_exit_code ..................... Passed 0.06 sec test 286 Start 286: Test_VDB_Copy_Should_Fail_On_Invalid_Accession 286: Test command: /usr/bin/bash "-c" "./return_code_on_error.sh /build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" 286: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/vdb-copy 286: Test timeout computed to be: 1500 286: 2024-05-29T09:34:06 vdb-copy.3.0.9 int: item not found while copying within virtual database module - the path 'NOT_EXISTING_DIR' cannot be opened as vdb-database or vdb-table 286: SUCCESS: vdb-copy returned 3 if ask to copy a none-existing object. 181/187 Test #286: Test_VDB_Copy_Should_Fail_On_Invalid_Accession .... Passed 0.07 sec test 288 Start 288: Test_VDB_Diff_Check_exit_code 288: Test command: /usr/bin/python3 "/build/reproducible-path/sra-sdk-3.0.9+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-diff" 288: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/internal/vdb-diff 288: Test timeout computed to be: 1500 288: WARNING[TEST1] help message is in 'STDOUT' 288: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin/vdb-diff] 182/187 Test #288: Test_VDB_Diff_Check_exit_code ..................... Passed 0.06 sec test 291 Start 291: Test_qa-stat 291: Test command: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/test-tools/qa-stats/runtests.sh "/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/test-tools/qa-stats" 291: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/test-tools/qa-stats 291: Test timeout computed to be: 1500 291: Testing with default parameters. 291: Testing with one biological read. 291: Testing with one technical read. 291: Testing with two biological read. 291: Testing with one biological and one technical read. 291: Testing with multiple layouts. 183/187 Test #291: Test_qa-stat ...................................... Passed 3.50 sec test 292 Start 292: Test_Scripts_prepare-sra-names 292: Test command: /usr/bin/perl "test-prepare-sra-names.pl" 292: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/scripts 292: Test timeout computed to be: 1500 184/187 Test #292: Test_Scripts_prepare-sra-names .................... Passed 0.48 sec test 293 Start 293: Test_Scripts_fix-sra-names 293: Test command: /usr/bin/perl "test-fix-sra-names.pl" 293: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/scripts 293: Test timeout computed to be: 1500 185/187 Test #293: Test_Scripts_fix-sra-names ........................ Passed 0.08 sec test 294 Start 294: Test_Scripts_prepare-sra-names-py 294: Test command: /usr/bin/perl "test-prepare-sra-names-py.pl" 294: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/scripts 294: Test timeout computed to be: 1500 186/187 Test #294: Test_Scripts_prepare-sra-names-py ................. Passed 0.83 sec test 295 Start 295: Test_Scripts_fix-sra-names-py 295: Test command: /usr/bin/perl "test-fix-sra-names-py.pl" 295: Working Directory: /build/reproducible-path/sra-sdk-3.0.9+dfsg/test/scripts 295: Test timeout computed to be: 1500 187/187 Test #295: Test_Scripts_fix-sra-names-py ..................... Passed 0.85 sec 100% tests passed, 0 tests failed out of 187 Total Test time (real) = 94.71 sec make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake debian/rules override_dh_prep make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_prep -X debian/tmp make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/sra-sdk-3.0.9\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sra-sdk-3.0.9+dfsg -B/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/default.kfg': No such file or directory mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/certs.kfg': No such file or directory mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/vdb-copy.kfg': No such file or directory -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++-static.a -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/include/ncbi-vdb/NGS.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/share/examples/FragTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/share/examples/AlignTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/share/examples/AlignSliceTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/share/examples/PileupTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/share/examples/RefTest.cpp -- Installing: 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/build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-info.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-info.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-info -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/bam-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/bam-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/bam-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+ -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+meta.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+meta.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kar+meta -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/dump-blob-boundaries.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/dump-blob-boundaries.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/dump-blob-boundaries -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort-cg.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort-cg.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sra-sort-cg -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/latf-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/latf-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/latf-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sff-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sff-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sff-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastq-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastq-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastq-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/srf-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/srf-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/srf-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/abi-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/abi-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/abi-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/illumina-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/illumina-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/illumina-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/helicos-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/helicos-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/helicos-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-loadxml.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-loadxml.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-loadxml -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/cg-load.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/cg-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/cg-load -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/general-loader.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/general-loader.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/general-loader -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-lock.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-lock.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-lock -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-unlock.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-unlock.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-unlock -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/align-cache.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/align-cache.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/align-cache -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/ccextract.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/ccextract.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/ccextract -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/copycat.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/copycat.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/copycat -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/make-read-filter.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/make-read-filter.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/make-read-filter -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/md5cp.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/md5cp.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/md5cp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-cmp.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-cmp.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-cmp -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-copy.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-copy.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-copy -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-repair.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-repair.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/meta-repair -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-read-write-cursor.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-read-write-cursor.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-read-write-cursor -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/read-filter-redact.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/read-filter-redact.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/read-filter-redact -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-copy.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-copy.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-copy -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-diff.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-diff.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-diff -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-sql.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-sql.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/vdb-sql -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastconv.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastconv.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/fastconv -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/check-redact.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/check-redact.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/check-redact -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/crc32sum.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/crc32sum.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/crc32sum -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-download.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-download.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/test-download -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kdb-index.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kdb-index.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/kdb-index -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-correct.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-correct.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pacbio-correct -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/schema-replace.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/schema-replace.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/schema-replace -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sortreadtest.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sortreadtest.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/sortreadtest -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/rowwritetest.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/rowwritetest.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/rowwritetest -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview-util.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview-util.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/samview-util -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/testld.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/testld.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/testld -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/txt2kdb.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/txt2kdb.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/txt2kdb -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pileup-stats.3.0.9 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pileup-stats.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/bin/pileup-stats make[2]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg/obj-x86_64-linux-gnu' # build/install.sh /usr/include/ncbi-vdb/kfg/ncbi \ # /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy \ # debian/sra-toolkit/etc/ncbi \ # debian/sra-toolkit/etc/ncbi \ # debian/sra-toolkit/usr/bin \ # debian/sra-toolkit/usr/lib/x86_64-linux-gnu \ # /build/reproducible-path/sra-sdk-3.0.9+dfsg/shared/kfgsums build/install-kfg.sh default.kfg /usr/include/ncbi-vdb/kfg/ncbi debian/sra-toolkit/etc/ncbi \ /usr/include/ncbi-vdb/kfg/ncbi/kfgsums build/install-kfg.sh certs.kfg /usr/include/ncbi-vdb/kfg/ncbi debian/sra-toolkit/etc/ncbi \ /usr/include/ncbi-vdb/kfg/ncbi/kfgsums build/install-kfg.sh vdb-copy.kfg /build/reproducible-path/sra-sdk-3.0.9+dfsg/tools/internal/vdb-copy \ debian/sra-toolkit/etc/ncbi /build/reproducible-path/sra-sdk-3.0.9+dfsg/shared/kfgsums d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ --exclude-la \ --movedev "debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.a*" \ usr/lib/x86_64-linux-gnu \ --override "s/libncbi-vdb3-dev/libncbi-vdb-dev/" \ debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.so Library package automatic movement utility --> libncbi-vdb-dev package exists. set -e install -d -m 755 debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3.0.9 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu PKGDEV=libncbi-ngs-dev PKGSHL=libncbi-ngs3 install -d -m 755 debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu mv debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.a* debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ --exclude-la \ --movedev "debian/*/usr/lib/x86_64-linux-gnu/lib*c++.a*" \ usr/lib/x86_64-linux-gnu \ --movedev "debian/tmp/usr/include/*" usr/include \ --ignorelibdep \ debian/*/usr/lib/x86_64-linux-gnu/libngs-c++.so | \ tee /dev/stderr | LC_ALL=C grep '^[a-z]' | sh tee: /dev/stderr: Permission denied Error occurred, aborting make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' # upstream installs versioned *.a libs - we only want a single version for d in debian/lib*-dev/usr/lib/x86_64-linux-gnu ; do \ for slib in $d/lib*.a ; do \ mv $d/`readlink $slib` $slib ; \ mv $d/`readlink $slib` $slib ; \ done ; \ done ls -l debian/tmp/usr/bin total 65556 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 abi-dump -> abi-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 abi-dump.3 -> abi-dump.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 269200 May 28 21:29 abi-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 abi-load -> abi-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 abi-load.3 -> abi-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 639488 May 28 21:30 abi-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 align-cache -> align-cache.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 align-cache.3 -> align-cache.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 249200 May 28 21:30 align-cache.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 align-info -> align-info.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 align-info.3 -> align-info.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 97392 May 28 21:30 align-info.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 bam-load -> bam-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 bam-load.3 -> bam-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 12596800 May 28 21:31 bam-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 cache-mgr -> cache-mgr.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 cache-mgr.3 -> cache-mgr.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 124752 May 28 21:30 cache-mgr.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 ccextract -> ccextract.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 ccextract.3 -> ccextract.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 273248 May 28 21:30 ccextract.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 cg-load -> cg-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 cg-load.3 -> cg-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 655944 May 28 21:30 cg-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 check-corrupt -> check-corrupt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 May 28 21:34 check-corrupt.3 -> check-corrupt.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 239792 May 28 21:30 check-corrupt.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 check-redact -> check-redact.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 check-redact.3 -> check-redact.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 93648 May 28 21:30 check-redact.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 copycat -> copycat.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 copycat.3 -> copycat.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 482104 May 28 21:30 copycat.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 crc32sum -> crc32sum.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 crc32sum.3 -> crc32sum.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 79368 May 28 21:30 crc32sum.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 22 May 28 21:34 dump-blob-boundaries -> dump-blob-boundaries.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 26 May 28 21:34 dump-blob-boundaries.3 -> dump-blob-boundaries.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 31528 May 28 21:30 dump-blob-boundaries.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 fastconv -> fastconv.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 fastconv.3 -> fastconv.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 4963984 May 28 21:31 fastconv.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 fasterq-dump -> fasterq-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 901584 May 28 21:30 fasterq-dump-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 fasterq-dump.3 -> fasterq-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 fasterq-dump.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 fastq-dump -> fastq-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 349400 May 28 21:30 fastq-dump-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 fastq-dump.3 -> fastq-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 fastq-dump.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 fastq-load -> fastq-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 fastq-load.3 -> fastq-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 699120 May 28 21:30 fastq-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 general-loader -> general-loader.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 May 28 21:34 general-loader.3 -> general-loader.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 1335768 May 28 21:30 general-loader.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 helicos-load -> helicos-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 helicos-load.3 -> helicos-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 605728 May 28 21:30 helicos-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 illumina-dump -> illumina-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 May 28 21:34 illumina-dump.3 -> illumina-dump.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 251320 May 28 21:29 illumina-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 illumina-load -> illumina-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 May 28 21:34 illumina-load.3 -> illumina-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 654616 May 28 21:30 illumina-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 5 May 28 21:34 kar -> kar.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 6 May 28 21:34 kar+ -> kar+.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 kar+.3 -> kar+.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 237800 May 28 21:30 kar+.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 kar+meta -> kar+meta.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 kar+meta.3 -> kar+meta.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 158576 May 28 21:30 kar+meta.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 kar.3 -> kar.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 191648 May 28 21:30 kar.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 kdb-index -> kdb-index.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 kdb-index.3 -> kdb-index.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 78216 May 28 21:30 kdb-index.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 kdbmeta -> kdbmeta.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 kdbmeta.3 -> kdbmeta.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 124464 May 28 21:30 kdbmeta.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 latf-load -> latf-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 latf-load.3 -> latf-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 507208 May 28 21:30 latf-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 make-read-filter -> make-read-filter.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 22 May 28 21:34 make-read-filter.3 -> make-read-filter.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 158936 May 28 21:30 make-read-filter.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 7 May 28 21:34 md5cp -> md5cp.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 md5cp.3 -> md5cp.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 89640 May 28 21:30 md5cp.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 meta-cmp -> meta-cmp.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 meta-cmp.3 -> meta-cmp.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 82024 May 28 21:30 meta-cmp.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 meta-copy -> meta-copy.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 meta-copy.3 -> meta-copy.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 81960 May 28 21:30 meta-copy.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 meta-repair -> meta-repair.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 meta-repair.3 -> meta-repair.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 135584 May 28 21:30 meta-repair.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 ngs-pileup -> ngs-pileup.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 ngs-pileup.3 -> ngs-pileup.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 2543576 May 28 21:30 ngs-pileup.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 pacbio-correct -> pacbio-correct.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 May 28 21:34 pacbio-correct.3 -> pacbio-correct.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 76016 May 28 21:30 pacbio-correct.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 pacbio-load -> pacbio-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 pacbio-load.3 -> pacbio-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 477896 May 28 21:30 pacbio-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 pacbio-loadxml -> pacbio-loadxml.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 May 28 21:34 pacbio-loadxml.3 -> pacbio-loadxml.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 589400 May 28 21:30 pacbio-loadxml.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 pileup-stats -> pileup-stats.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 pileup-stats.3 -> pileup-stats.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 2724088 May 28 21:31 pileup-stats.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 prefetch -> prefetch.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 466640 May 28 21:30 prefetch-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 prefetch.3 -> prefetch.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 prefetch.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 May 28 21:34 rcexplain -> rcexplain.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 rcexplain.3 -> rcexplain.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 63384 May 28 21:30 rcexplain.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 May 28 21:34 read-filter-redact -> read-filter-redact.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 24 May 28 21:34 read-filter-redact.3 -> read-filter-redact.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 111720 May 28 21:30 read-filter-redact.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 ref-variation -> ref-variation.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 May 28 21:34 ref-variation.3 -> ref-variation.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 2904424 May 28 21:31 ref-variation.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 rowwritetest -> rowwritetest.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 rowwritetest.3 -> rowwritetest.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 88528 May 28 21:30 rowwritetest.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sam-dump -> sam-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 826784 May 28 21:30 sam-dump-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sam-dump.3 -> sam-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sam-dump.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 samview -> samview.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 samview-util -> samview-util.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 samview-util.3 -> samview-util.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 64120 May 28 21:30 samview-util.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 samview.3 -> samview.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 307736 May 28 21:30 samview.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 schema-replace -> schema-replace.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 May 28 21:34 schema-replace.3 -> schema-replace.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 82928 May 28 21:30 schema-replace.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sff-dump -> sff-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sff-dump.3 -> sff-dump.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 234392 May 28 21:29 sff-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sff-load -> sff-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sff-load.3 -> sff-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 650232 May 28 21:30 sff-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sortreadtest -> sortreadtest.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 sortreadtest.3 -> sortreadtest.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 79736 May 28 21:30 sortreadtest.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sra-info -> sra-info.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sra-info.3 -> sra-info.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 2162240 May 28 21:30 sra-info.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 sra-pileup -> sra-pileup.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 443544 May 28 21:30 sra-pileup-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 sra-pileup.3 -> sra-pileup.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sra-pileup.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 sra-search -> sra-search.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 sra-search.3 -> sra-search.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 3905040 May 28 21:31 sra-search.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sra-sort -> sra-sort.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 sra-sort-cg -> sra-sort-cg.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 sra-sort-cg.3 -> sra-sort-cg.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 807424 May 28 21:30 sra-sort-cg.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sra-sort.3 -> sra-sort.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 807496 May 28 21:30 sra-sort.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sra-stat -> sra-stat.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sra-stat.3 -> sra-stat.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 336072 May 28 21:30 sra-stat.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 srapath -> srapath.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 254912 May 28 21:30 srapath-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 srapath.3 -> srapath.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 srapath.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 sratools -> sratools.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 sratools.3 -> sratools.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 4928768 May 28 21:30 sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 srf-load -> srf-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 srf-load.3 -> srf-load.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 829520 May 28 21:30 srf-load.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 May 28 21:34 test-download -> test-download.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 May 28 21:34 test-download.3 -> test-download.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 93792 May 28 21:30 test-download.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 24 May 28 21:34 test-read-write-cursor -> test-read-write-cursor.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 28 May 28 21:34 test-read-write-cursor.3 -> test-read-write-cursor.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 75432 May 28 21:30 test-read-write-cursor.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 test-sra -> test-sra.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 test-sra.3 -> test-sra.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 342072 May 28 21:30 test-sra.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 8 May 28 21:34 testld -> testld.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 testld.3 -> testld.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 76440 May 28 21:30 testld.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 txt2kdb -> txt2kdb.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 txt2kdb.3 -> txt2kdb.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 82904 May 28 21:30 txt2kdb.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 var-expand -> var-expand.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 var-expand.3 -> var-expand.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 1986472 May 28 21:31 var-expand.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 vdb-config -> vdb-config.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 vdb-config.3 -> vdb-config.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 2872568 May 28 21:31 vdb-config.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 vdb-copy -> vdb-copy.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-copy.3 -> vdb-copy.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 329840 May 28 21:30 vdb-copy.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 vdb-decrypt -> vdb-decrypt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 vdb-decrypt.3 -> vdb-decrypt.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 121696 May 28 21:30 vdb-decrypt.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 vdb-diff -> vdb-diff.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-diff.3 -> vdb-diff.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 155248 May 28 21:30 vdb-diff.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 vdb-dump -> vdb-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 901144 May 28 21:30 vdb-dump-orig.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-dump.3 -> vdb-dump.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-dump.3.0.9 -> sratools.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 vdb-encrypt -> vdb-encrypt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 May 28 21:34 vdb-encrypt.3 -> vdb-encrypt.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 120040 May 28 21:30 vdb-encrypt.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 May 28 21:34 vdb-lock -> vdb-lock.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-lock.3 -> vdb-lock.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 68336 May 28 21:30 vdb-lock.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 May 28 21:34 vdb-sql -> vdb-sql.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 May 28 21:34 vdb-sql.3 -> vdb-sql.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 5217120 May 28 21:31 vdb-sql.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 May 28 21:34 vdb-unlock -> vdb-unlock.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 May 28 21:34 vdb-unlock.3 -> vdb-unlock.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 68344 May 28 21:30 vdb-unlock.3.0.9 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 May 28 21:34 vdb-validate -> vdb-validate.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 May 28 21:34 vdb-validate.3 -> vdb-validate.3.0.9 -rwxr-xr-x 1 pbuilder1 pbuilder1 261128 May 28 21:30 vdb-validate.3.0.9 cd debian/tmp/usr/bin && \ for bin in *-orig.* ; do \ base=${bin%-orig.*} && \ vbase=$(readlink "$(readlink $base)") && \ vdriver=$(readlink "$vbase") && \ mv -v $bin $base-orig && \ ln -snfv ${vdriver%%.[0-9]*} $vbase || exit $? ; \ done && \ for bin in *[a-z+] ; do \ bin2=$(readlink $bin) ; \ bin3=$(readlink "$bin2") ; \ case $bin2 in \ $bin.* ) rm -v $bin2 && mv -v $bin3 $bin || exit $? ;; \ esac ; \ done renamed 'fasterq-dump-orig.3.0.9' -> 'fasterq-dump-orig' 'fasterq-dump.3.0.9' -> 'sratools' renamed 'fastq-dump-orig.3.0.9' -> 'fastq-dump-orig' 'fastq-dump.3.0.9' -> 'sratools' renamed 'prefetch-orig.3.0.9' -> 'prefetch-orig' 'prefetch.3.0.9' -> 'sratools' renamed 'sam-dump-orig.3.0.9' -> 'sam-dump-orig' 'sam-dump.3.0.9' -> 'sratools' renamed 'sra-pileup-orig.3.0.9' -> 'sra-pileup-orig' 'sra-pileup.3.0.9' -> 'sratools' renamed 'srapath-orig.3.0.9' -> 'srapath-orig' 'srapath.3.0.9' -> 'sratools' renamed 'vdb-dump-orig.3.0.9' -> 'vdb-dump-orig' 'vdb-dump.3.0.9' -> 'sratools' removed 'abi-dump.3' renamed 'abi-dump.3.0.9' -> 'abi-dump' removed 'abi-load.3' renamed 'abi-load.3.0.9' -> 'abi-load' removed 'align-cache.3' renamed 'align-cache.3.0.9' -> 'align-cache' removed 'align-info.3' renamed 'align-info.3.0.9' -> 'align-info' removed 'bam-load.3' renamed 'bam-load.3.0.9' -> 'bam-load' removed 'cache-mgr.3' renamed 'cache-mgr.3.0.9' -> 'cache-mgr' removed 'ccextract.3' renamed 'ccextract.3.0.9' -> 'ccextract' removed 'cg-load.3' renamed 'cg-load.3.0.9' -> 'cg-load' removed 'check-corrupt.3' renamed 'check-corrupt.3.0.9' -> 'check-corrupt' removed 'check-redact.3' renamed 'check-redact.3.0.9' -> 'check-redact' removed 'copycat.3' renamed 'copycat.3.0.9' -> 'copycat' removed 'crc32sum.3' renamed 'crc32sum.3.0.9' -> 'crc32sum' removed 'dump-blob-boundaries.3' renamed 'dump-blob-boundaries.3.0.9' -> 'dump-blob-boundaries' removed 'fastconv.3' renamed 'fastconv.3.0.9' -> 'fastconv' removed 'fasterq-dump.3' renamed 'fasterq-dump.3.0.9' -> 'fasterq-dump' removed 'fastq-dump.3' renamed 'fastq-dump.3.0.9' -> 'fastq-dump' removed 'fastq-load.3' renamed 'fastq-load.3.0.9' -> 'fastq-load' removed 'general-loader.3' renamed 'general-loader.3.0.9' -> 'general-loader' removed 'helicos-load.3' renamed 'helicos-load.3.0.9' -> 'helicos-load' removed 'illumina-dump.3' renamed 'illumina-dump.3.0.9' -> 'illumina-dump' removed 'illumina-load.3' renamed 'illumina-load.3.0.9' -> 'illumina-load' removed 'kar.3' renamed 'kar.3.0.9' -> 'kar' removed 'kar+.3' renamed 'kar+.3.0.9' -> 'kar+' removed 'kar+meta.3' renamed 'kar+meta.3.0.9' -> 'kar+meta' removed 'kdb-index.3' renamed 'kdb-index.3.0.9' -> 'kdb-index' removed 'kdbmeta.3' renamed 'kdbmeta.3.0.9' -> 'kdbmeta' removed 'latf-load.3' renamed 'latf-load.3.0.9' -> 'latf-load' removed 'make-read-filter.3' renamed 'make-read-filter.3.0.9' -> 'make-read-filter' removed 'md5cp.3' renamed 'md5cp.3.0.9' -> 'md5cp' removed 'meta-cmp.3' renamed 'meta-cmp.3.0.9' -> 'meta-cmp' removed 'meta-copy.3' renamed 'meta-copy.3.0.9' -> 'meta-copy' removed 'meta-repair.3' renamed 'meta-repair.3.0.9' -> 'meta-repair' removed 'ngs-pileup.3' renamed 'ngs-pileup.3.0.9' -> 'ngs-pileup' removed 'pacbio-correct.3' renamed 'pacbio-correct.3.0.9' -> 'pacbio-correct' removed 'pacbio-load.3' renamed 'pacbio-load.3.0.9' -> 'pacbio-load' removed 'pacbio-loadxml.3' renamed 'pacbio-loadxml.3.0.9' -> 'pacbio-loadxml' removed 'pileup-stats.3' renamed 'pileup-stats.3.0.9' -> 'pileup-stats' removed 'prefetch.3' renamed 'prefetch.3.0.9' -> 'prefetch' removed 'rcexplain.3' renamed 'rcexplain.3.0.9' -> 'rcexplain' removed 'read-filter-redact.3' renamed 'read-filter-redact.3.0.9' -> 'read-filter-redact' removed 'ref-variation.3' renamed 'ref-variation.3.0.9' -> 'ref-variation' removed 'rowwritetest.3' renamed 'rowwritetest.3.0.9' -> 'rowwritetest' removed 'sam-dump.3' renamed 'sam-dump.3.0.9' -> 'sam-dump' removed 'samview.3' renamed 'samview.3.0.9' -> 'samview' removed 'samview-util.3' renamed 'samview-util.3.0.9' -> 'samview-util' removed 'schema-replace.3' renamed 'schema-replace.3.0.9' -> 'schema-replace' removed 'sff-dump.3' renamed 'sff-dump.3.0.9' -> 'sff-dump' removed 'sff-load.3' renamed 'sff-load.3.0.9' -> 'sff-load' removed 'sortreadtest.3' renamed 'sortreadtest.3.0.9' -> 'sortreadtest' removed 'sra-info.3' renamed 'sra-info.3.0.9' -> 'sra-info' removed 'sra-pileup.3' renamed 'sra-pileup.3.0.9' -> 'sra-pileup' removed 'sra-search.3' renamed 'sra-search.3.0.9' -> 'sra-search' removed 'sra-sort.3' renamed 'sra-sort.3.0.9' -> 'sra-sort' removed 'sra-sort-cg.3' renamed 'sra-sort-cg.3.0.9' -> 'sra-sort-cg' removed 'sra-stat.3' renamed 'sra-stat.3.0.9' -> 'sra-stat' removed 'srapath.3' renamed 'srapath.3.0.9' -> 'srapath' removed 'sratools.3' renamed 'sratools.3.0.9' -> 'sratools' removed 'srf-load.3' renamed 'srf-load.3.0.9' -> 'srf-load' removed 'test-download.3' renamed 'test-download.3.0.9' -> 'test-download' removed 'test-read-write-cursor.3' renamed 'test-read-write-cursor.3.0.9' -> 'test-read-write-cursor' removed 'test-sra.3' renamed 'test-sra.3.0.9' -> 'test-sra' removed 'testld.3' renamed 'testld.3.0.9' -> 'testld' removed 'txt2kdb.3' renamed 'txt2kdb.3.0.9' -> 'txt2kdb' removed 'var-expand.3' renamed 'var-expand.3.0.9' -> 'var-expand' removed 'vdb-config.3' renamed 'vdb-config.3.0.9' -> 'vdb-config' removed 'vdb-copy.3' renamed 'vdb-copy.3.0.9' -> 'vdb-copy' removed 'vdb-decrypt.3' renamed 'vdb-decrypt.3.0.9' -> 'vdb-decrypt' removed 'vdb-diff.3' renamed 'vdb-diff.3.0.9' -> 'vdb-diff' removed 'vdb-dump.3' renamed 'vdb-dump.3.0.9' -> 'vdb-dump' removed 'vdb-encrypt.3' renamed 'vdb-encrypt.3.0.9' -> 'vdb-encrypt' removed 'vdb-lock.3' renamed 'vdb-lock.3.0.9' -> 'vdb-lock' removed 'vdb-sql.3' renamed 'vdb-sql.3.0.9' -> 'vdb-sql' removed 'vdb-unlock.3' renamed 'vdb-unlock.3.0.9' -> 'vdb-unlock' removed 'vdb-validate.3' renamed 'vdb-validate.3.0.9' -> 'vdb-validate' mkdir debian/tmp/usr/lib/sra-toolkit mv debian/tmp/usr/bin/sratools debian/tmp/usr/lib/sra-toolkit for x in debian/tmp/usr/bin/*-orig; do \ mv -v $x debian/tmp/usr/lib/sra-toolkit ; \ ln -snfv ../lib/sra-toolkit/sratools ${x%-orig} ; \ done renamed 'debian/tmp/usr/bin/fasterq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fasterq-dump-orig' 'debian/tmp/usr/bin/fasterq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/fastq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fastq-dump-orig' 'debian/tmp/usr/bin/fastq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/prefetch-orig' -> 'debian/tmp/usr/lib/sra-toolkit/prefetch-orig' 'debian/tmp/usr/bin/prefetch' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sam-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sam-dump-orig' 'debian/tmp/usr/bin/sam-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sra-pileup-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sra-pileup-orig' 'debian/tmp/usr/bin/sra-pileup' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/srapath-orig' -> 'debian/tmp/usr/lib/sra-toolkit/srapath-orig' 'debian/tmp/usr/bin/srapath' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/vdb-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/vdb-dump-orig' 'debian/tmp/usr/bin/vdb-dump' -> '../lib/sra-toolkit/sratools' dh_install # remove susipcious file which is not executable and conflicts with package magic rm -f debian/*/usr/bin/magic # Formally supply a standard installation ID to satisfy sratools echo '/LIBS/GUID = "806b5c3b-0088-4732-8359-51630950d723"' >debian/sra-toolkit/etc/ncbi/debian.kfg set -e && for i in 3.12 3.11; do \ cd ngs/ngs-python; \ python$i ./setup.py install --install-layout=deb \ --root /build/reproducible-path/sra-sdk-3.0.9+dfsg/debian/python3-ngs; \ cd ../..; \ done /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/ngs/LibManager.py:123: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() find debian -name "*.pyc" -delete find debian -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' jh_installjavadoc -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_installexamples find debian/*/ -name .gitignore -delete make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' dh_python3 -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake debian/rules execute_before_dh_link make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' # Putting the upstream version number (without the dfsg part) at the end of # symlink source in the -jni package. sed -e 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\13.0.9+dfsg/' \ -e 's/#STRIPPED_UPSTREAM_VERSION#\(.*\)+dfsg[0-9]*/\1/' \ -e 's/\$[({]DEB_HOST_MULTIARCH[)}]/x86_64-linux-gnu/g' \ debian/libngs-jni.links.in > debian/libngs-jni.links make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.9+dfsg' 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 mh_installpoms -O--buildsystem=cmake mh_linkjars --skip-clean-poms -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 dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol string_cmp used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol xcColumnEmpty used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol VDBManagerMakeSchema used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol KDBManagerMakeRead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol string_size used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol KNSManagerSetUserAgent used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol xcParamUnexpected used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol xcUnimplemented used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol VDBManagerOpenDBRead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: symbol KRefcountAdd used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.9 found in none of the libraries dpkg-shlibdeps: warning: 133 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 libngs-jni: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libncbi-ngs-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libngs-c++3' in '../libngs-c++3_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'sra-toolkit-dbgsym' in '../sra-toolkit-dbgsym_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libngs-c++-dev' in '../libngs-c++-dev_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libngs-c++3-dbgsym' in '../libngs-c++3-dbgsym_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3' in '../libncbi-ngs3_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3-dbgsym' in '../libncbi-ngs3-dbgsym_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libncbi-ngs-dev' in '../libncbi-ngs-dev_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libngs-jni' in '../libngs-jni_3.0.9+dfsg-3_amd64.deb'. dpkg-deb: building package 'libngs-java-doc' in '../libngs-java-doc_3.0.9+dfsg-3_all.deb'. dpkg-deb: building package 'python3-ngs' in '../python3-ngs_3.0.9+dfsg-3_all.deb'. dpkg-deb: building package 'libngs-java' in '../libngs-java_3.0.9+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sra-sdk_3.0.9+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../sra-sdk_3.0.9+dfsg-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: 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/3289361 and its subdirectories I: Current time: Tue May 28 21:35:39 -12 2024 I: pbuilder-time-stamp: 1716975339 Wed May 29 09:35:40 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed May 29 09:35:40 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed May 29 09:40:50 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed May 29 09:40:50 UTC 2024 I: sra-sdk_3.0.9+dfsg-3_amd64.changes: Format: 1.8 Date: Sun, 05 May 2024 22:45:27 -0400 Source: sra-sdk Binary: libncbi-ngs-dev libncbi-ngs3 libncbi-ngs3-dbgsym libngs-c++-dev libngs-c++3 libngs-c++3-dbgsym libngs-java libngs-java-doc libngs-jni python3-ngs sra-toolkit sra-toolkit-dbgsym Architecture: amd64 all Version: 3.0.9+dfsg-3 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Aaron M. Ucko Description: libncbi-ngs-dev - Next Generation Sequencing language Bindings (C++ development) libncbi-ngs3 - Next Generation Sequencing language Bindings (full runtime) libngs-c++-dev - Next Generation Sequencing language Bindings (C++ development) libngs-c++3 - Next Generation Sequencing language Bindings (C++ runtime) libngs-java - Next Generation Sequencing language Bindings (Java bindings) libngs-java-doc - Next Generation Sequencing language Bindings (Java documentation) libngs-jni - Next Generation Sequencing language Bindings (Java native binding python3-ngs - Next Generation Sequencing language Bindings (Python3 bindings) sra-toolkit - utilities for the NCBI Sequence Read Archive Closes: 1053411 Changes: sra-sdk (3.0.9+dfsg-3) experimental; urgency=medium . * debian/control: Build depend on libabsl-dev so binaries using libre2 (sharq and relevant tests) can unconditionally link against -labsl_string_view for simplicitly. * debian/patches/support_libre2-11.patch (new): Prepare for (but don't require!) newer libre2 versions where re2::StringPiece has changed from a custom class to a typedef for absl::string_view, whose API is somewhat different. (Closes: #1053411.) 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command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.640s) 0.640s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.297s) 0.297s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 971ms CPU time consumed: 972ms Wed May 29 09:40:53 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Wed May 29 09:40:53 UTC 2024 I: sra-sdk from experimental built successfully and reproducibly on amd64. Wed May 29 09:40:54 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 29 09:40:54 UTC 2024 I: Submitting 20K b1/sra-sdk_3.0.9+dfsg-3_amd64.buildinfo.asc Wed May 29 09:40:55 UTC 2024 I: Submitting 20K b2/sra-sdk_3.0.9+dfsg-3_amd64.buildinfo.asc Wed May 29 09:40:56 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 29 09:40:56 UTC 2024 I: Done submitting .buildinfo files. Wed May 29 09:40:56 UTC 2024 I: Removing signed sra-sdk_3.0.9+dfsg-3_amd64.buildinfo.asc files: removed './b1/sra-sdk_3.0.9+dfsg-3_amd64.buildinfo.asc' removed './b2/sra-sdk_3.0.9+dfsg-3_amd64.buildinfo.asc'