I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 24 00:01:42 -12 2024 I: pbuilder-time-stamp: 1724500902 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sra-sdk_3.0.3+dfsg-6~deb12u1.dsc] I: copying [./sra-sdk_3.0.3+dfsg.orig.tar.xz] I: copying [./sra-sdk_3.0.3+dfsg-6~deb12u1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 14 09:42:24 2023 -12 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.3+dfsg-6~deb12u1.dsc: no acceptable signature found dpkg-source: info: extracting sra-sdk in sra-sdk-3.0.3+dfsg dpkg-source: info: unpacking sra-sdk_3.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking sra-sdk_3.0.3+dfsg-6~deb12u1.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 fix_javadoc_build.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/428083/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4e0de03298ee40e89b0d9b6c4311fb28' 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='428083' 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.3t3OzlOC/pbuilderrc_RhhU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3t3OzlOC/b1 --logfile b1/build.log sra-sdk_3.0.3+dfsg-6~deb12u1.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-1 (2023-07-14) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/428083/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, libncbi-vdb-dev (>= 3.0.1+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, python3-distutils, 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 ... 19555 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 libncbi-vdb-dev (>= 3.0.1+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 python3-distutils; however: Package python3-distutils 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} 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} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hdf5-helpers{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} java-common{a} javahelper{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libasound2{a} libasound2-data{a} libassuan0{a} libatk1.0-0{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} libcups2{a} libcurl4{a} libcurl4-openssl-dev{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} libelf1{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} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{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} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm15{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-dev{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{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} libnpth0{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} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libre2-9{a} libre2-dev{a} libreadline8{a} libregexp-ipv6-perl{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} libssh2-1{a} libssl-dev{a} libsub-override-perl{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} libuv1{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} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{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 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 libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-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 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, 275 newly installed, 0 to remove and 0 not upgraded. Need to get 266 MB of archives. After unpacking 847 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 flex amd64 2.6.4-8.2 [422 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.9-1 [1416 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.37-2 [43.3 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.8-2~deb12u1 [201 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u1 [244 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.7+7-1~deb12u1 [43.7 MB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B] Get: 72 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230103 [11.4 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u1 [292 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u1 [759 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u1 [192 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.7+7-1~deb12u1 [184 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B] Get: 165 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.7+7-1~deb12u1 [71.3 MB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B] Get: 167 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.7+7-1~deb12u1 [3590 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 187 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 206 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.4 [1073 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130+deb12u1 [104 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 javahelper all 0.78 [97.2 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-10 [487 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libsepol-dev amd64 3.4-2.1 [351 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libpcre2-32-0 amd64 10.42-1 [234 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libpcre2-posix3 amd64 10.42-1 [55.4 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libpcre2-dev amd64 10.42-1 [753 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libselinux1-dev amd64 3.4-1+b6 [157 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libfuse-dev amd64 2.9.9-6+b1 [1021 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.9-1 [2428 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libmagic-dev amd64 1:5.44-3 [116 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 libncbi-wvdb3 amd64 3.0.2+dfsg-2 [1078 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 libncbi-wvdb-dev amd64 3.0.2+dfsg-2 [1188 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb-dev amd64 3.0.2+dfsg-2 [1461 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 libre2-9 amd64 20220601+dfsg-1+b1 [179 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 libre2-dev amd64 20220601+dfsg-1+b1 [241 kB] Get: 270 http://deb.debian.org/debian bookworm/main amd64 libsam-extract3 amd64 3.0.2+dfsg-2 [43.0 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 libsam-extract-dev amd64 3.0.2+dfsg-2 [44.5 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.3~deb12u1 [782 kB] Get: 273 http://deb.debian.org/debian bookworm/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Fetched 266 MB in 8s (31.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (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 ... 19555 files and directories currently installed.) Preparing to unpack .../archives/m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package flex. Preparing to unpack .../flex_2.6.4-8.2_amd64.deb ... Unpacking flex (2.6.4-8.2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20053 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20487 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package netbase. Preparing to unpack .../001-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.0.9-1_amd64.deb ... Unpacking openssl (3.0.9-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../008-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../011-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../014-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package hicolor-icon-theme. Preparing to unpack .../016-hicolor-icon-theme_0.17-2_all.deb ... Unpacking hicolor-icon-theme (0.17-2) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../017-libgdk-pixbuf2.0-common_2.42.10+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../018-libglib2.0-0_2.74.6-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../019-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../020-libxml2_2.9.14+dfsg-1.3~deb12u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../021-shared-mime-info_2.2-1_amd64.deb ... Unpacking shared-mime-info (2.2-1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../023-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../024-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../025-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../026-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../027-libwebp7_1.2.4-0.2_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.2) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../028-libtiff6_4.5.0-6_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-6) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../029-libgdk-pixbuf-2.0-0_2.42.10+dfsg-1+b1_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Selecting previously unselected package gtk-update-icon-cache. Preparing to unpack .../030-gtk-update-icon-cache_3.24.37-2_amd64.deb ... Unpacking gtk-update-icon-cache (3.24.37-2) ... Selecting previously unselected package adwaita-icon-theme. Preparing to unpack .../031-adwaita-icon-theme_43-1_all.deb ... Unpacking adwaita-icon-theme (43-1) ... Selecting previously unselected package at-spi2-common. Preparing to unpack .../032-at-spi2-common_2.46.0-5_all.deb ... Unpacking at-spi2-common (2.46.0-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../033-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../034-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../035-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../036-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package bison. Preparing to unpack .../037-bison_2%3a3.8.2+dfsg-1+b1_amd64.deb ... Unpacking bison (2:3.8.2+dfsg-1+b1) ... Selecting previously unselected package java-common. Preparing to unpack .../038-java-common_0.74_all.deb ... Unpacking java-common (0.74) ... Selecting previously unselected package libavahi-common-data:amd64. 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Setting up libksba8:amd64 (1.6.3-2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up wdiff (1.2.2-5) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libre2-9:amd64 (20220601+dfsg-1+b1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libzstd-dev:amd64 (1.5.4+dfsg2-5) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up java-common (0.74) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up libio-pty-perl (1:1.17-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libglvnd0:amd64 (1.6.0-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.31-2) ... Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libnpth0:amd64 (1.6-3) ... Setting up file (1:5.44-3) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libmagic-dev:amd64 (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libasound2-data (1.2.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libpcre2-32-0:amd64 (10.42-1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libx11-data (2:1.8.4-2+deb12u1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Setting up libnspr4:amd64 (2:4.35-1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libdbus-1-3:amd64 (1.14.8-2~deb12u1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libssl-dev:amd64 (3.0.9-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-12) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up d-shlibs (0.104) ... Setting up libipc-run-perl (20220807.0-1) ... Setting up libsepol-dev:amd64 (3.4-2.1) ... Setting up libpcsclite1:amd64 (1.9.9-2) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up libgif7:amd64 (5.2.1-2.5) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libpcre2-posix3:amd64 (10.42-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libtiff6:amd64 (4.5.0-6) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libasound2:amd64 (1.2.8-1+b1) ... 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 libsub-override-perl (0.09-4) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libsam-extract3:amd64 (3.0.2+dfsg-2) ... Setting up cmake-data (3.25.1-1) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libre2-dev:amd64 (20220601+dfsg-1+b1) ... Setting up openssl (3.0.9-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up liburi-perl (5.17-1) ... Setting up libsam-extract-dev:amd64 (3.0.2+dfsg-2) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up markdown (1.0.1-12) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+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 (1.2.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up flex (2.6.4-8.2) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libpcre2-dev:amd64 (10.42-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libselinux1-dev:amd64 (3.4-1+b6) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libaec-dev:amd64 (1.0.6-1+b1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libnss3:amd64 (2:3.87.1-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libfuse-dev:amd64 (2.9.9-6+b1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libncbi-wvdb3:amd64 (3.0.2+dfsg-2) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libcurl4:amd64 (7.88.1-10) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libncbi-wvdb-dev:amd64 (3.0.2+dfsg-2) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up gpg (2.2.40-1.1) ... Setting up gnupg-utils (2.2.40-1.1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up gpgsm (2.2.40-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libcurl4-openssl-dev:amd64 (7.88.1-10) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up gpg-wks-server (2.2.40-1.1) ... Setting up libcups2:amd64 (2.4.2-3+deb12u1) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ... Setting up cmake (3.25.1-1) ... Setting up libncbi-vdb-dev:amd64 (3.0.2+dfsg-2) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up gpg-wks-client (2.2.40-1.1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libhdf5-fortran-102:amd64 (1.10.8+repack1-1) ... Setting up gnupg (2.2.40-1.1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up libgtk2.0-0:amd64 (2.24.33-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... 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 default-jre-headless (2:1.17-74) ... Setting up libwww-perl (6.68-1) ... Setting up maven-repo-helper (1.11) ... Setting up devscripts (2.23.4) ... Setting up openjdk-17-jre-headless:amd64 (17.0.7+7-1~deb12u1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up javahelper (0.78) ... Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up openjdk-17-jre:amd64 (17.0.7+7-1~deb12u1) ... Setting up default-jre (2:1.17-74) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.7+7-1~deb12u1) ... 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 openjdk-17-jdk:amd64 (17.0.7+7-1~deb12u1) ... 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 (2:1.17-74) ... Setting up default-jdk (2:1.17-74) ... Processing triggers for libc-bin (2.36-9+deb12u1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/sra-sdk-3.0.3+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_3.0.3+dfsg-6~deb12u1_source.changes dpkg-buildpackage: info: source package sra-sdk dpkg-buildpackage: info: source version 3.0.3+dfsg-6~deb12u1 dpkg-buildpackage: info: source distribution bookworm 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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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 cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -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 .. CMAKE_VERSION=3.25.1 -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done VERSION=3.0.3 -- Performing Test COMPILER_OPTION_SSE42_SUPPORTED -- Performing Test COMPILER_OPTION_SSE42_SUPPORTED - Success -- 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 "2.9.14") LIBXML2_INCLUDE_DIR=/usr/include/libxml2 LIBXML2_LIBRARIES=/usr/lib/x86_64-linux-gnu/libxml2.so -- Found Java: /usr/bin/java (found version "17.0.7") found components: Development -- Found Python3: /usr/bin/python3 (found version "3.11.2") 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 BUILD_TOOLS_INTERNAL=ON BUILD_TOOLS_LOADERS=ON BUILD_TOOLS_TEST_TOOLS=ON CMake Warning at tools/external/sra-search/test/CMakeLists.txt:219 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-search is not found. The corresponding tests are skipped. -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.0.9") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- 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 -- 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 "1.10.8") found components: C CMake Warning at test/external/align-info/CMakeLists.txt:34 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/align-info is not found. The corresponding tests are skipped. CMake Warning at test/external/fasterq-dump/CMakeLists.txt:58 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump is not found. The corresponding tests are skipped. CMake Warning at test/external/kdbmeta/CMakeLists.txt:43 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta is not found. The corresponding tests are skipped. CMake Warning at test/external/ngs-pileup/CMakeLists.txt:147 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ngs-pileup is not found. The corresponding tests are skipped. CMake Warning at test/external/prefetch/CMakeLists.txt:114 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/prefetch is not found. The corresponding tests are skipped. CMake Warning at test/external/sam-dump/CMakeLists.txt:51 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sam-dump is not found. The corresponding tests are skipped. CMake Warning at test/external/srapath/CMakeLists.txt:61 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/srapath is not found. The corresponding tests are skipped. CMake Warning at test/external/sra-pileup/CMakeLists.txt:50 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-pileup is not found. The corresponding tests are skipped. CMake Warning at test/external/sra-stat/CMakeLists.txt:61 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-stat is not found. The corresponding tests are skipped. CMake Warning at test/external/vdb-config/CMakeLists.txt:40 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config is not found. The corresponding tests are skipped. CMake Warning at test/external/vdb-validate/CMakeLists.txt:41 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-validate is not found. The corresponding tests are skipped. CMake Warning at test/loaders/bam-load/CMakeLists.txt:62 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/bam-load is not found. The corresponding tests are skipped. CMake Warning at test/loaders/fastq-loader/CMakeLists.txt:219 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/latf-load is not found. The corresponding tests are skipped. CMake Warning at test/loaders/kar/CMakeLists.txt:50 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kar is not found. The corresponding tests are skipped. CMake Warning at test/loaders/sra-sort/CMakeLists.txt:47 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-sort is not found. The corresponding tests are skipped. CMake Warning at test/internal/align-cache/CMakeLists.txt:42 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/align-cache is not found. The corresponding tests are skipped. CMake Warning at test/internal/copycat/CMakeLists.txt:68 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/copycat is not found. The corresponding tests are skipped. CMake Warning at test/internal/make-read-filter/CMakeLists.txt:72 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/make-read-filter is not found. The corresponding tests are skipped. CMake Warning at test/internal/read-filter-redact/CMakeLists.txt:40 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-unlock is not found. The corresponding tests are skipped. CMake Warning at test/internal/read-filter-redact/CMakeLists.txt:60 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/read-filter-redact is not found. The corresponding tests are skipped. CMake Warning at test/internal/vdb-copy/CMakeLists.txt:43 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-copy is not found. The corresponding tests are skipped. CMake Warning at test/internal/vdb-diff/CMakeLists.txt:75 (message): /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-diff is not found. The corresponding tests are skipped. -- Configuring done CMake Warning (dev) at tools/loaders/sharq/CMakeLists.txt:96 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg' jh_linkjars -O--buildsystem=cmake dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sra-sdk-3.0.3+dfsg -B/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared/CMakeFiles/tk-version.dir/DependInfo.cmake --color= 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[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs/CMakeFiles/ngs.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/DependInfo.cmake --color= make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/DependInfo.cmake --color= 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 -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/DependInfo.cmake --color= 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[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/DependInfo.cmake --color= 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake --color= make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/depend make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/build 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+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]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 [ 0%] Building C object shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD 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-I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_Manager.c [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_String.c [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o [ 1%] Building C object ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py/py_Manager.c [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NCBI-NGS.c [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_ErrorMsg.c [ 1%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o [ 1%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o [ 1%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_PileupEvent.c [ 1%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadCollectionItf.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Pileup.c [ 2%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Alignment.c [ 2%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadCollectionItf.cpp [ 2%] Building Java objects for ngs-java.jar cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadCollectionItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -h ./jni @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 2%] Linking C static library ../ilib/libtk-version.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -P CMakeFiles/tk-version.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceSequence.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 3%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -E cmake_link_script CMakeFiles/tk-version.dir/link.txt --verbose=1 /usr/bin/ar qc ../ilib/libtk-version.a "CMakeFiles/tk-version.dir/toolkit.vers.c.o" /usr/bin/ranlib ../ilib/libtk-version.a [ 3%] Linking C static library ../../../ilib/libngs-py.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -P CMakeFiles/ngs-py.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp [ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupItf.cpp [ 4%] Built target tk-version 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/ar qc ../../../ilib/libngs-py.a "CMakeFiles/ngs-py.dir/py_Manager.c.o" [ 4%] Linking C static library ../../../ilib/libngs-jni.a /usr/bin/ranlib ../../../ilib/libngs-py.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -P CMakeFiles/ngs-jni.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javadoc -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs cd /build/sra-sdk-3.0.3+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 [ 4%] Built target ngs-py make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/kxml /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml/CMakeFiles/kxml.dir/DependInfo.cmake --color= /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" /usr/bin/ranlib ../../../ilib/libngs-jni.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-jni make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader/CMakeFiles/loader.dir/DependInfo.cmake --color= [ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/kxml/xml.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Building C object libs/loader/CMakeFiles/loader.dir/progressbar.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/progressbar.c.o -MF CMakeFiles/loader.dir/progressbar.c.o.d -o CMakeFiles/loader.dir/progressbar.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/progressbar.c [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp [ 5%] Building C object libs/loader/CMakeFiles/loader.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/loader-file.c.o -MF CMakeFiles/loader.dir/loader-file.c.o.d -o CMakeFiles/loader.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/loader-file.c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadCollectionItf; C = NGS_ReadCollection_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 5%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Reference.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupEventItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceItf.cpp [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReadCollection.c [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Read.c [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/EBI_ReferenceSequence.c [ 5%] Building C object libs/loader/CMakeFiles/loader.dir/loader-meta.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/loader-meta.c [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp [ 5%] Building C object libs/loader/CMakeFiles/loader.dir/queue-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/queue-file.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o -MF CMakeFiles/ngs.dir/SRA_Statistics.c.o.d -o CMakeFiles/ngs.dir/SRA_Statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Statistics.c [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp Loading source files for package gov.nih.nlm.ncbi.ngs... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Loading source files for package ngs... [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_DB_ReadCollection.c [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Read.c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceSequenceItf; C = NGS_ReferenceSequence_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ [ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o [ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp [ 5%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc-parsexml.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroup.c [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp [ 5%] Building C object libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o -MF CMakeFiles/loader.dir/alignment-writer.c.o.d -o CMakeFiles/loader.dir/alignment-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/alignment-writer.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/AlignmentItf.cpp Constructing Javadoc information... [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroupInfo.c [ 6%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadCollection.c [ 6%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o [ 7%] Building C object libs/loader/CMakeFiles/loader.dir/common-reader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/common-reader.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReferenceSequence.c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 7%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupItf; C = NGS_Pileup_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupItf; C = NGS_Pileup_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -MF CMakeFiles/ngs.dir/NGS_Statistics.c.o.d -o CMakeFiles/ngs.dir/NGS_Statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Statistics.c [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadCollection.c [ 7%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadGroupItf.cpp [ 7%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 8%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o [ 8%] Building C object libs/loader/CMakeFiles/loader.dir/common-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_PileupEvent.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/loader/CMakeFiles/loader.dir/common-writer.c.o -MF CMakeFiles/loader.dir/common-writer.c.o.d -o CMakeFiles/loader.dir/common-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/loader/common-writer.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Pileup.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Creating destination directory: "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/" Building index for all the packages and classes... [ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o Standard Doclet version 17.0.7+7-Debian-1deb12u1 Building tree for all the packages and classes... cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 8%] Linking C static library ../../ilib/libkxml.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake [ 8%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 /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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 8%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... /usr/bin/ranlib ../../ilib/libkxml.a cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/FragmentItf.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp [ 8%] Built target kxml make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadGroup.c [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o -MF CMakeFiles/ngs.dir/NGS_Alignment.c.o.d -o CMakeFiles/ngs.dir/NGS_Alignment.c.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Alignment.c [ 9%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 9%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:217: warning: @return has already been specified * @return '-' if negative strand is transcribed ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:218: warning: @return has already been specified * @return '?' if unknown ^ [ 9%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 9%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | ^ /build/sra-sdk-3.0.3+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 ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /build/sra-sdk-3.0.3+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 ^ [ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Reference.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:38:7: warning: 'jlong Cast(ngs::PileupEventItf*)' defined but not used [-Wunused-function] 38 | jlong Cast ( PileupEventItf * obj ) | ^~~~ [ 11%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StatisticsItf.cpp [ 11%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StringItf.cpp [ 11%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadItf; C = NGS_Read_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadItf; C = NGS_Read_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... [ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ [ 12%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp [ 12%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -MD -MT 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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceSequence.c [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp public class NGS ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Read.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Note: ngs/itf/Refcount.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | static int insertion = 0x08; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ [ 13%] Generating CMakeFiles/ngs-java.dir/java_class_filelist cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/Refcount.cpp [ 13%] Creating Java archive ngs-java.jar Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar @java_class_filelist [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrorMsg.cpp Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:35: warning: no comment public interface Read ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Fragment.c [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... [ 13%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Cursor.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StatisticsItf; C = NGS_Statistics_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Refcount.c Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Built target ngs-java make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/DependInfo.cmake --color= Building index for all classes... make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index-all.html... [ 13%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o [ 13%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -c /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -MF CMakeFiles/ngs-disp.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-disp.dir/Refcount.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'const char* ngs::StringItf::data() const': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:62:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 62 | if ( this != 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'size_t ngs::StringItf::size() const': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:97:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 97 | if ( this != 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StringItf; C = NGS_String_v1]': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o 46 warnings cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrBlock.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_String.c [ 14%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Id.c [ 14%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 14%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/mmarray.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 14%] Built target ngs-doc_javadoc 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/DependInfo.cmake --color= [ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o -MF CMakeFiles/ngs-disp.dir/VTable.cpp.o.d -o CMakeFiles/ngs-disp.dir/VTable.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/VTable.cpp [ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrBlock.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Building CXX object libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ErrBlock.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_makedb.cpp [ 15%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/reference-writer.c [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlob.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlobIterator.c [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void ngs::OpaqueRefcount::Release()': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:69:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 69 | if ( this != 0 ) | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void* ngs::OpaqueRefcount::Duplicate() const': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:100:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this != 0 ) | ^~ [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT 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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrorMsg.cpp cd /build/sra-sdk-3.0.3+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 [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o /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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp [ 15%] Building C object libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/loader/sequence-writer.c /usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlob.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlobIterator.c [ 15%] Built target ngs-adapt-c++ make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp [ 15%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/ascp/ascp.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlobIterator.cpp [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp [ 15%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/VByteBlob.c [ 15%] Linking C static library ../../ilib/libloader.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Statistics.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 15%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /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" [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp /usr/bin/ranlib ../../ilib/libloader.a [ 15%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Built target loader make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend [ 15%] Linking CXX static library ../../../ilib/libngs-disp.a make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Linking C static library ../../../ilib/libngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake /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" [ 15%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c [ 15%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/diagnose/diagnose.c /usr/bin/ranlib ../../../ilib/libngs-disp.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Built target ngs-disp /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 make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 /usr/bin/ranlib ../../../ilib/libngs.a make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 15%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlob.cpp /build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c: In function 'run_ascp': /build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:425:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | write(pipeto[1], answer, sizeof y - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:460:49: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 460 | write(pipeto[1], | ^~~~~~~~~~~~~~~~ 461 | answer, sizeof y - 1); | ~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 16%] Built target ngs 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/DependInfo.cmake --color= [ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 17%] Building CXX object tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_cpp.cpp [ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp [ 17%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp [ 17%] Building C object libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/general-writer/utf8-like-int-codec.c [ 17%] Building C object libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/ascp/linux/ascp-path.c [ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp [ 17%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlob.cpp [ 17%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp [ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp [ 18%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlobIterator.cpp [ 18%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReference.hpp:32, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 18%] Linking C static library ../../ilib/libascp.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 18%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake /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" [ 19%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp /usr/bin/ranlib ../../ilib/libascp.a cd /build/sra-sdk-3.0.3+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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ar qc ../../../../ilib/libngs-bind-c++.a "CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" [ 19%] Built target ascp 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui.dir/DependInfo.cmake --color= /usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbAlignment.hpp:30, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o [ 19%] Built target ngs-bind-c++ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/dir_dlg.c 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/fastq-dump.dir/DependInfo.cmake --color= make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c [ 19%] Linking CXX static library ../../../../ilib/libngs-bind-java.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -P CMakeFiles/ngs-bind-java.dir/cmake_clean_target.cmake [ 19%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c cd /build/sra-sdk-3.0.3+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 /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" /usr/bin/ranlib ../../../../ilib/libngs-bind-java.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/NGS-VDB.cpp [ 19%] Linking CXX executable ../../../test-bin/ngs-makedb cd /build/sra-sdk-3.0.3+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 [ 19%] Built target ngs-bind-java make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/illumina-dump.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp [ 19%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c [ 19%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3vdb.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = short unsigned int; uint8_t = unsigned char]': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:646:17: warning: unused variable 'ret2' [-Wunused-variable] 646 | int ret2 = decode_uint16 ( start, start + ret, & val2 ); | ^~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = unsigned int; uint8_t = unsigned char]': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:659:17: warning: unused variable 'ret2' [-Wunused-variable] 659 | int ret2 = decode_uint32 ( start, start + ret, & val2 ); | ^~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = long unsigned int; uint8_t = unsigned char]': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:672:17: warning: unused variable 'ret2' [-Wunused-variable] 672 | int ret2 = decode_uint64 ( start, start + ret, & val2 ); | ^~~~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/NGS-VDB.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/NGS-VDB.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/eventring.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/file_dlg.c [ 19%] Linking CXX static library ../../../../ilib/libtui_cpp.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui_cpp.dir/cmake_clean_target.cmake /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~ [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o /usr/bin/ar qc ../../../../ilib/libtui_cpp.a CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp /usr/bin/ranlib ../../../../ilib/libtui_cpp.a In file included from /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:11540: /build/sra-sdk-3.0.3+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) ); | ^~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Built target ngs-makedb 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/abi-dump.dir/DependInfo.cmake --color= /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~ [ 19%] Built target tui_cpp 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+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) ); | ^~~~~~ 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c [ 19%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/line_policy.c [ 19%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -c /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp:30: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 20%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 20%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c [ 20%] Linking CXX static library ../../ilib/libngs-vdb.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -P CMakeFiles/ngs-vdb.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-vdb.dir/link.txt --verbose=1 [ 21%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/core.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.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" [ 21%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/screen.c /usr/bin/ranlib ../../ilib/libngs-vdb.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Built target ngs-vdb make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sam-dump.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/DependInfo.cmake --color= [ 21%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/inputfiles.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+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]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/core.c.o cd /build/sra-sdk-3.0.3+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 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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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/helper.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c: In function 'foreach_argument': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:443:20: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 443 | if ( rc == 0 && path != NULL ) { | ^ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:394:10: note: 'rc' was declared here 394 | rc_t rc; | ^~ [ 23%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/rna_splice_log.c [ 23%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/arg_helper.c [ 23%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c [ 24%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/string_cache.c [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump-opts.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump-opts.c [ 24%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c [ 24%] Linking CXX static library ../../../../ilib/libngs-bind-python.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o -MF CMakeFiles/sam-dump.dir/out_redir.c.o.d -o CMakeFiles/sam-dump.dir/out_redir.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c cd /build/sra-sdk-3.0.3+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 [ 24%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/dflt_defline.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" [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr.c /usr/bin/ranlib ../../../../ilib/libngs-bind-python.a [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/perf_log.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 25%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/abi.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 25%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui.c [ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o cd /build/sra-sdk-3.0.3+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 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/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/DependInfo.cmake --color= [ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o -MF CMakeFiles/fasterq-dump.dir/inspector.c.o.d -o CMakeFiles/fasterq-dump.dir/inspector.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/inspector.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr1.c [ 25%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-context.c [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c [ 25%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg.c [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o -MF CMakeFiles/sam-dump.dir/matecache.c.o.d -o CMakeFiles/sam-dump.dir/matecache.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/matecache.c In function 'report_ref_table2', inlined from 'report_ref_obj' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:367:14, inlined from 'report_ref_database' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:408:34, inlined from 'report_references' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:432:41, inlined from 'report_on_reference' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:479:34: /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:175:14: warning: 'max_ev_at' may be used uninitialized [-Wmaybe-uninitialized] 175 | rc = KOutMsg( "max. EV:\t%,u\tat row #%,i ( from pos: %,u ... %,u )\n", max_ev, max_ev_at, from, from + 4999 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c: In function 'report_on_reference': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:137:46: note: 'max_ev_at' was declared here 137 | int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | ^~~~~~~~~ In function 'report_ref_table2', inlined from 'report_ref_obj' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:367:14, inlined from 'report_ref_database' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:408:34, inlined from 'report_references' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:432:41, inlined from 'report_on_reference' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:479:34: /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:171:14: warning: 'max_sec_at' may be used uninitialized [-Wmaybe-uninitialized] 171 | rc = KOutMsg( "max. SEC:\t%,u\tat row #%,i ( from pos: %,u ... %,u )\n", max_sec, max_sec_at, from, from + 4999 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c: In function 'report_on_reference': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:137:34: note: 'max_sec_at' was declared here 137 | int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | ^~~~~~~~~~ In function 'report_ref_table2', inlined from 'report_ref_obj' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:367:14, inlined from 'report_ref_database' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:408:34, inlined from 'report_references' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:432:41, inlined from 'report_on_reference' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:479:34: /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:166:41: warning: 'max_prim_at' may be used uninitialized [-Wmaybe-uninitialized] 166 | uint64_t from = ( ( max_prim_at - start ) * 5000 ) + 1; | ~~~~~~~~~~~~~~^~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c: In function 'report_on_reference': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/reref.c:137:21: note: 'max_prim_at' was declared here 137 | int64_t row_id, max_prim_at, max_sec_at, max_ev_at; | ^~~~~~~~~~~ [ 25%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o -MF CMakeFiles/fasterq-dump.dir/sbuffer.c.o.d -o CMakeFiles/fasterq-dump.dir/sbuffer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/sbuffer.c [ 25%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c [ 25%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o [ 26%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/libs/diagnose/endpoint.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | ^~ [ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/err_msg.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/err_msg.c [ 26%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fastq.c [ 26%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o [ 26%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o -MF CMakeFiles/sam-dump.dir/read_fkt.c.o.d -o CMakeFiles/sam-dump.dir/read_fkt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/read_fkt.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-aligned.c [ 26%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg_helper.c [ 26%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_tools.c.o -MF CMakeFiles/fasterq-dump.dir/file_tools.c.o.d -o CMakeFiles/fasterq-dump.dir/file_tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/file_tools.c [ 26%] Linking C static library ../../ilib/libdiagnose.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -P CMakeFiles/diagnose.dir/cmake_clean_target.cmake [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o -MF CMakeFiles/sam-dump.dir/sam-unaligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-unaligned.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c [ 27%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -E cmake_link_script CMakeFiles/diagnose.dir/link.txt --verbose=1 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o -MF CMakeFiles/sff-dump.dir/sff.c.o.d -o CMakeFiles/sff-dump.dir/sff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/sff.c [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/md_flag.c /usr/bin/ar qc ../../ilib/libdiagnose.a CMakeFiles/diagnose.dir/diagnose.c.o CMakeFiles/diagnose.dir/endpoint.c.o /usr/bin/ranlib ../../ilib/libdiagnose.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 27%] Built target diagnose 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/illumina.c [ 27%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o -MF CMakeFiles/vdb-validate.dir/vdb-validate.c.o.d -o CMakeFiles/vdb-validate.dir/vdb-validate.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c [ 27%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c: In function 'print_sliced_quality': [ 27%] Linking C executable ../../../bin/sff-dump /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:407:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 407 | return rc; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:391:10: note: 'rc' was declared here 391 | rc_t rc; | ^~ cd /build/sra-sdk-3.0.3+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 [ 27%] Linking C executable ../../../bin/abi-dump cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 28%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/var_fmt.c [ 28%] Linking CXX static library ../../ilib/libgeneral-writer.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -P CMakeFiles/general-writer.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-writer.dir/link.txt --verbose=1 /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | ^~ /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 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../../../bin/illumina-dump cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3.0.3 sff-dump.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3 sff-dump /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-dump.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 29%] Building CXX object tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/check-corrupt.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-dump abi-dump.3.0.3 [ 29%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-tools.c [ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3.0.3 abi-dump.3 /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c: In function 'KTUI_Menu_Remove_Id': /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:408:22: warning: 'idx' may be used uninitialized [-Wmaybe-uninitialized] 408 | rc = VectorRemove ( &parent->children, idx, &removed ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:401:22: note: 'idx' was declared here 401 | uint32_t idx; | ^~~ [ 29%] Built target sff-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3 abi-dump make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 29%] Built target abi-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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/DependInfo.cmake --color= [ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-decrypt.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-dump.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-dump illumina-dump.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3.0.3 illumina-dump.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3 illumina-dump make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 29%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-encrypt.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpQuality': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:1096:37: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] 1096 | char const newValue = ((param->qualQuant && param->qualQuantSingle)?param->qualQuantSingle:30) + 33; | ^~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here 205 | uint8_t qualQuant[256]; | ^~~~~~~~~ [ 29%] Built target illumina-dump make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath/CMakeFiles/srapath.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SetupColumns': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:3230:10: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] 3230 | if ( param -> qualQuant && param -> qualQuantSingle ) { /** we don't really need quality ***/ | ^~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here 205 | uint8_t qualQuant[256]; | ^~~~~~~~~ [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o -MF CMakeFiles/tui.dir/tui_palette.c.o.d -o CMakeFiles/tui.dir/tui_palette.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_palette.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SAM_Dump_Main': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 1579 | return rc; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here 1547 | rc_t rc; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:4380:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4380 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1574:13: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1574 | KOutMsg( "%d%c", total_cnt, op ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here 1549 | int i, total_cnt, cnt; | ^~~~~~~~~ [ 30%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/srapath/helper.c [ 30%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o -MF CMakeFiles/vdb-decrypt.dir/shared.c.o.d -o CMakeFiles/vdb-decrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c [ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/report_deletes.c [ 31%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o -MF CMakeFiles/vdb-encrypt.dir/shared.c.o.d -o CMakeFiles/vdb-encrypt.dir/shared.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c [ 31%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_std_dlg.c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c: In function 'ric_align_generic.constprop': /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1393:12: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 1393 | if (chunk == last) | ^ /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1384:17: note: 'last' was declared here 1384 | int64_t last; | ^~~~ [ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o -MF CMakeFiles/fasterq-dump.dir/flex_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/flex_printer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/flex_printer.c [ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_regions.c [ 31%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_button.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 1579 | return rc; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here 1547 | rc_t rc; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1574:13: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1574 | KOutMsg( "%d%c", total_cnt, op ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here 1549 | int i, total_cnt, cnt; | ^~~~~~~~~ [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_dir.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_checkbox.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o -MF CMakeFiles/sam-dump.dir/sam-dump3.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump3.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:557:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 557 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o -MF CMakeFiles/fasterq-dump.dir/progress_thread.c.o.d -o CMakeFiles/fasterq-dump.dir/progress_thread.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/progress_thread.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_grid.c [ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/line_iter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/srapath/line_iter.c In function 'samdump_main', inlined from 'KMain' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:558:26: /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:510:10: warning: 'mode' may be used uninitialized [-Wmaybe-uninitialized] 510 | rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:502:25: note: 'mode' was declared here 502 | enum out_redir_mode mode; | ^~~~ [ 32%] Linking C executable ../../../bin/vdb-decrypt cd /build/sra-sdk-3.0.3+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 [ 32%] Linking C executable ../../../bin/vdb-encrypt cd /build/sra-sdk-3.0.3+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 [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/4na_ascii.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat/CMakeFiles/sra-stat.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker_0.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f 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CMakeFiles/sra-stat.dir/assembly-statistics.c.o.d -o CMakeFiles/sra-stat.dir/assembly-statistics.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/assembly-statistics.c [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -MF CMakeFiles/fasterq-dump.dir/cleanup_task.c.o.d -o CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cleanup_task.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/walk_debug.c [ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/srapath/repository-mgr.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-decrypt.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-decrypt vdb-decrypt.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3.0.3 vdb-decrypt.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-encrypt.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3 vdb-decrypt cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-encrypt vdb-encrypt.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3.0.3 vdb-encrypt.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3 vdb-encrypt [ 32%] Built target vdb-decrypt make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/rcexplain/CMakeFiles/rcexplain.dir/build.make tools/external/rcexplain/CMakeFiles/rcexplain.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/rcexplain /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain/CMakeFiles/rcexplain.dir/DependInfo.cmake --color= [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_inputline.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_inputline.c [ 32%] Built target vdb-encrypt make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 32%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/services.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/services.c.o -MF CMakeFiles/srapath.dir/services.c.o.d -o CMakeFiles/srapath.dir/services.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/index.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_counters.c [ 32%] Building C object tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o -MF CMakeFiles/rcexplain.dir/rcexplain.c.o.d -o CMakeFiles/rcexplain.dir/rcexplain.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/rcexplain/rcexplain.c [ 32%] Building C object tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o -MF CMakeFiles/kdbmeta.dir/kdbmeta.c.o.d -o CMakeFiles/kdbmeta.dir/kdbmeta.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta/kdbmeta.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c: In function 'json_print_named_url': /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:338:10: warning: unused variable 'rc' [-Wunused-variable] 338 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c: In function 'json_print_named_urls_and_service': /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:356:14: warning: unused variable 'rc' [-Wunused-variable] 356 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); | ^~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_label.c In function 'make_cursor_ids', inlined from 'ref_walker_add_iterator.constprop' at /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:591:15: /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:534:14: warning: 'ids' may be used uninitialized [-Wmaybe-uninitialized] 534 | rc = VectorAppend ( cursor_id_vector, NULL, ids ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:34: /usr/include/ncbi-vdb/klib/vector.h: In function 'ref_walker_add_iterator.constprop': /usr/include/ncbi-vdb/klib/vector.h:401:21: note: by argument 3 of type 'const void *' to 'VectorAppend' declared here 401 | KLIB_EXTERN rc_t CC VectorAppend ( Vector *self, uint32_t *idx, const void *item ); | ^~~~~~~~~~~~ [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o -MF CMakeFiles/sra-pileup.dir/pileup_index.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_index.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_index.c [ 32%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra.c.o -MF CMakeFiles/sra-stat.dir/sra.c.o.d -o CMakeFiles/sra-stat.dir/sra.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/sra.c [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_progress.c [ 32%] Linking C executable ../../../bin/rcexplain cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cmake -E cmake_link_script CMakeFiles/rcexplain.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 32%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/lookup_writer.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_radiobox.c [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_indels.c [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_varcount.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_varcount.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rcexplain.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rcexplain rcexplain.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3.0.3 rcexplain.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3 rcexplain make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_spin_edit.c [ 33%] Built target rcexplain make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/align-info /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info/CMakeFiles/align-info.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/lookup_reader.c [ 33%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_stat.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_stat.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_string_list.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_v2.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_v2.c [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o [ 33%] Building C object tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o -MF CMakeFiles/sra-stat.dir/sra-stat.c.o.d -o CMakeFiles/sra-stat.dir/sra-stat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/sra-stat.c [ 34%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_tabhdr.c /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c:1415:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1415 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ [ 34%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/linux/systui.c [ 34%] Linking CXX executable ../../../bin/check-corrupt cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o -MF CMakeFiles/srapath.dir/cgi_request.c.o.d -o CMakeFiles/srapath.dir/cgi_request.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/srapath/cgi_request.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/test-sra /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra/CMakeFiles/test-sra.dir/DependInfo.cmake --color= [ 34%] Linking C executable ../../../bin/fastq-dump [ 34%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/srapath/srapath.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Linking C executable ../../../bin/vdb-validate cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E 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/build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/test-sra.c [ 36%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/locked_file_list.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-validate.dir/vdb-validate.c.o" -o ../../../bin/vdb-validate /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/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpCGSAM.part.0': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:2455:32: warning: 'last_cig_op' may be used uninitialized [-Wmaybe-uninitialized] 2455 | if( last_cig_oplen > 0 && last_cig_op == OP){ \ | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:2445:14: note: 'last_cig_op' was declared here 2445 | char last_cig_op; | ^~~~~~~~~~~ [ 36%] Linking C executable ../../../bin/kdbmeta cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-dump.3.0.3 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 36%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-dump fastq-dump.3.0.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/locked_value.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3.0.3 fastq-dump.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3 fastq-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fastq-dump-driver cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f check-corrupt.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv check-corrupt check-corrupt.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3.0.3 check-corrupt.3 [ 36%] Built target fastq-dump make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3 check-corrupt make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdbmeta kdbmeta.3.0.3 [ 37%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3.0.3 kdbmeta.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o -MF CMakeFiles/sratools.dir/sratools.cpp.o.d -o CMakeFiles/sratools.dir/sratools.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp [ 37%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3 kdbmeta make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -MF CMakeFiles/fasterq-dump.dir/merge_sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/merge_sorter.c [ 37%] Built target kdbmeta cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-validate.3.0.3 make -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/bam-load.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-validate vdb-validate.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3.0.3 vdb-validate.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3 vdb-validate make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Linking C executable ../../../bin/align-info make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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 -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/samview.dir/DependInfo.cmake --color= [ 38%] Built target vdb-validate make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar.dir/DependInfo.cmake --color= /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 38%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/build cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o -MF CMakeFiles/bam-load.dir/bam-loader.c.o.d -o CMakeFiles/bam-load.dir/bam-loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/build [ 38%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c [ 38%] Linking C executable ../../../bin/sra-pileup cd /build/sra-sdk-3.0.3+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 [ 38%] Linking C static library ../../../../ilib/libtui.a /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t Usage(const Args*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:579:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 579 | for(i = 0; i < argsQty; i++ ) { | ~~^~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:585:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 585 | for(i = 0; i < argsQty; i++ ) { | ~~^~~~~~~~~ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui.dir/cmake_clean_target.cmake /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t KMain(int, char**)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1304:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1304 | argv[1] = "--help"; | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1309:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1309 | argv[1] = "--version"; | ^~~~~~~~~~~ cd /build/sra-sdk-3.0.3+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 [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/sorter.c /usr/bin/ar qc ../../../../ilib/libtui.a CMakeFiles/tui.dir/dir_dlg.c.o CMakeFiles/tui.dir/eventring.c.o CMakeFiles/tui.dir/file_dlg.c.o CMakeFiles/tui.dir/line_policy.c.o CMakeFiles/tui.dir/screen.c.o CMakeFiles/tui.dir/string_cache.c.o CMakeFiles/tui.dir/tui.c.o CMakeFiles/tui.dir/tui_dlg.c.o CMakeFiles/tui.dir/tui_dlg_helper.c.o CMakeFiles/tui.dir/tui_menu.c.o CMakeFiles/tui.dir/tui_palette.c.o CMakeFiles/tui.dir/tui_std_dlg.c.o CMakeFiles/tui.dir/tui_widget.c.o CMakeFiles/tui.dir/tui_widget_button.c.o CMakeFiles/tui.dir/tui_widget_checkbox.c.o CMakeFiles/tui.dir/tui_widget_grid.c.o CMakeFiles/tui.dir/tui_widget_inputline.c.o CMakeFiles/tui.dir/tui_widget_label.c.o CMakeFiles/tui.dir/tui_widget_progress.c.o CMakeFiles/tui.dir/tui_widget_radiobox.c.o 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 /usr/bin/ranlib ../../../../ilib/libtui.a [ 38%] Linking C executable ../../../bin/srapath cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-info.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cmake -E cmake_link_script CMakeFiles/srapath.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-info align-info.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3.0.3 align-info.3 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 38%] Built target tui cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3 align-info make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Built target align-info cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-pileup.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-pileup sra-pileup.3.0.3 make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+meta.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3.0.3 sra-pileup.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3 sra-pileup cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sra-pileup-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/build cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Built target sra-pileup make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/DependInfo.cmake --color= [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srapath.3.0.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-args.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srapath srapath.3.0.3 [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3.0.3 srapath.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cmn_iter.c [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dump-blob-boundaries.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3 srapath [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/raw_read_iter.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 srapath-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Built target srapath 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/DependInfo.cmake --color= [ 38%] Linking C executable ../../../bin/cache-mgr cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat 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CMakeFiles/kar+.dir/kar+args.c.o.d -o CMakeFiles/kar+.dir/kar+args.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+args.c [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 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-fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cache-mgr.3.0.3 [ 38%] Linking C executable ../../../bin/sam-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cache-mgr cache-mgr.3.0.3 cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3.0.3 cache-mgr.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3 cache-mgr /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c [ 38%] Built target cache-mgr make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f dump-blob-boundaries.3.0.3 [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+meta.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv dump-blob-boundaries dump-blob-boundaries.3.0.3 [ 38%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -MF CMakeFiles/fasterq-dump.dir/fastq_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fastq_iter.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3.0.3 dump-blob-boundaries.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3 dump-blob-boundaries make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 39%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/db_join.c [ 40%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o [ 40%] Built target dump-blob-boundaries [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/depend cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+print.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sam-dump.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sam-dump sam-dump.3.0.3 [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3.0.3 sam-dump.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3 sam-dump make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sam-dump-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c [ 41%] Built target sam-dump make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.py.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/sharq.py /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq.py make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o In function 'kar_persist_karalias', inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1067:14, inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1038:9: /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1032:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 1032 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c: In function 'kar_persist': /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:988:28: note: 'total_written' was declared here 988 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ In function 'kar_persist_karfile', inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1054:14, inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1038:9: /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:964:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 964 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c: In function 'kar_persist': /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:919:28: note: 'total_written' was declared here 919 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c [ 41%] Built target sharq.py 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/sff-load.dir/DependInfo.cmake --color= /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:690:14: warning: 'value' may be used uninitialized [-Wmaybe-uninitialized] 690 | unsigned value; | ^~~~~ In function 'ParseSQ', inlined from 'ParseHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:917:47, inlined from 'ProcessHeaderText' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1063:25: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:739:21: warning: 'tag' may be used uninitialized [-Wmaybe-uninitialized] 739 | if (strcmp(&hdata[tag], "SN") == 0) | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:689:14: note: 'tag' was declared here 689 | unsigned tag; | ^~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT 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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c [ 41%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c [ 41%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tbl_join.c [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o -MF CMakeFiles/sff-load.dir/common-xml.c.o.d -o CMakeFiles/sff-load.dir/common-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c [ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:68: /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: In lambda function: /usr/include/ncbi-vdb/klib/debug.h:547:27: warning: statement has no effect [-Wunused-value] 547 | #define KDbgSetString(s) ((rc_t)0) | ~^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:464:13: note: in expansion of macro 'KDbgSetString' 464 | KDbgSetString(arg.argument); | ^~~~~~~~~~~~~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:690:14: warning: 'value' may be used uninitialized [-Wmaybe-uninitialized] 690 | unsigned value; | ^~~~~ In function 'ParseSQ', inlined from 'ParseHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:917:47, inlined from 'ProcessHeaderText' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1063:25: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:739:21: warning: 'tag' may be used uninitialized [-Wmaybe-uninitialized] 739 | if (strcmp(&hdata[tag], "SN") == 0) | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'ProcessHeaderText': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:689:14: note: 'tag' was declared here 689 | unsigned tag; | ^~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' 42 | FILE_ENTRY ( except ); | ^~~~~~~~~~ [ 42%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ [ 42%] Linking C executable ../../../bin/kar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar.dir/link.txt --verbose=1 /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c: In function 'readThread': /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] 691 | if ( rr->type == rr_fileDone ) | ~~^~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here 647 | free(rr); | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] 691 | if ( rr->type == rr_fileDone ) | ~~^~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here 647 | free(rr); | ^~~~~~~~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 42%] Linking C executable ../../../bin/kar+meta cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+meta.dir/link.txt --verbose=1 [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' 32 | FILE_ENTRY ( idx-mapping ); | ^~~~~~~~~~ In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' 42 | FILE_ENTRY ( except ); | ^~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: At global scope: /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:390:13: warning: 'void sratools::do_sratools(const CommandLine&)' defined but not used [-Wunused-function] 390 | static void do_sratools [[noreturn]] (CommandLine const &argv) | ^~~~~~~~~~~ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar kar.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3.0.3 kar.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3 kar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+meta.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+meta kar+meta.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3.0.3 kar+meta.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3 kar+meta In function 'ProcessBAMHeader', inlined from 'BAM_FileMakeWithKFileAndHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1421:14, inlined from 'BAM_FileMake' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1479:14: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1321:18: warning: 'refSeq' may be used uninitialized [-Wmaybe-uninitialized] 1321 | self->refSeq = refSeq; | ~~~~~~~~~~~~~^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMake': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: note: 'refSeq' was declared here 1282 | BAMRefSeq *refSeq; | ^~~~~~ [ 42%] Built target kar make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/fastq-load.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' 32 | FILE_ENTRY ( idx-mapping ); | ^~~~~~~~~~ [ 42%] Built target kar+meta make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/srf-load.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o -MF CMakeFiles/fastq-load.dir/pstring.c.o.d -o CMakeFiles/fastq-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In function 'kar_persist_karalias', inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:761:14, inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:720:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 720 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:676:28: note: 'total_written' was declared here 676 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ In function 'kar_persist_karfile', inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:748:14, inlined from 'kar_persist' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:652:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 652 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': /build/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:607:28: note: 'total_written' was declared here 607 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o -MF CMakeFiles/srf-load.dir/pstring.c.o.d -o CMakeFiles/srf-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_registry.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o -MF CMakeFiles/sra-sort-cg.dir/map-file.c.o.d -o CMakeFiles/sra-sort-cg.dir/map-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c [ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/copy_machine.c [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o -MF CMakeFiles/sff-load.dir/experiment-xml.c.o.d -o CMakeFiles/sff-load.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c [ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c [ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o -MF CMakeFiles/fasterq-dump.dir/concatenator.c.o.d -o CMakeFiles/fasterq-dump.dir/concatenator.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/concatenator.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c In function 'ProcessBAMHeader', inlined from 'BAM_FileMakeWithKFileAndHeader' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1421:14, inlined from 'BAM_FileMake' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1479:14: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1321:18: warning: 'refSeq' may be used uninitialized [-Wmaybe-uninitialized] 1321 | self->refSeq = refSeq; | ~~~~~~~~~~~~~^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMake': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: note: 'refSeq' was declared here 1282 | BAMRefSeq *refSeq; | ^~~~~~ [ 42%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fasterq-dump.c [ 42%] Linking C executable ../../../bin/kar+ cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c [ 42%] Building C object tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/test-sra\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/test-sra/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/test-sra/unix/PrintOS.c [ 42%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-str.c [ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c [ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+ kar+.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3.0.3 kar+.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3 kar+ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Built target kar+ 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/abi-load.dir/DependInfo.cmake --color= [ 42%] Linking C executable ../../../bin/test-sra cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Linking C executable ../../../bin/fasterq-dump cd /build/sra-sdk-3.0.3+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 [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o -MF CMakeFiles/abi-load.dir/pstring.c.o.d -o CMakeFiles/abi-load.dir/pstring.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/fastq_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/concatenator.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 [ 43%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c [ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-sra.3.0.3 [ 44%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-helper.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-sra test-sra.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3.0.3 test-sra.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3 test-sra make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fasterq-dump.3.0.3 [ 44%] Built target test-sra make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fasterq-dump fasterq-dump.3.0.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/illumina-load.dir/DependInfo.cmake --color= make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3.0.3 fasterq-dump.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/helicos-load.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3 fasterq-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fasterq-dump-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c [ 44%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c [ 44%] Built target fasterq-dump make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load 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/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort.dir/simple-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic 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45%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort.dir/mapping-row-set.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c [ 45%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-formats.c [ 45%] Linking C executable ../../../bin/sra-stat cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c [ 46%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c [ 46%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 46%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-stat.3.0.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-redir.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-stat sra-stat.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3.0.3 sra-stat.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3 sra-stat make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 46%] Built target sra-stat make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/DependInfo.cmake --color= [ 47%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 47%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o -MF CMakeFiles/samview.dir/samview.c.o.d -o CMakeFiles/samview.dir/samview.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/samview.c [ 47%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5arrayfile.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined 750 | #define YY_BUF_SIZE 16777216 | /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition 204 | #define YY_BUF_SIZE 16384 | /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1115 | if ( ! yyg->yy_state_buf ) | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1117 | if ( ! yyg->yy_state_buf ) | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1120 | if ( ! yyg->yy_start ) | ^~ [ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) | ^~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] 2395 | static int yy_top_state (yyscan_t yyscanner) | ^~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] 1837 | static int input (yyscan_t yyscanner) | ^~~~~ [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 47%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-fastq.c [ 47%] Linking C executable ../../../bin/samview cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o -MF CMakeFiles/sff-load.dir/loader-fmt.c.o.d -o CMakeFiles/sff-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 48%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview.3.0.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 48%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5dir.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview samview.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3.0.3 samview.3 [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3 samview [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o [ 49%] Built target samview cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/depend [ 50%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/alignment-writer.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load/CMakeFiles/cg-load.dir/DependInfo.cmake --color= /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 50%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/cg-load.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 51%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c: In function 'DB_Fini': /build/sra-sdk-3.0.3+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 ) { | ^~~~~~~~ [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 51%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5file.c [ 51%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o [ 52%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o -MF CMakeFiles/bam-load.dir/reference-writer.c.o.d -o CMakeFiles/bam-load.dir/reference-writer.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/reference-writer.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o -MF CMakeFiles/sff-load.dir/loader.c.o.d -o CMakeFiles/sff-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 52%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o [ 52%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o -MF CMakeFiles/fastq-load.dir/loader-fmt.c.o.d -o CMakeFiles/fastq-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o -MF CMakeFiles/srf-load.dir/loader-file.c.o.d -o CMakeFiles/srf-load.dir/loader-file.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 53%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o -MF CMakeFiles/pacbio-load.dir/pl-context.c.o.d -o CMakeFiles/pacbio-load.dir/pl-context.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-context.c [ 53%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c [ 53%] Linking C static library ../../../ilib/libfastqloader.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -P CMakeFiles/fastqloader.dir/cmake_clean_target.cmake [ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastqloader.dir/link.txt --verbose=1 /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 /usr/bin/ranlib ../../../ilib/libfastqloader.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT 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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 54%] Built target fastqloader 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/CMakeFiles/general-loader.dir/DependInfo.cmake --color= /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c: In function 'SequenceWhack': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c:490:14: warning: unused variable 'rc' [-Wunused-variable] 490 | rc_t rc = VDatabaseOpenTableUpdate(self->db, &tbl, "SEQUENCE"); | ^~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 54%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-tools.c [ 54%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/general-loader.cpp [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 54%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT 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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 54%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c [ 54%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c In function 'inspect_line', inlined from 'parse_buffer' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:602:29, inlined from 'get_meta_bam_hdr' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:639:21, inlined from 'get_meta_info' at /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:681:5: /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:575:43: warning: 'line' may be used uninitialized [-Wmaybe-uninitialized] 575 | case 'P' : if ( 'G' == line[ 2 ] ) ( bam_hdr -> PG_lines )++; break; | ~~~~^~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c: In function 'get_meta_info': /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:582:12: note: 'line' was declared here 582 | char * line; | ^~~~ [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o -MF CMakeFiles/fastq-load.dir/loader.c.o.d -o CMakeFiles/fastq-load.dir/loader.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 54%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-intervals.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o -MF CMakeFiles/abi-load.dir/loader-fmt.c.o.d -o CMakeFiles/abi-load.dir/loader-fmt.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 54%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o -MF CMakeFiles/pacbio-load.dir/pl-zmw.c.o.d -o CMakeFiles/pacbio-load.dir/pl-zmw.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-zmw.c [ 54%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-basecalls_cmn.c [ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o [ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-sequence.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp:101:13: warning: 'bool sratools::forceInstallID()' defined but not used [-Wunused-function] 101 | static bool forceInstallID(void) | ^~~~~~~~~~~~~~ [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o cd 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/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load 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-I/build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 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-I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/sra-sdk-3.0.3+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 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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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sff-fmt.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | 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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-passes.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-fmt.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c [ 59%] Linking C executable ../../../bin/sff-load cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c [ 59%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-metrics.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-load.3.0.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sff-load sff-load.3.0.3 [ 59%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3.0.3 sff-load.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 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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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings15_Read': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:225:14: note: 'tmp' declared here 225 | char tmp[2]; | ^~~ [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/absolid-fmt.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings22_Read': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:287:14: note: 'tmp' declared here 287 | char tmp[2]; | ^~~ [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-helicos.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o /build/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings25_Read': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:358:14: note: 'tmp' declared here 358 | char tmp[2]; | ^~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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 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/build/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/fastq-fmt.c [ 60%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c [ 60%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/helicos-fmt.c [ 61%] Linking C executable ../../../bin/vdb-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump.dir/link.txt --verbose=1 [ 62%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-regions.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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_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 [ 62%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pacbio-fmt.c [ 62%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c [ 62%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c [ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-reads.c [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c [ 63%] Linking C executable ../../../bin/pacbio-loadxml cd /build/sra-sdk-3.0.3+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%] Linking C executable ../../../bin/abi-load cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-dump.3.0.3 [ 63%] Linking C executable ../../../bin/helicos-load cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-dump vdb-dump.3.0.3 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3.0.3 vdb-dump.3 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3 vdb-dump cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 vdb-dump-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Built target vdb-dump 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+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/depend [ 63%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-gw-dumper.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f helicos-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv helicos-load helicos-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3.0.3 helicos-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3 helicos-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-load.3.0.3 [ 63%] Linking C executable ../../../bin/sra-sort [ 63%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-progress.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:32: /build/sra-sdk-3.0.3+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 ); | ^~~~~~~~ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-load abi-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3.0.3 abi-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-loadxml.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-loadxml pacbio-loadxml.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3 abi-load [ 63%] Built target helicos-load make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3.0.3 pacbio-loadxml.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/DependInfo.cmake --color= /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3 pacbio-loadxml make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:619:86: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 619 | REQUIRE_EQ ( string ( __DATE__), GetDbMetadataAttr ( "SOFTWARE/loader", "date" ) ); | ^ make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Built target abi-load 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/DependInfo.cmake --color= [ 63%] Built target pacbio-loadxml 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 [ 63%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/DependInfo.cmake --color= [ 63%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/makeinputs.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/makeinputs.cpp [ 63%] Linking C executable ../../../bin/fastq-load cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-tag-lfr.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c [ 63%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp [ 63%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-illumina.c [ 63%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort sra-sort.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3.0.3 sra-sort.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3 sra-sort make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c: In function 'pacbio_meta_entry': In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger-inl.h:12, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger.h:446, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/details/registry-inl.h:12, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/details/registry.h:114, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/spdlog.h:13, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:101: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h: In constructor 'spdlog::pattern_formatter::pattern_formatter(std::string, spdlog::pattern_time_type, std::string, custom_flags)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:110:18: warning: 'spdlog::pattern_formatter::custom_handlers_' will be initialized after [-Wreorder] 110 | custom_flags custom_handlers_; | ^~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:106:10: warning: 'bool spdlog::pattern_formatter::need_localtime_' [-Wreorder] 106 | bool need_localtime_; | ^~~~~~~~~~~~~~~ In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:126: /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1017:15: warning: when initialized here [-Wreorder] 1017 | SPDLOG_INLINE pattern_formatter::pattern_formatter( | ^~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+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() ); | ^~~~~~~~ [ 63%] Built target sra-sort /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h: In constructor 'spdlog::pattern_formatter::pattern_formatter(spdlog::pattern_time_type, std::string)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:108:26: warning: 'spdlog::pattern_formatter::last_log_secs_' will be initialized after [-Wreorder] 108 | std::chrono::seconds last_log_secs_; | ^~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:106:10: warning: 'bool spdlog::pattern_formatter::need_localtime_' [-Wreorder] 106 | bool need_localtime_; | ^~~~~~~~~~~~~~~ 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 /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1031:15: warning: when initialized here [-Wreorder] 1031 | SPDLOG_INLINE pattern_formatter::pattern_formatter(pattern_time_type time_type, std::string eol) | ^~~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/checklookup.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-load fastq-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3.0.3 fastq-load.3 [ 63%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3 fastq-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 63%] Built target fastq-load 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/DependInfo.cmake --color= [ 63%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_3.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 64%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c [ 64%] Building C object tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock/vdb-lock.c [ 64%] Linking C executable ../../../bin/pacbio-load cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 64%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_5.c [ 64%] Linking C executable ../../../bin/vdb-lock cd /build/sra-sdk-3.0.3+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 [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/illumina-fmt.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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-cg.dir/csra-tbl.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_7.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-lock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-lock vdb-lock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3.0.3 vdb-lock.3 [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-absolid.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3 vdb-lock /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:54:20: note: 'gw' was declared here 54 | GeneralWriter *gw; | ^~ In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/sra-sdk-3.0.3+dfsg/libs/inc/general-writer/general-writer.hpp:34, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:30: In static member function 'static std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:423:21, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:418:7, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy_chars(_CharT*, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:477:16, inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::forward_iterator_tag) [with _FwdIterator = const char*; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.tcc:243:21, 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++/12/bits/basic_string.h:642:14, inlined from 'void run(const char*, TestCaseType, const std::string*, int)' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:77:25: /usr/include/c++/12/bits/char_traits.h:431:56: warning: 'db_schema' may be used uninitialized [-Wmaybe-uninitialized] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:57:21: note: 'db_schema' was declared here 57 | const char* db_schema; | ^~~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:45:20: note: 'gw' was declared here 45 | GeneralWriter *gw; | ^~ [ 65%] Built target vdb-lock make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/DependInfo.cmake --color= [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_0.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock/vdb-unlock.c /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp: In constructor 'data_sources::data_sources(const CommandLine&, const Arguments&, bool)': /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp:480:16: warning: unused variable 'havePerm' [-Wunused-variable] 480 | auto const havePerm = perm != nullptr; | ^~~~~~~~ [ 65%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp [ 65%] Linking CXX executable ../../../../test-bin/test-gw-dumper cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-load.3.0.3 cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-load pacbio-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3.0.3 pacbio-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3 pacbio-load /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+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 ); | ^~~~~~~~ [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_2.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_2.c [ 65%] Built target pacbio-load 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/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/DependInfo.cmake --color= [ 65%] Linking C executable ../../../bin/vdb-unlock cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/test-read-write-cursor.c [ 65%] Linking CXX executable ../../../../../test-bin/bio-end-makeinputs cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 65%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_4.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-huffman.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-unlock.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-unlock vdb-unlock.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3.0.3 vdb-unlock.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3 vdb-unlock make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 65%] Built target test-gw-dumper 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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/DependInfo.cmake --color= [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c [ 65%] Built target vdb-unlock make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/depend [ 65%] Linking C executable ../../../bin/illumina-load cd /build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat/CMakeFiles/copycat.dir/DependInfo.cmake --color= [ 66%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_5.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/build [ 66%] Building C object tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 66%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/copycat.c [ 66%] Built target bio-end-makeinputs [ 67%] Linking C executable ../../../bin/test-read-write-cursor make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/depend cd /build/sra-sdk-3.0.3+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 [ 67%] Linking CXX executable ../../../../../test-bin/idx-text-makeinputs make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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 [ 67%] Linking C executable ../../../bin/sra-sort-cg cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c: In function 'enter_date_name_vers': /build/sra-sdk-3.0.3+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__ ); | ^~~~~~~~ [ 67%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/context.c [ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-read-write-cursor.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-read-write-cursor test-read-write-cursor.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3.0.3 test-read-write-cursor.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort-cg.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3 test-read-write-cursor cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort-cg sra-sort-cg.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3.0.3 sra-sort-cg.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3 sra-sort-cg make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 67%] Built target test-read-write-cursor make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/depend [ 68%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/DependInfo.cmake --color= [ 68%] Built target sra-sort-cg 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]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-load illumina-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3.0.3 illumina-load.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3 illumina-load make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o [ 68%] Building C object tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/namelist_tools.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c [ 68%] Built target illumina-load 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/align-cache /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache/CMakeFiles/align-cache.dir/DependInfo.cmake --color= [ 68%] Built target idx-text-makeinputs cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/helper.c make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract/CMakeFiles/ccextract.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/build [ 68%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/align-cache.cpp make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:33: /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h: In function 'rowCount': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h:124:16: warning: unused variable 'rc' [-Wunused-variable] 124 | rc_t const rc = VCursorIdRange(curs, cid, first, &count); | ^~ [ 68%] Building C object tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'main_1': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:598:9: warning: ignoring return value of 'chdir' declared with attribute 'warn_unused_result' [-Wunused-result] 598 | chdir(wd); | ^~~~~~~~~ cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/ccextract/ccextract.c /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'temporaryDirectory': /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:938:5: warning: ignoring return value of 'mkdtemp' declared with attribute 'warn_unused_result' [-Wunused-result] 938 | mkdtemp(pattern); | ^~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: At top level: /build/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:692:13: warning: 'test' defined but not used [-Wunused-function] 692 | static void test(void) | ^~~~ [ 68%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-absolid.c [ 69%] Linking C executable ../../../bin/read-filter-redact cd /build/sra-sdk-3.0.3+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 [ 69%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file-version-factory.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 69%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfileformat.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f read-filter-redact.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv read-filter-redact read-filter-redact.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3.0.3 read-filter-redact.3 [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/coldefs.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3 read-filter-redact make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/coldefs.c [ 70%] Built target read-filter-redact make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp/CMakeFiles/md5cp.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/formats.c [ 70%] Building C object tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/md5cp/md5cp.c [ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cccat.c [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-algn.c [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff-context.c [ 70%] Linking C executable ../../../bin/srf-load cd /build/sra-sdk-3.0.3+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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 70%] Linking C executable ../../../bin/ccextract cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cmake -E cmake_link_script CMakeFiles/ccextract.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o -MF CMakeFiles/vdb-diff.dir/cmn.c.o.d -o CMakeFiles/vdb-diff.dir/cmn.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/cmn.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srf-load srf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3.0.3 srf-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3 srf-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Linking C executable ../../../bin/md5cp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cmake -E cmake_link_script CMakeFiles/md5cp.dir/link.txt --verbose=1 [ 70%] Built target srf-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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-cmp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/DependInfo.cmake --color= /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/row_by_row.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/get_platform.c [ 70%] Building C object tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o cd /build/sra-sdk-3.0.3+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 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'/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f md5cp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv md5cp md5cp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3.0.3 md5cp.3 [ 70%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/helper.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3 md5cp [ 70%] Built target ccextract make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/depend make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy 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/build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/namelist_tools.c [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/col_by_col.c [ 70%] Built target md5cp make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Linking C executable ../../../bin/meta-cmp [ 70%] Building C object tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build [ 70%] Linking C executable ../../../bin/make-read-filter [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-dnbs.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 71%] Building C object tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum/crc32sum.c /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:330:23: warning: unused variable 'diffs' [-Wunused-variable] 330 | unsigned long int diffs = 0; | ^~~~~ /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: At top level: /build/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:186:13: warning: 'cleanup_rc' defined but not used [-Wunused-function] 186 | static void cleanup_rc( void ) { | ^~~~~~~~~~ [ 71%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-cmp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-cmp meta-cmp.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3.0.3 meta-cmp.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3 meta-cmp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f make-read-filter.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv make-read-filter make-read-filter.3.0.3 [ 71%] Built target meta-cmp [ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/depend cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3.0.3 make-read-filter.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download/CMakeFiles/test-download.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3 make-read-filter make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 71%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 71%] Built target make-read-filter make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/depend [ 71%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-intervals.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/DependInfo.cmake --color= [ 72%] Building C object tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download/test-download.c [ 72%] Linking C executable ../../../bin/crc32sum cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cmake -E cmake_link_script CMakeFiles/crc32sum.dir/link.txt --verbose=1 [ 72%] Linking C executable ../../../bin/meta-copy make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-copy.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c: In function 'enter_date_name_vers': /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c:349:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 349 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 72%] Building C object tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index/kdb-index.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f crc32sum.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-copy meta-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv crc32sum crc32sum.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3.0.3 meta-copy.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3 meta-copy cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3.0.3 crc32sum.3 [ 72%] Linking C executable ../../../bin/vdb-diff cd /build/sra-sdk-3.0.3+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[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s crc32sum.3 crc32sum make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 72%] Built target meta-copy /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 72%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o 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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-seq.c [ 73%] Linking C executable ../../../bin/kdb-index make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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 [ 73%] Built target crc32sum [ 73%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree-dump.c [ 74%] Linking CXX executable ../../../../../test-bin/idx-text-checklookup /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/depend cd /build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/schema-replace /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 74%] Building C object tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -MF CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o.d -o CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct/pacbio-correct.c make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/type_matcher.c [ 74%] Building C object tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/schema-replace.c.o -MF CMakeFiles/schema-replace.dir/schema-replace.c.o.d -o CMakeFiles/schema-replace.dir/schema-replace.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/test-tools/schema-replace/schema-replace.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-diff.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-diff vdb-diff.3.0.3 [ 74%] Linking C executable ../../../bin/cg-load cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3.0.3 vdb-diff.3 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-diff.3 vdb-diff make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdb-index.3.0.3 [ 74%] Built target vdb-diff make -f tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build.make tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdb-index kdb-index.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdb-index.3.0.3 kdb-index.3 [ 74%] Linking C executable ../../../bin/pacbio-correct cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdb-index.3 kdb-index cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 74%] Built target kdb-index [ 74%] Building C object tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cc -DLINUX 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/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/DependInfo.cmake --color= [ 74%] Linking C executable ../../../bin/test-download make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-download.dir/link.txt --verbose=1 [ 74%] Linking C executable ../../../bin/schema-replace make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c [ 74%] Built target idx-text-checklookup make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util/CMakeFiles/samview-util.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cg-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cg-load cg-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-correct.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3.0.3 cg-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-correct pacbio-correct.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3 cg-load make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3.0.3 pacbio-correct.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3 pacbio-correct make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building C object tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util/samview.c [ 74%] Built target cg-load /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'run': /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:287: warning: "STATUS" redefined 287 | #define STATUS(action) (action FORMAT, tablePath, name) | In file included from /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:11: /usr/include/ncbi-vdb/klib/status.h:139: note: this is the location of the previous definition 139 | #define STATUS( lvl, ... ) \ | make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld/CMakeFiles/testld.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f schema-replace.3.0.3 [ 74%] Built target pacbio-correct cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv schema-replace schema-replace.3.0.3 make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/depend make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/DependInfo.cmake --color= make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3.0.3 schema-replace.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-download.3.0.3 [ 74%] Linking C executable ../../../bin/sortreadtest cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3 schema-replace cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-download test-download.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3.0.3 test-download.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building C object tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/testld/testld.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3 test-download make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target schema-replace [ 74%] Building C object tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb/txt2kdb.c 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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/DependInfo.cmake --color= [ 74%] Linking C executable ../../../bin/samview-util cd /build/sra-sdk-3.0.3+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 [ 74%] Built target test-download make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 74%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building Java objects for test-ngs-java.jar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sortreadtest.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sortreadtest sortreadtest.3.0.3 [ 74%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -MF CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-build-version.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3.0.3 sortreadtest.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3 sortreadtest cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_sources make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target sortreadtest make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/DependInfo.cmake --color= /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c: In function 'what_header_type': /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:1015:42: warning: the comparison will always evaluate as 'true' for the address of 'fullsize' will never be NULL [-Waddress] 1015 | header->suntar.extcount && | ^~ /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:598:25: note: 'fullsize' declared here 598 | sun_fullsize fullsize; /* 502 non-conformant */ | ^~~~~~~~ [ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/redactval.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview-util.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview-util samview-util.3.0.3 [ 75%] Linking C executable ../../../bin/testld make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cmake -E cmake_link_script CMakeFiles/testld.dir/link.txt --verbose=1 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3.0.3 samview-util.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3 samview-util [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -MF CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o.d -o CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-filepath.cpp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 75%] Built target samview-util make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/DependInfo.cmake --color= [ 75%] Linking CXX executable ../../../../test-bin/makeinputs make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'KMain': /build/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:383:17: warning: '__builtin_strncpy' specified bound 512 equals destination size [-Wstringop-truncation] 383 | strncpy (tablePath, pc, sizeof (tablePath)); | ^ [ 75%] Linking C executable ../../../bin/txt2kdb cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/txt2kdb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-command-line.cpp /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f testld.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv testld testld.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3.0.3 testld.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3 testld make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Linking C executable ../../../bin/rowwritetest [ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/config_values.c [ 75%] Built target testld /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f txt2kdb.3.0.3 [ 75%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o [ 76%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv txt2kdb txt2kdb.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsra.c cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/main.cpp make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3.0.3 txt2kdb.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3 txt2kdb make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -MF CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o.d -o CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-json-parse.cpp [ 76%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.c [ 76%] 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rowwritetest.3.0.3 [ 76%] Built target makeinputs make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/depend cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rowwritetest rowwritetest.3.0.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3.0.3 rowwritetest.3 [ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3 rowwritetest cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-sdl-response.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 76%] Built target rowwritetest make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/depend [ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-accession.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/DependInfo.cmake --color= [ 77%] Linking CXX executable ../../../bin/align-cache cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-uuid.cpp [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsubchunk.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsubchunk.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c: In function 'rc_t FixOverhangingAlignment(KDataBuffer*, uint32_t*, uint32_t, uint32_t, uint32_t)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1540:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1540 | if (refend > refLen) { | ~~~~~~~^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1544:26: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1544 | if (left * 2 > readlen) { | ~~~~~~~~~^~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c: In function 'rc_t ProcessBAM(const char*, context_t*, VDatabase*, Reference*, Sequence*, Alignment*, bool*, bool*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1850:60: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1850 | if (ctx->m_isSingleGroup && ctx->m_emptyGroupIndex == -1) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfile.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2340:41: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 2340 | if (!isPrimary && AR_MAPQ(data) < G.minMapQual) cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-cache.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-cache align-cache.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3.0.3 align-cache.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3 align-cache make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target align-cache [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o -MF CMakeFiles/copycat.dir/kff/fileformat.c.o.d -o CMakeFiles/copycat.dir/kff/fileformat.c.o -c /build/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/fileformat.c [ 77%] Linking C executable ../../../bin/vdb-copy cd /build/sra-sdk-3.0.3+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 [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffext.c /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/namelist_tools.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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-copy vdb-copy.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3.0.3 vdb-copy.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3 vdb-copy [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E copy /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/vdb-copy.kfg cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffkey.c [ 77%] Linking CXX executable ../../../bin/general-loader cd /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 77%] Built target vdb-copy 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffmagic.c [ 77%] Building CXX object test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/vdb-config/test-vdb-config-model.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f general-loader.3.0.3 [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_BuildVersion cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv general-loader general-loader.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3.0.3 general-loader.3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o" -o ../../../test-bin/Test_Drivertool_BuildVersion cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3 general-loader make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target general-loader 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/DependInfo.cmake --color= [ 77%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/mem-bank.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/vdb-dump/makedb.cpp [ 77%] Linking C executable ../../../bin/copycat cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_BuildVersion 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building C object test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/test/loaders/loader/qfiletest.c cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f copycat.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv copycat copycat.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3.0.3 copycat.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3 copycat make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target copycat make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Note: ngs_test_lib_load.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. [ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/loaders/loader/test-loaderfile.cpp [ 77%] Linking C executable ../../../test-bin/Test_KAPP_qfile cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_compiled_test-ngs-java [ 77%] Generating CMakeFiles/test-ngs-java.dir/java_class_filelist cd /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake [ 77%] Creating Java archive test-ngs-java.jar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar @java_class_filelist make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADER.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_UUID cd /build/sra-sdk-3.0.3+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 [ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o" -o ../../../test-bin/Test_Drivertool_UUID [ 77%] Linking CXX executable ../../../test-bin/vdb-dump-makedb cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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" ) ); | ^ cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+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-3.25/Modules/UseJava/Symlinks.cmake make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_UUID make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-regexpr.dir/DependInfo.cmake --color= [ 77%] Built target test-ngs-java 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/Test_Align_samextract.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -MF CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o.d -o CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp [ 77%] Building CXX object test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/internal/align/test-samextract.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_Accession cd /build/sra-sdk-3.0.3+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 [ 77%] Built target vdb-dump-makedb /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o" -o ../../../test-bin/Test_Drivertool_Accession [ 77%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -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/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/low-match-count.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_Accession make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/depend [ 77%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_CommandLine cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o" -o ../../../test-bin/Test_Drivertool_CommandLine In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_CommandLine 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/bin/jar\ -cf\ /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-doc.jar\ . [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.cpp [ 77%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+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 /usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" /usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3.0.3 libncbi-ngs-c++.a.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ncbi-ngs-c++ 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java && bash -c /usr/bin/jar\ -cf\ /build/sra-sdk-3.0.3+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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ngs-doc-jar make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building Java objects for ngs-examples.jar cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClearClassFiles.cmake cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/javac -classpath :/build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar -d /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/gw-dumper.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ngs-src-jar make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test/CMakeFiles/test-general-writer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp [ 77%] Linking CXX executable ../../../test-bin/Test_LOADERFILE cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADERFILE.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp: In member function 'void Construction::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp:40:22: warning: parentheses were disambiguated as a function declaration [-Wvexing-parse] 40 | CRegExprMatcher m( string() ); | ^~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp:40:22: note: replace parentheses with braces to declare a variable 40 | CRegExprMatcher m( string() ); | ^~~~~~~~~~~~ | - | { - | } make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_LOADERFILE make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/prefetch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch/CMakeFiles/prefetch.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3SelectNew': [ 77%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/prefetch/kfile-no-q.c /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] 115649 | return pNew; | ^~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'void gw_dump::check_vers_component(const char*, const char*, long int, long unsigned int, char)': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1198:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare] 1198 | if ( num < 0 || num > max ) | ~~~~^~~~~ /build/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here 115609 | Select standin; | ^~~~~~~ [ 78%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfMain.c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'const char* gw_dump::metadata_node_root_name(metadata_node_root)': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1315:5: warning: control reaches end of non-void function [-Wreturn-type] 1315 | } | ^ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: At global scope: /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:732:17: warning: 'char gw_dump::hex(uint8_t)' defined but not used [-Wunused-function] 732 | static char hex(uint8_t const x) { | ^~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:441:10: warning: 'void gw_dump::whack_colname(const T&, char*) [with T = gw_column_evt_v1]' defined but not used [-Wunused-function] 441 | void whack_colname < :: gw_column_evt_v1 > ( const :: gw_column_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:418:12: warning: 'char* gw_dump::read_colname(const T&, FILE*) [with T = gw_column_evt_v1]' defined but not used [-Wunused-function] 418 | char * read_colname < :: gw_column_evt_v1 > ( const :: gw_column_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:368:10: warning: 'void gw_dump::whack_2string(const T&, char*) [with T = gw_2string_evt_v1]' defined but not used [-Wunused-function] 368 | void whack_2string < :: gw_2string_evt_v1 > ( const :: gw_2string_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:345:12: warning: 'char* gw_dump::read_2string(const T&, FILE*) [with T = gw_2string_evt_v1]' defined but not used [-Wunused-function] 345 | char * read_2string < :: gw_2string_evt_v1 > ( const :: gw_2string_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:293:10: warning: 'void gw_dump::whack_1string(const T&, char*) [with T = gw_1string_evt_v1]' defined but not used [-Wunused-function] 293 | void whack_1string < :: gw_1string_evt_v1 > ( const :: gw_1string_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:270:12: warning: 'char* gw_dump::read_1string(const T&, FILE*) [with T = gw_status_evt_v1]' defined but not used [-Wunused-function] 270 | char * read_1string < :: gw_status_evt_v1 > ( const :: gw_status_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:255:12: warning: 'char* gw_dump::read_1string(const T&, FILE*) [with T = gw_1string_evt_v1]' defined but not used [-Wunused-function] 255 | char * read_1string < :: gw_1string_evt_v1 > ( const :: gw_1string_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/CMakeFiles/vdb-config.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 78%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/configure.cpp [ 78%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/uuid.cpp [ 78%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/prefetch/prefetch.c /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp: In function 'void ncbi::runTest(int, const char**, const char*, const char*)': /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:271:20: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 271 | delete gw; | ^~ /build/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:217:24: note: 'gw' was declared here 217 | GeneralWriter *gw; | ^~ cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -E touch /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples [ 78%] Generating CMakeFiles/ngs-examples.dir/java_class_filelist cd /build/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.25/Modules/UseJava/ClassFilelist.cmake [ 78%] Creating Java archive ngs-examples.jar cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/jar -cf /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-examples.jar @java_class_filelist [ 79%] Linking CXX executable ../../../test-bin/test-general-writer cd /build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.25/Modules/UseJava/Symlinks.cmake /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 79%] Built target ngs-examples 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 80%] Linking CXX executable ../../../test-bin/Test_LOADER cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADER.dir/link.txt --verbose=1 [ 81%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target test-general-writer make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o [ 81%] Building CXX object tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/accession.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/. -I/build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/../../.. -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o -MF CMakeFiles/sharq.dir/fastq_parse.cpp.o.d -o CMakeFiles/sharq.dir/fastq_parse.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Built target Test_LOADER [ 81%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/service.cpp [ 81%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c [ 82%] Linking CXX executable ../../../test-bin/Test_Drivertool_JsonParsing cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o" -o ../../../test-bin/Test_Drivertool_JsonParsing /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c: In function 'readThread': /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] 691 | if ( rr->type == rr_fileDone ) | ~~^~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here 647 | free(rr); | ^~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:691:16: warning: pointer 'rslt' may be used after 'free' [-Wuse-after-free] 691 | if ( rr->type == rr_fileDone ) | ~~^~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c:647:13: note: call to 'free' here 647 | free(rr); | ^~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target Test_Drivertool_JsonParsing make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Linking CXX static library ../../lib/libngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ngs-c++.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++.dir/link.txt --verbose=1 /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.dir/jni_ErrorMsg.c.o" /usr/bin/ranlib ../../lib/libngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libngs-c++.a libngs-c++.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3.0.3 libngs-c++.a.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3 libngs-c++.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a libngs-c++-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Linking CXX executable ../../../test-bin/test-regexpr cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-regexpr.dir/link.txt --verbose=1 [ 83%] Linking CXX shared library ../../lib/libngs-c++.so cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o" -o ../../../test-bin/test-regexpr /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 -lre2 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libngs-c++.so.3 -o ../../lib/libngs-c++.so.3.0.3 "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.dir/jni_ErrorMsg.c.o" [ 83%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c [ 83%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/json-parse.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libngs-c++.so.3.0.3 ../../lib/libngs-c++.so.3 ../../lib/libngs-c++.so make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target test-regexpr make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target ngs-c++-shared make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend [ 84%] Linking CXX static library ../../lib/libncbi-ngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ncbi-ngs.dir/cmake_clean_target.cmake make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs.dir/link.txt --verbose=1 [ 84%] Linking CXX shared library ../../lib/libncbi-ngs.so cd /build/sra-sdk-3.0.3+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 /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" 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../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" [ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libncbi-ngs.so.3 -o ../../lib/libncbi-ngs.so.3.0.3 "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" 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../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 /usr/bin/ranlib ../../lib/libncbi-ngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs.a libncbi-ngs.a.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3.0.3 libncbi-ngs.a.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3 libncbi-ngs.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a libncbi-ngs-static.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target ncbi-ngs 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp [ 84%] Linking CXX executable ../../../test-bin/Test_Align_samextract cd /build/sra-sdk-3.0.3+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 [ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libncbi-ngs.so.3.0.3 ../../lib/libncbi-ngs.so.3 ../../lib/libncbi-ngs.so In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ld: CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o: in function `extract_buf(char const*, unsigned long, SAMExtractor**) [clone .constprop.0]': ./obj-x86_64-linux-gnu/test/internal/align/./test/internal/align/test-samextract.cpp:117: warning: the use of `tempnam' is dangerous, better use `mkstemp' [ 84%] Built target ncbi-ngs-shared 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp [ 84%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/SDL-response.cpp [ 84%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/util.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o [ 84%] Built target Test_Align_samextract cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/var-expand.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp [ 84%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfRetrier.c [ 84%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfOutFile.c /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': /build/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] 97 | bool next = i -> nextPileup (); | ^~~~ [ 84%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp [ 85%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp [ 85%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined 750 | #define YY_BUF_SIZE 16777216 | /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition 204 | #define YY_BUF_SIZE 16384 | /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1115 | if ( ! yyg->yy_state_buf ) | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1117 | if ( ! yyg->yy_state_buf ) | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1120 | if ( ! yyg->yy_start ) | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) | ^~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] 2395 | static int yy_top_state (yyscan_t yyscanner) | ^~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] 1837 | static int input (yyscan_t yyscanner) | ^~~~~ [ 85%] Linking C executable ../../../bin/prefetch cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/prefetch.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f prefetch.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv prefetch prefetch.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3.0.3 prefetch.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3 prefetch cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 prefetch-driver make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Linking CXX executable ../../../test-bin/Test_Drivertool_FilePath cd /build/sra-sdk-3.0.3+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 [ 85%] Built target prefetch 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/CMakeFiles/sra-search.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/main.cpp [ 86%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/tool-args.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/main.cpp:38: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target Test_Drivertool_FilePath 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 86%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search.cpp [ 86%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search.cpp:29: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-loader.c [ 87%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/main.cpp [ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp [ 87%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp:8: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 87%] Linking CXX executable ../../bin/gw-dumper cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:42: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:19, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parser.hpp:48, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp:44: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/strict_fstream.hpp:136:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 136 | catch (std::ios_base::failure e) {} | ^ [ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:20: /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp: In function 'bxz::Compression bxz::detect_type(char*, char*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:33:19: warning: unused variable 'b3' [-Wunused-variable] 33 | unsigned char b3 = *reinterpret_cast< unsigned char * >(in_buff_start + 3); | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:34:19: warning: unused variable 'b4' [-Wunused-variable] 34 | unsigned char b4 = *reinterpret_cast< unsigned char * >(in_buff_start + 4); | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:35:19: warning: unused variable 'b5' [-Wunused-variable] 35 | unsigned char b5 = *reinterpret_cast< unsigned char * >(in_buff_start + 5); | ^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c: In function 'WriteLoaderSignature': /build/sra-sdk-3.0.3+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]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target gw-dumper 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp [ 87%] Linking C executable ../../../bin/latf-load cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp:28: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f latf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv latf-load latf-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3.0.3 latf-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3 latf-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target latf-load 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-searchblock.cpp /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp: In instantiation of 'int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, coverage_info*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]': /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:853:47: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, coverage_info*) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:893:43: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector*, TLock*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:933:51: required from 'void NSRefVariation::find_alignments(const char*, const std::vector*, TLock*, size_t, const CInputRuns*, KApp::CProgressBar*) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:1024:25: required from here /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:570:28: warning: unused variable 'allele_size' [-Wunused-variable] 570 | size_t allele_size = obj.GetAlleleSize(); | ^~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp: In instantiation of 'int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, coverage_info*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]': /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:853:47: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, coverage_info*) [with TLock = CNoMutex; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:893:43: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector*, TLock*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:933:51: required from 'void NSRefVariation::find_alignments(const char*, const std::vector*, TLock*, size_t, const CInputRuns*, KApp::CProgressBar*) [with TLock = CNoMutex; size_t = long unsigned int]' /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:1051:29: required from here /build/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:570:28: warning: unused variable 'allele_size' [-Wunused-variable] [ 87%] Linking CXX executable ../../../bin/var-expand cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 88%] Linking CXX executable ../../../bin/ngs-pileup cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 88%] Linking CXX executable ../../../test-bin/Test_Drivertool_SDLResponse cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o" -o ../../../test-bin/Test_Drivertool_SDLResponse cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f var-expand.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv var-expand var-expand.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3.0.3 var-expand.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3 var-expand make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target var-expand 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ngs-pileup.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ngs-pileup ngs-pileup.3.0.3 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3.0.3 ngs-pileup.3 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3 ngs-pileup make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp [ 88%] Built target ngs-pileup 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp:29: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 88%] Building CXX object test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp [ 88%] Built target Test_Drivertool_SDLResponse 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:1: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 88%] Building CXX object test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp [ 88%] Linking CXX executable ../../../test-bin/test-vdb-config-model cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:31, from /build/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp:37: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target test-vdb-config-model 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/sra-sdk-3.0.3+dfsg -I/build/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp:52: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:3: /usr/include/ncbi-vdb/kfc/ctx.h:68:19: warning: 's_src_loc' defined but not used [-Wunused-variable] 68 | static KSourceLoc s_src_loc = { __mod__, __file__, __fext__ }; | ^~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] 97 | bool next = i -> nextPileup (); | ^~~~ [ 88%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config.c [ 89%] Linking CXX executable ../../../../test-bin/testy-the-bear cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 89%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/build-version.cpp [ 89%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 89%] Built target testy-the-bear make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 89%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 90%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp [ 90%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/file-path.posix.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 90%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp [ 90%] Linking CXX executable ../../../bin/pileup-stats [ 90%] Linking CXX executable ../../../test-bin/FragTest cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 90%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o -MF CMakeFiles/vdb-config.dir/interactive.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive.cpp.o -c /build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Linking CXX executable ../../../bin/ref-variation cd /build/sra-sdk-3.0.3+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 [ 90%] Built target FragTest make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pileup-stats.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pileup-stats pileup-stats.3.0.3 [ 90%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3.0.3 pileup-stats.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3 pileup-stats make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Built target pileup-stats make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ref-variation.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ref-variation ref-variation.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3.0.3 ref-variation.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3 ref-variation make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp [ 90%] Built target ref-variation make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Linking CXX executable ../../../../test-bin/test-searchblock cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target test-searchblock make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/RefTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/RefTest.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Linking CXX executable ../../../test-bin/AlignTest cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 91%] Linking CXX executable ../../../test-bin/AlignSliceTest cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignSliceTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 91%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp [ 91%] Built target AlignTest make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o [ 91%] Linking CXX executable ../../../test-bin/PileupTest cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/PileupTest.dir/link.txt --verbose=1 cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target AlignSliceTest 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target PileupTest 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sra.cpp [ 91%] Linking CXX executable ../../../test-bin/RefTest cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target RefTest 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp: In member function 'POSIX::Process::ExitStatus POSIX::Process::wait() const': /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:246:28: warning: 'void std::unexpected()' is deprecated [-Wdeprecated-declarations] 246 | std::unexpected(); | ~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/12/ios:39, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:42: /usr/include/c++/12/exception:109:8: note: declared here 109 | void unexpected() __attribute__ ((__noreturn__)); | ^~~~~~~~~~ [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp [ 91%] Linking CXX executable ../../../test-bin/DumpReferenceFASTA cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 91%] Linking CXX executable ../../../test-bin/test-ngs cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target DumpReferenceFASTA 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o [ 91%] Built target test-ngs cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp 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 [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/DependInfo.cmake --color= cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o [ 91%] Linking CXX executable ../../../test-bin/Test_Ngs_Pileup cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_readcollection.cpp cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive2.cpp make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target Test_Ngs_Pileup 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o [ 91%] Linking CXX executable ../../../test-bin/SlowTest_Align_estimator cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp: In function 'rc_t KMain(int, char**)': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp:864:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 864 | putenv("NCBI_VDB_QUALITY=R"); | ^~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target SlowTest_Align_estimator 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp [ 91%] Linking CXX executable ../../../bin/sratools cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp [ 92%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceWindow_Slice_Filtered::Instance::test_method()': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound::Instance::test_method()': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound_StartInWindow::Instance::test_method()': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound::Instance::test_method()': /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound_StartInWindow::Instance::test_method()': /build/sra-sdk-3.0.3+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." ) | ^ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sratools.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sratools sratools.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sratools.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3 sratools make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target sratools 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 92%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_reference.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIterator_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:191:10: warning: unused variable 'base' [-Wunused-variable] 191 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIteratorSlice_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:386:10: warning: unused variable 'base' [-Wunused-variable] 386 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 93%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config-model.cpp [ 93%] Linking CXX executable ../../../bin/sra-search cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 93%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-search.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-search sra-search.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3.0.3 sra-search.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3 sra-search make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ [ 93%] Built target sra-search make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/depend /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_fragmentblob.cpp [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_referenceblob.cpp [ 94%] Linking CXX executable ../../../../test-bin/test-sra-search cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 94%] Linking CXX executable ../../../bin/vdb-config cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/interactive.cpp.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 [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-config.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-config vdb-config.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3.0.3 vdb-config.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3 vdb-config cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E copy /usr/include/ncbi-vdb/kfg/ncbi/default.kfg /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/default.kfg make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target test-sra-search 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/DependInfo.cmake --color= [ 94%] Built target vdb-config 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/DependInfo.cmake --color= In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_byteblob.cpp [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ [ 94%] Linking CXX executable ../../../../test-bin/test-sra-search-slow cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 94%] Linking CXX executable ../../../../test-bin/test-general-loader cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target test-general-loader 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 make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target test-sra-search-slow 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1test.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1test.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp: In function 'rc_t KMain(int, char**)': /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:530:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 530 | putenv("NCBI_VDB_QUALITY=R"); | ^~~~~~~~~~~~~~~~~~~~ [ 94%] Linking CXX executable ../../../test-bin/test-byteblob cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1PileupTest.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1PileupTest.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 94%] Linking CXX executable ../../../test-bin/test-fragmentblob cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target test-fragmentblob 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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -I/build/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -rdynamic -Wall -std=c++11 -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/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/test-ngs-vdb.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/NGS-VDB.hpp:31, from /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/test-ngs-vdb.cpp:31: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1_pileup cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_csra1_pileup [ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1_refwin cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_csra1_refwin [ 95%] Linking CXX executable ../../../test-bin/test-ngs_sra_c++ cd /build/sra-sdk-3.0.3+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 [ 95%] Linking CXX executable ../../../test-bin/test-ngs_reference cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_reference make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_sra_c++ [ 95%] Linking CXX executable ../../../test-bin/test-ngs_csra1pileup++ cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_csra1pileup++ [ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1_readcollection cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 96%] Linking C static library ../../ilib/libvdb-sqlite.a cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -P CMakeFiles/vdb-sqlite.dir/cmake_clean_target.cmake cd /build/sra-sdk-3.0.3+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" make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-ngs_csra1_readcollection /usr/bin/ranlib ../../ilib/libvdb-sqlite.a make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] 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 -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/fastconv.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+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]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] Building C object tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/fastconv.c [ 97%] Building C object tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o cd /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c11 -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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/vdb_shell.c [ 97%] Linking CXX executable ../../../test-bin/test-referenceblob cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 97%] Linking C executable ../../../bin/fastconv cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-referenceblob [ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastconv.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastconv fastconv.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3.0.3 fastconv.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3 fastconv make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target fastconv make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_sradb [ 97%] Linking CXX executable ../../../test-bin/test-ngs_sradb_c++ cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_sradb_c++ [ 98%] Linking CXX executable ../../../test-bin/test-ngs_sra cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target test-ngs_sra [ 98%] Linking C executable ../../../bin/vdb-sql cd /build/sra-sdk-3.0.3+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 -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 98%] Linking CXX executable ../../../test-bin/test-ngs_csra1 cd /build/sra-sdk-3.0.3+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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-sql.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-sql vdb-sql.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3.0.3 vdb-sql.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3 vdb-sql make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target vdb-sql make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target test-ngs_csra1 [ 98%] Linking CXX executable ../../../test-bin/test-ngs-vdb cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target test-ngs-vdb In file included from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/../utility/traits.hpp:29, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/graph.hpp:5, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/task.hpp:3, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/observer.hpp:3, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/core/executor.hpp:3, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./taskflow/taskflow.hpp:3, from /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:109: In member function 'constexpr _Tp std::optional<_Tp>::value_or(_Up&&) const & [with _Up = bool; _Tp = bool]', inlined from 'rc_t ProcessBAM(const char*, context_t*, VDatabase*, Reference*, Sequence*, Alignment*, bool*, bool*)' at /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2466:53: /usr/include/c++/12/optional:1030:33: warning: '*(unsigned char*)((char*)&opt_is_unmated + offsetof(std::optional,std::optional::.std::_Optional_base::))' may be used uninitialized [-Wmaybe-uninitialized] 1030 | return this->_M_get(); | ^ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c: In function 'rc_t ProcessBAM(const char*, context_t*, VDatabase*, Reference*, Sequence*, Alignment*, bool*, bool*)': /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1894:25: note: '*(unsigned char*)((char*)&opt_is_unmated + offsetof(std::optional,std::optional::.std::_Optional_base::))' was declared here 1894 | std::optional opt_is_unmated; | ^~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2438:38: warning: '*(unsigned char*)((char*)&opt_is_primary + offsetof(std::optional,std::optional::.std::_Optional_base::))' may be used uninitialized [-Wmaybe-uninitialized] 2438 | if (!opt_is_primary.value()) { | ~~~~~~~~~~~~~~~~~~~~^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1893:25: note: '*(unsigned char*)((char*)&opt_is_primary + offsetof(std::optional,std::optional::.std::_Optional_base::))' was declared here 1893 | std::optional opt_is_primary; | ^~~~~~~~~~~~~~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2447:62: warning: '*(unsigned char*)((char*)&opt_pcr_dup + offsetof(std::optional,std::optional::.std::_Optional_base::))' may be used uninitialized [-Wmaybe-uninitialized] 2447 | if (!opt_pcr_dup.has_value() || opt_pcr_dup.value() != (o_pcr_dup & n_pcr_dup)) { | ~~~~~~~~~~~~~~~~~^~ /build/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1892:25: note: '*(unsigned char*)((char*)&opt_pcr_dup + offsetof(std::optional,std::optional::.std::_Optional_base::))' was declared here 1892 | std::optional opt_pcr_dup; | ^~~~~~~~~~~ [ 98%] Linking CXX executable ../../../test-bin/test-ngs_csra1_c++ cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target test-ngs_csra1_c++ [ 98%] Linking CXX executable ../../../bin/bam-load cd /build/sra-sdk-3.0.3+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++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -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/libssl.so /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 /usr/lib/x86_64-linux-gnu/libcrypto.so cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f bam-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv bam-load bam-load.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3.0.3 bam-load.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3 bam-load make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target bam-load [ 99%] Linking CXX executable ../../../bin/sharq cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/sharq.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sharq.dir/fastq_parse.cpp.o -o ../../../bin/sharq -lstdc++fs /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so -lre2 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sharq.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sharq sharq.3.0.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sharq.3.0.3 sharq.3 cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sharq.3 sharq make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target sharq make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/depend make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/depend make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sra-sdk-3.0.3+dfsg /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/../../../tools/loaders/sharq -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o -MF CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o.d -o CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-parser.cpp cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /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/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/sra-sdk-3.0.3+dfsg/libs/inc -I/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/../../../tools/loaders/sharq -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -rdynamic -Wall -std=c++17 -MD -MT test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o -MF CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o.d -o CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o -c /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-writer.cpp In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/bxzstr.hpp:19, from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/fastq_parser.hpp:48, from /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-parser.cpp:37: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*)': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/strict_fstream.hpp:136:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 136 | catch (std::ios_base::failure e) {} | ^ In file included from /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/bxzstr.hpp:20: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp: In function 'bxz::Compression bxz::detect_type(char*, char*)': /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:33:19: warning: unused variable 'b3' [-Wunused-variable] 33 | unsigned char b3 = *reinterpret_cast< unsigned char * >(in_buff_start + 3); | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:34:19: warning: unused variable 'b4' [-Wunused-variable] 34 | unsigned char b4 = *reinterpret_cast< unsigned char * >(in_buff_start + 4); | ^~ /build/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:35:19: warning: unused variable 'b5' [-Wunused-variable] 35 | unsigned char b5 = *reinterpret_cast< unsigned char * >(in_buff_start + 5); | ^~ [ 99%] Linking CXX executable ../../../test-bin/test-sharq-writer cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sharq-writer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o" -o ../../../test-bin/test-sharq-writer /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/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-sharq-writer [100%] Linking CXX executable ../../../test-bin/test-sharq-parser cd /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sharq-parser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o" -o ../../../test-bin/test-sharq-parser -lstdc++fs /usr/lib/x86_64-linux-gnu/libz.so /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/lib/x86_64-linux-gnu/libbz2.so -lre2 make[3]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [100%] Built target test-sharq-parser make[2]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg' cd obj-x86_64-linux-gnu && \ ctest --force-new-ctest-process --verbose -j1 -LE online UpdateCTestConfiguration from :/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/ngs/ngs-python/setup.py" "-q" "install" "--user" 9: Working Directory: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-python 9: Environment variables: 9: PYTHONUSERBASE=/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/tmp/python 9: Test timeout computed to be: 1500 9: /build/sra-sdk-3.0.3+dfsg/ngs/ngs-python/setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives 9: from distutils.core import setup 1/114 Test #9: Test_NGS_Python_install ......................... Passed 0.50 sec test 15 Start 15: Ngs_MakeDB 15: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/ngs-makedb 15: Working Directory: /build/sra-sdk-3.0.3+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) 2/114 Test #15: Ngs_MakeDB ...................................... Passed 0.15 sec test 16 Start 16: Test_Ngs 16: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-ngs 16: Working Directory: /build/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test 16: Test timeout computed to be: 1500 16: 16: *** No errors detected (0 s total) 3/114 Test #16: Test_Ngs ........................................ Passed 0.03 sec test 32 Start 32: GeneralWriterTest 32: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-writer 32: Working Directory: /build/sra-sdk-3.0.3+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: --------------------------------- 4/114 Test #32: GeneralWriterTest ............................... Passed 0.02 sec test 33 Start 33: Ref-Variation-1.0 33: Test command: /bin/sh "./have-access.sh" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "ref-variation" 33: Working Directory: /build/sra-sdk-3.0.3+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... 5/114 Test #33: Ref-Variation-1.0 ............................... Passed 0.02 sec test 34 Start 34: Var-Expand-1.0 34: Test command: /bin/sh "./have-access.sh" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "var-expand" 34: Working Directory: /build/sra-sdk-3.0.3+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... 6/114 Test #34: Var-Expand-1.0 .................................. Passed 0.01 sec test 35 Start 35: SearchBlockWhiteBox 35: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-searchblock 35: Working Directory: /build/sra-sdk-3.0.3+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) 7/114 Test #35: SearchBlockWhiteBox ............................. Passed 0.03 sec test 38 Start 38: GeneralLoaderWhiteBox 38: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-loader 38: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 38: Test timeout computed to be: 1500 38: Unpacked protocol: Running 62 test cases... 38: EmptyInput (0 s) 38: ShortInput (0 s) 38: BadSignature (0 s) 38: BadEndianness (0 s) 38: ReverseEndianness (0 s) 38: LaterVersion (0 s) 38: BadSchemaFileName (0 s) 38: BadSchemaFileName_Long (0 s) 38: BadSchemaName (0 s) 38: BadSchemaName_Long (0 s) 38: BadTableName (0 s) 38: BadTableName_Long (0 s) 38: DuplicateTableId (0 s) 38: BadColumnName (0 s) 38: BadTableId (0 s) 38: DuplicateColumnName (0 s) 38: DuplicateColumnId (0 s) 38: NoOpenStreamEvent (0 s) 38: NoCloseStreamEvent (0 s) 38: NoColumns (0 s) 38: SoftwareName (0 s) 38: SoftwareName_BadVersion (0 s) 38: DBAddDatabase (0 s) 38: DBAddSubDatabase (0 s) 38: DBAddTable (0 s) 38: DBAddTableToSubDb (0 s) 38: DBMetadataNode (0 s) 38: SubDBMetadataNode (0 s) 38: TblMetadataNode (0 s) 38: ColMetadataNode (0 s) 38: NoData (0 s) 38: Chunk_BadColumnId (0 s) 38: WriteNoCommit (0 s) 38: CommitBadTableId (0 s) 38: OneColumnOneCellOneChunk (0 s) 38: OneColumnOneCellOneChunk_Long (0 s) 38: OneColumnOneCellManyChunks (0 s) 38: IntegerCompression_MinimumCompression (0 s) 38: IntegerCompression_MaximumCompression (0 s) 38: IntegerCompression_MultipleValues (0 s) 38: OneColumnDefaultNoWrite (0 s) 38: OneColumnDefaultNoWrite_Long (0 s) 38: MoveAhead (0 s) 38: OneColumnDefaultOverwite (0 s) 38: OneColumnChangeDefault (0 s) 38: OneColumnDataAndDefaultsMixed (0 s) 38: TwoColumnsFullRow (0 s) 38: TwoColumnsIncompleteRow (0 s) 38: TwoColumnsPartialRowWithDefaults (0 s) 38: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 38: EmptyDefault_String (0 s) 38: EmptyDefault_Int (0 s) 38: MultipleTables_Multiple_Columns_MultipleRows (0 s) 38: AdditionalSchemaIncludePaths_Single (0 s) 38: AdditionalSchemaIncludePaths_Multiple (0 s) 38: AdditionalSchemaFiles_Single (0 s) 38: AdditionalSchemaFiles_Multiple (0 s) 38: ErrorMessage (0 s) 38: ErrorMessage_Long (0 s) 38: LogMessage (0 s) 38: ProgressMessage (0 s) 38: TargetOverride (0 s) 38: 38: *** No errors detected (0 s total) 38: Packed protocol: Running 62 test cases... 38: EmptyInput (0 s) 38: ShortInput (0 s) 38: BadSignature (0 s) 38: BadEndianness (0 s) 38: ReverseEndianness (0 s) 38: LaterVersion (0 s) 38: BadSchemaFileName (0 s) 38: BadSchemaFileName_Long (0 s) 38: BadSchemaName (0 s) 38: BadSchemaName_Long (0 s) 38: BadTableName (0 s) 38: BadTableName_Long (0 s) 38: DuplicateTableId (0 s) 38: BadColumnName (0 s) 38: BadTableId (0 s) 38: DuplicateColumnName (0 s) 38: DuplicateColumnId (0 s) 38: NoOpenStreamEvent (0 s) 38: NoCloseStreamEvent (0 s) 38: NoColumns (0 s) 38: SoftwareName (0 s) 38: SoftwareName_BadVersion (0 s) 38: DBAddDatabase (0 s) 38: DBAddSubDatabase (0 s) 38: DBAddTable (0 s) 38: DBAddTableToSubDb (0 s) 38: DBMetadataNode (0 s) 38: SubDBMetadataNode (0 s) 38: TblMetadataNode (0 s) 38: ColMetadataNode (0 s) 38: NoData (0 s) 38: Chunk_BadColumnId (0 s) 38: WriteNoCommit (0 s) 38: CommitBadTableId (0 s) 38: OneColumnOneCellOneChunk (0 s) 38: OneColumnOneCellOneChunk_Long (0 s) 38: OneColumnOneCellManyChunks (0 s) 38: IntegerCompression_MinimumCompression (0 s) 38: IntegerCompression_MaximumCompression (0 s) 38: IntegerCompression_MultipleValues (0 s) 38: OneColumnDefaultNoWrite (0 s) 38: OneColumnDefaultNoWrite_Long (0 s) 38: MoveAhead (0 s) 38: OneColumnDefaultOverwite (0 s) 38: OneColumnChangeDefault (0 s) 38: OneColumnDataAndDefaultsMixed (0 s) 38: TwoColumnsFullRow (0 s) 38: TwoColumnsIncompleteRow (0 s) 38: TwoColumnsPartialRowWithDefaults (0 s) 38: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 38: EmptyDefault_String (0 s) 38: EmptyDefault_Int (0 s) 38: MultipleTables_Multiple_Columns_MultipleRows (0 s) 38: AdditionalSchemaIncludePaths_Single (0 s) 38: AdditionalSchemaIncludePaths_Multiple (0 s) 38: AdditionalSchemaFiles_Single (0 s) 38: AdditionalSchemaFiles_Multiple (0 s) 38: ErrorMessage (0 s) 38: ErrorMessage_Long (0 s) 38: LogMessage (0 s) 38: ProgressMessage (0 s) 38: TargetOverride (0 s) 38: 38: *** No errors detected (1 s total) 8/114 Test #38: GeneralLoaderWhiteBox ........................... Passed 2.19 sec test 39 Start 39: GWDumper 39: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-gw-dumper 39: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test 39: Test timeout computed to be: 1500 9/114 Test #39: GWDumper ........................................ Passed 0.02 sec test 40 Start 40: makeinputs 40: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/makeinputs 40: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 40: Test timeout computed to be: 1500 10/114 Test #40: makeinputs ...................................... Passed 0.04 sec test 41 Start 41: GeneralLoader-1.0-Basic-Unpacked 41: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1" "0" "-I/usr/include/ncbi-vdb" 41: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 41: Test timeout computed to be: 1500 41: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1 0 -I/usr/include/ncbi-vdb 41: running test case 1 41: cat input/1.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stderr 41: Load succeeded, dumping and matching stdout 41: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stderr 11/114 Test #41: GeneralLoader-1.0-Basic-Unpacked ................ Passed 0.65 sec test 42 Start 42: GeneralLoader-1.1-Basic-Packed 42: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1packed" "0" "-I/usr/include/ncbi-vdb" 42: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 42: Test timeout computed to be: 1500 42: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1packed 0 -I/usr/include/ncbi-vdb 42: running test case 1packed 42: cat input/1packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stderr 42: Load succeeded, dumping and matching stdout 42: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stderr 12/114 Test #42: GeneralLoader-1.1-Basic-Packed .................. Passed 0.60 sec test 43 Start 43: GeneralLoader-1.2-TargetDbOverride 43: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb --target actual/1override/db" 43: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 43: Test timeout computed to be: 1500 43: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb --target actual/1override/db 43: running test case 1override 43: cat input/1override.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb --target actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 43: Load succeeded, dumping and matching stdout 43: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 13/114 Test #43: GeneralLoader-1.2-TargetDbOverride .............. Passed 0.60 sec test 44 Start 44: GeneralLoader-1.3-TargetDbOverrideShorthand 44: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb -T actual/1override/db" 44: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 44: Test timeout computed to be: 1500 44: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb -T actual/1override/db 44: running test case 1override 44: cat input/1override.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -T actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 44: Load succeeded, dumping and matching stdout 44: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 14/114 Test #44: GeneralLoader-1.3-TargetDbOverrideShorthand ..... Passed 0.56 sec test 45 Start 45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked 45: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "2" "3" "-I/usr/include/ncbi-vdb -L=err" 45: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 45: Test timeout computed to be: 1500 45: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 2 3 -I/usr/include/ncbi-vdb -L=err 45: running test case 2 45: cat input/2.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stderr 45: Load failed as expected, matching stderr 15/114 Test #45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked .... Passed 0.36 sec test 46 Start 46: GeneralLoader-2.1-ErrorMessageEvent-Packed 46: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "2packed" "3" "-I/usr/include/ncbi-vdb -L=err" 46: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 46: Test timeout computed to be: 1500 46: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 2packed 3 -I/usr/include/ncbi-vdb -L=err 46: running test case 2packed 46: cat input/2packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stderr 46: Load failed as expected, matching stderr 16/114 Test #46: GeneralLoader-2.1-ErrorMessageEvent-Packed ...... Passed 0.39 sec test 47 Start 47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked 47: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 47: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 47: Test timeout computed to be: 1500 47: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 47: running test case 3 47: cat input/3.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 47: Load succeeded, dumping and matching stdout 47: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 17/114 Test #47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked ... Passed 0.53 sec test 48 Start 48: GeneralLoader-3.1-EmptyDefaultValues-Packed 48: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 48: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 48: Test timeout computed to be: 1500 48: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 48: running test case 3 48: cat input/3.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 48: Load succeeded, dumping and matching stdout 48: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 18/114 Test #48: GeneralLoader-3.1-EmptyDefaultValues-Packed ..... Passed 0.52 sec test 49 Start 49: GeneralLoader-4.0-MoveAheadEvent-Unpacked 49: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "4" "0" "-I/usr/include/ncbi-vdb" 49: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 49: Test timeout computed to be: 1500 49: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 4 0 -I/usr/include/ncbi-vdb 49: running test case 4 49: cat input/4.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stderr 49: Load succeeded, dumping and matching stdout 49: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stderr 19/114 Test #49: GeneralLoader-4.0-MoveAheadEvent-Unpacked ....... Passed 0.57 sec test 50 Start 50: GeneralLoader-4.1-MoveAheadEvent-Packed 50: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "4packed" "0" "-I/usr/include/ncbi-vdb" 50: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 50: Test timeout computed to be: 1500 50: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 4packed 0 -I/usr/include/ncbi-vdb 50: running test case 4packed 50: cat input/4packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stderr 50: Load succeeded, dumping and matching stdout 50: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stderr 20/114 Test #50: GeneralLoader-4.1-MoveAheadEvent-Packed ......... Passed 0.47 sec test 51 Start 51: GeneralLoader-5.0-IntegerConversion 51: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "5packed" "0" "-I/usr/include/ncbi-vdb" 51: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 51: Test timeout computed to be: 1500 51: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 5packed 0 -I/usr/include/ncbi-vdb 51: running test case 5packed 51: cat input/5packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stderr 51: Load succeeded, dumping and matching stdout 51: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/db 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stderr 21/114 Test #51: GeneralLoader-5.0-IntegerConversion ............. Passed 0.54 sec test 52 Start 52: GeneralLoader-6.0-SoftwareName-Unpacked 52: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "6" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 52: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 52: Test timeout computed to be: 1500 52: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 6 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 52: running test case 6 52: cat input/6.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stderr 52: Load succeeded, dumping and matching stdout 52: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/db SOFTWARE/formatter 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stderr 22/114 Test #52: GeneralLoader-6.0-SoftwareName-Unpacked ......... Passed 0.40 sec test 53 Start 53: GeneralLoader-6.1-SoftwareName-Packed 53: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "6packed" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 53: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 53: Test timeout computed to be: 1500 53: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 6packed 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 53: running test case 6packed 53: cat input/6packed.gl | /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stderr 53: Load succeeded, dumping and matching stdout 53: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/db SOFTWARE/formatter 1>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stdout 2>/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stderr 23/114 Test #53: GeneralLoader-6.1-SoftwareName-Packed ........... Passed 0.20 sec test 54 Start 54: bio-end-makeinputs 54: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/bio-end-makeinputs 54: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 54: Test timeout computed to be: 1500 24/114 Test #54: bio-end-makeinputs .............................. Passed 0.01 sec test 55 Start 55: BioEnd-Excl-1 55: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" "-L=debug" 55: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 55: Test timeout computed to be: 1500 55: running test bio-end:excl-1 25/114 Test #55: BioEnd-Excl-1 ................................... Passed 0.48 sec test 56 Start 56: BioEnd-Excl-2 56: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-2" "0" "n" "-I/usr/include/ncbi-vdb" 56: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 56: Test timeout computed to be: 1500 56: running test bio-end:excl-2 26/114 Test #56: BioEnd-Excl-2 ................................... Passed 0.48 sec test 57 Start 57: BioEnd-Excl-3 57: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-3" "0" "n" "-I/usr/include/ncbi-vdb" 57: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 57: Test timeout computed to be: 1500 57: running test bio-end:excl-3 27/114 Test #57: BioEnd-Excl-3 ................................... Passed 0.48 sec test 58 Start 58: BioEnd-Excl-4 58: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-4" "0" "n" "-I/usr/include/ncbi-vdb" 58: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 58: Test timeout computed to be: 1500 58: running test bio-end:excl-4 28/114 Test #58: BioEnd-Excl-4 ................................... Passed 0.43 sec test 59 Start 59: BioEnd-Incl-1 59: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "incl-1" "0" "n" "-I/usr/include/ncbi-vdb" 59: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 59: Test timeout computed to be: 1500 59: running test bio-end:incl-1 29/114 Test #59: BioEnd-Incl-1 ................................... Passed 0.49 sec test 60 Start 60: IdxText-CI-1 60: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" 60: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 60: Test timeout computed to be: 1500 60: running test bio-end:excl-1 30/114 Test #60: IdxText-CI-1 .................................... Passed 0.36 sec test 61 Start 61: idx-text-makeinputs 61: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-makeinputs 61: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 61: Test timeout computed to be: 1500 31/114 Test #61: idx-text-makeinputs ............................. Passed 0.01 sec test 62 Start 62: IdxText-ci-1 62: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-1" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 62: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 62: Test timeout computed to be: 1500 62: running test idx-text:ci-1 32/114 Test #62: IdxText-ci-1 .................................... Passed 0.54 sec test 63 Start 63: IdxText-ci-2 63: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-2" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 63: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 63: Test timeout computed to be: 1500 63: running test idx-text:ci-2 33/114 Test #63: IdxText-ci-2 .................................... Passed 0.50 sec test 64 Start 64: IdxText-ci-3 64: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-3" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 64: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 64: Test timeout computed to be: 1500 64: running test idx-text:ci-3 34/114 Test #64: IdxText-ci-3 .................................... Passed 0.59 sec test 65 Start 65: IdxText-ci-4 65: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-4" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 65: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 65: Test timeout computed to be: 1500 65: running test idx-text:ci-4 35/114 Test #65: IdxText-ci-4 .................................... Passed 0.48 sec test 66 Start 66: IdxText-ci-5 66: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-5" "0" "n" "-I/usr/include/ncbi-vdb" 66: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 66: Test timeout computed to be: 1500 66: running test idx-text:ci-5 36/114 Test #66: IdxText-ci-5 .................................... Passed 0.33 sec test 67 Start 67: IdxText-cs-1 67: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-1" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 67: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 67: Test timeout computed to be: 1500 67: running test idx-text:cs-1 37/114 Test #67: IdxText-cs-1 .................................... Passed 0.56 sec test 68 Start 68: IdxText-cs-2 68: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-2" "0" "y" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 68: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 68: Test timeout computed to be: 1500 68: running test idx-text:cs-2 38/114 Test #68: IdxText-cs-2 .................................... Passed 0.59 sec test 69 Start 69: IdxText-cs-3 69: Test command: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-3" "0" "n" "-I/usr/include/ncbi-vdb" 69: Working Directory: /build/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 69: Test timeout computed to be: 1500 69: running test idx-text:cs-3 39/114 Test #69: IdxText-cs-3 .................................... Passed 0.43 sec test 70 Start 70: PileupStats-Version 70: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -V | grep --quiet `head -n 1 /build/sra-sdk-3.0.3+dfsg/shared/toolkit.vers`" 70: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 70: Test timeout computed to be: 1500 40/114 Test #70: PileupStats-Version ............................. Passed 0.06 sec test 71 Start 71: PileupStats-Help 71: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -h | grep --quiet Usage" 71: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 71: Test timeout computed to be: 1500 41/114 Test #71: PileupStats-Help ................................ Passed 0.05 sec test 72 Start 72: PileupStats-NoArgs 72: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats; if [ $? == 0 ] ; then exit 1; fi;" 72: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 72: Test timeout computed to be: 1500 72: 72: Usage: 72: pileup-stats [options] 72: 72: Options: 72: -o|--output-file file for output 72: (default pipe to stdout) 72: -r|--remote-db name of remote database to create 72: (default .pileup_stat) 72: -x|--depth-cutoff cutoff for depth <= value (default 1) 72: -e|--event-cutoff cutoff for number of events > value (default 1) 72: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 72: -a|--align-category the types of alignments to pile up: 72: { primary, secondary, all } (default primary) 72: --buffer-size bytes size of output pipe buffer - default 32K bytes 72: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 72: -h|--help output brief explanation of the program 72: -v|--verbose increase the verbosity of the program. 72: -V|--version display the version of the program then quit. 72: use multiple times for more verbosity. 72: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 72: 72: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 72: 72: /bin/sh: 1: [: 3: unexpected operator 42/114 Test #72: PileupStats-NoArgs .............................. Passed 0.02 sec test 73 Start 73: PileupStats-IgnoreArgs-L 73: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -L 1; if [ $? == 0 ] ; then exit 1; fi;" 73: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 73: Test timeout computed to be: 1500 73: 73: Usage: 73: pileup-stats [options] 73: 73: Options: 73: -o|--output-file file for output 73: (default pipe to stdout) 73: -r|--remote-db name of remote database to create 73: (default .pileup_stat) 73: -x|--depth-cutoff cutoff for depth <= value (default 1) 73: -e|--event-cutoff cutoff for number of events > value (default 1) 73: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 73: -a|--align-category the types of alignments to pile up: 73: { primary, secondary, all } (default primary) 73: --buffer-size bytes size of output pipe buffer - default 32K bytes 73: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 73: -h|--help output brief explanation of the program 73: -v|--verbose increase the verbosity of the program. 73: -V|--version display the version of the program then quit. 73: use multiple times for more verbosity. 73: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 73: 73: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 73: 73: /bin/sh: 1: [: 3: unexpected operator 43/114 Test #73: PileupStats-IgnoreArgs-L ........................ Passed 0.05 sec test 74 Start 74: PileupStats-IgnoreArgs-z 74: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -z ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 74: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 74: Test timeout computed to be: 1500 74: 74: Usage: 74: pileup-stats [options] 74: 74: Options: 74: -o|--output-file file for output 74: (default pipe to stdout) 74: -r|--remote-db name of remote database to create 74: (default .pileup_stat) 74: -x|--depth-cutoff cutoff for depth <= value (default 1) 74: -e|--event-cutoff cutoff for number of events > value (default 1) 74: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 74: -a|--align-category the types of alignments to pile up: 74: { primary, secondary, all } (default primary) 74: --buffer-size bytes size of output pipe buffer - default 32K bytes 74: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 74: -h|--help output brief explanation of the program 74: -v|--verbose increase the verbosity of the program. 74: -V|--version display the version of the program then quit. 74: use multiple times for more verbosity. 74: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 74: 74: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 74: 74: /bin/sh: 1: [: 3: unexpected operator 44/114 Test #74: PileupStats-IgnoreArgs-z ........................ Passed 0.02 sec test 75 Start 75: PileupStats-IgnoreArgs-loglevel 75: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --log-level 1; if [ $? == 0 ] ; then exit 1; fi;" 75: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 75: Test timeout computed to be: 1500 75: 75: Usage: 75: pileup-stats [options] 75: 75: Options: 75: -o|--output-file file for output 75: (default pipe to stdout) 75: -r|--remote-db name of remote database to create 75: (default .pileup_stat) 75: -x|--depth-cutoff cutoff for depth <= value (default 1) 75: -e|--event-cutoff cutoff for number of events > value (default 1) 75: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 75: -a|--align-category the types of alignments to pile up: 75: { primary, secondary, all } (default primary) 75: --buffer-size bytes size of output pipe buffer - default 32K bytes 75: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 75: -h|--help output brief explanation of the program 75: -v|--verbose increase the verbosity of the program. 75: -V|--version display the version of the program then quit. 75: use multiple times for more verbosity. 75: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 75: 75: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 75: 75: /bin/sh: 1: [: 3: unexpected operator 45/114 Test #75: PileupStats-IgnoreArgs-loglevel ................. Passed 0.03 sec test 76 Start 76: PileupStats-IgnoreArgs-xmllog 76: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 76: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 76: Test timeout computed to be: 1500 76: 76: Usage: 76: pileup-stats [options] 76: 76: Options: 76: -o|--output-file file for output 76: (default pipe to stdout) 76: -r|--remote-db name of remote database to create 76: (default .pileup_stat) 76: -x|--depth-cutoff cutoff for depth <= value (default 1) 76: -e|--event-cutoff cutoff for number of events > value (default 1) 76: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 76: -a|--align-category the types of alignments to pile up: 76: { primary, secondary, all } (default primary) 76: --buffer-size bytes size of output pipe buffer - default 32K bytes 76: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 76: -h|--help output brief explanation of the program 76: -v|--verbose increase the verbosity of the program. 76: -V|--version display the version of the program then quit. 76: use multiple times for more verbosity. 76: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 76: 76: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 76: 76: /bin/sh: 1: [: 3: unexpected operator 46/114 Test #76: PileupStats-IgnoreArgs-xmllog ................... Passed 0.05 sec test 77 Start 77: PileupStats-IgnoreArgs-xmllogfd 77: Test command: /bin/sh "-c" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log-fd ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 77: Working Directory: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 77: Test timeout computed to be: 1500 77: 77: Usage: 77: pileup-stats [options] 77: 77: Options: 77: -o|--output-file file for output 77: (default pipe to stdout) 77: -r|--remote-db name of remote database to create 77: (default .pileup_stat) 77: -x|--depth-cutoff cutoff for depth <= value (default 1) 77: -e|--event-cutoff cutoff for number of events > value (default 1) 77: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 77: -a|--align-category the types of alignments to pile up: 77: { primary, secondary, all } (default primary) 77: --buffer-size bytes size of output pipe buffer - default 32K bytes 77: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 77: -h|--help output brief explanation of the program 77: -v|--verbose increase the verbosity of the program. 77: -V|--version display the version of the program then quit. 77: use multiple times for more verbosity. 77: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 77: 77: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 77: 77: /bin/sh: 1: [: 3: unexpected operator 47/114 Test #77: PileupStats-IgnoreArgs-xmllogfd ................. Passed 0.04 sec test 78 Start 78: Test_NgsJava_lib_load 78: Test command: /usr/bin/java "-cp" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar:/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/sra-sdk-3.0.3+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" 78: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java 78: Test timeout computed to be: 1500 78: JUnit version 4.11 78: ......... 78: Time: 0.337 78: 78: OK (9 tests) 78: 48/114 Test #78: Test_NgsJava_lib_load ........................... Passed 1.22 sec test 82 Start 82: Test_Drivertool_BuildVersion 82: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_BuildVersion 82: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 82: Test timeout computed to be: 1500 82: Test_Version passed. 49/114 Test #82: Test_Drivertool_BuildVersion .................... Passed 0.02 sec test 83 Start 83: Test_Drivertool_FilePath 83: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_FilePath 83: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 83: Test timeout computed to be: 1500 83: Running 26 test cases... 83: DefaultConstruct (0 s) 83: Construct_Cstring (0 s) 83: Construct_String (0 s) 83: CopyConstruct_Empty (0 s) 83: CopyConstruct (0 s) 83: Assign_Empty (0 s) 83: Assign (0 s) 83: Copy (0 s) 83: Split (0 s) 83: BaseName (0 s) 83: Append (0 s) 83: RemoveSuffix_0 (0 s) 83: RemoveSuffix (0 s) 83: RemoveSuffix_Ext (0 s) 83: RemoveSuffix_Oversized (0 s) 83: CWD (0 s) 83: Exists (0 s) 83: CWD_Append (0 s) 83: Exists_Static (0 s) 83: Readable (0 s) 83: IsSame_Directory (0 s) 83: NotIsSame_Directory (0 s) 83: IsSame_File (0 s) 83: NotIsSame_File (0 s) 83: Current_Executable (0 s) 83: Executable_Yes (0 s) 83: 83: *** No errors detected (0 s total) 50/114 Test #83: Test_Drivertool_FilePath ........................ Passed 0.03 sec test 84 Start 84: Test_Drivertool_CommandLine 84: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_CommandLine 84: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 84: Test timeout computed to be: 1500 84: Test_CommandLine passed. 51/114 Test #84: Test_Drivertool_CommandLine ..................... Passed 0.02 sec test 85 Start 85: Test_Drivertool_JsonParsing 85: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_JsonParsing 85: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 85: Test timeout computed to be: 1500 52/114 Test #85: Test_Drivertool_JsonParsing ..................... Passed 0.05 sec test 86 Start 86: Test_Drivertool_SDLResponse 86: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_SDLResponse 86: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 86: Test timeout computed to be: 1500 53/114 Test #86: Test_Drivertool_SDLResponse ..................... Passed 0.02 sec test 87 Start 87: Test_Drivertool_Accession 87: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_Accession 87: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 87: Test timeout computed to be: 1500 54/114 Test #87: Test_Drivertool_Accession ....................... Passed 0.02 sec test 88 Start 88: Test_Drivertool_UUID 88: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_UUID 88: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/driver-tool 88: Test timeout computed to be: 1500 55/114 Test #88: Test_Drivertool_UUID ............................ Passed 2.07 sec test 90 Start 90: Test_VDB_Config_model 90: Test command: /build/sra-sdk-3.0.3+dfsg/test/external/vdb-config/model.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model" 90: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/vdb-config 90: Test timeout computed to be: 1500 90: testing /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model 90: Running 11 test cases... 90: get_config_changed (0 s) 90: prefetch_download_to_cache (0 s) 90: user_accept_aws_charges (0 s) 90: user_accept_gcp_charges (0 s) 90: temp_cache_location (0 s) 90: gcp_credential_file_location (0 s) 90: aws_credential_file_location (0 s) 90: aws_profile (0 s) 90: noCommit (0 s) 90: Commit (0 s) 90: Reload (0 s) 90: 90: *** No errors detected (0 s total) 90: VDB Copy model test is finished 56/114 Test #90: Test_VDB_Config_model ........................... Passed 0.25 sec test 91 Start 91: Test_Vdb_dump_Check_exit_code 91: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=.." "/usr/bin/python3" "/build/sra-sdk-3.0.3+dfsg/build/check-exit-code.py" "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" 91: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/external/vdb-dump 91: Test timeout computed to be: 1500 91: WARNING[TEST1] help message is in 'STDOUT' 91: [check-exit-code.py] test passed for [/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump] 57/114 Test #91: Test_Vdb_dump_Check_exit_code ................... Passed 0.38 sec test 93 Start 93: Test_KAPP_qfile 93: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_KAPP_qfile 93: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/loader 93: Test timeout computed to be: 1500 93: start-position : 0 93: queue-size : 1024 93: block-size : 0 93: chunk-size : 1024 58/114 Test #93: Test_KAPP_qfile ................................. Passed 0.02 sec test 94 Start 94: Test_LOADERFILE 94: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADERFILE 94: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/loader 94: Test timeout computed to be: 1500 94: Running 5 test cases... 94: KQueueFile_ReadTimeout_FGsleeps (2 s) 94: KQueueFile_ReadTimeout_BGsleeps (3 s) 94: KQueueFile_WriteTimeout (2 s) 94: KLoaderFile_eolBeforeEof (0 s) 94: KLoaderFile_noEolBeforeEof (0 s) 94: 94: *** No errors detected (7 s total) 59/114 Test #94: Test_LOADERFILE ................................. Passed 7.13 sec test 95 Start 95: Test_LOADER 95: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADER 95: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/loader 95: Test timeout computed to be: 1500 95: Running 2 test cases... 95: LoaderMeta_Write (0 s) 95: LoaderMeta_WriteWithVersion (0 s) 95: 95: *** No errors detected (0 s total) 60/114 Test #95: Test_LOADER ..................................... Passed 0.17 sec test 96 Start 96: Test_regexpr 96: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-regexpr 96: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 96: Test timeout computed to be: 1500 96: Running 4 test cases... 96: Construction (0 s) 96: LastInput (0 s) 96: NoMatch (0 s) 96: YesMatch (0 s) 96: 96: *** No errors detected (0 s total) 61/114 Test #96: Test_regexpr .................................... Passed 0.03 sec test 97 Start 97: Test_sharq_parser 97: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-sharq-parser 97: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 97: Test timeout computed to be: 1500 97: Running 93 test cases... 97: EmptyFile (0 s) 97: EndLines (0 s) 97: InvalidDefline (0 s) 97: InvalidDeflineError (0 s) 97: GoodRead (0 s) 97: GoodReadFollowedByJunk (0 s) 97: MultiLineRead (0 s) 97: NoLastLF (0 s) 97: InvalidSequence (0 s) 97: EmptyQuality (0 s) 97: EmptyQuality2 (0 s) 97: TestSequence (0 s) 97: TestSequence_Multi (0 s) 97: UridineTranslation (0 s) 97: IlluminaNew1 (0 s) 97: IlluminaNew2 (0 s) 97: IlluminaNew3 (0 s) 97: IlluminaNew4 (0 s) 97: IlluminaNew5 (0 s) 97: IlluminaNew6 (0 s) 97: IlluminaNew7 (0 s) 97: IlluminaNew8 (0 s) 97: IlluminaNew9 (0 s) 97: IlluminaNew10 (0 s) 97: IlluminaNew11 (0 s) 97: IlluminaNew12 (0 s) 97: IlluminaNew13 (0 s) 97: IlluminaNew14 (0 s) 97: IlluminaNew15 (0 s) 97: IlluminaNew16 (0 s) 97: IlluminaNew17 (0 s) 97: IlluminaNew18 (0 s) 97: IlluminaNew19 (0 s) 97: IlluminaNew20 (0 s) 97: IlluminaNew21 (0 s) 97: IlluminaNew22 (0 s) 97: IlluminaNewDataGroup1 (0 s) 97: BGI1 (0 s) 97: BGI2 (0 s) 97: BGI3 (0 s) 97: BGIOld1 (0 s) 97: BgiOld8 (0 s) 97: BgiNewd8 (0 s) 97: SequenceGetSpotGroupBarcode (0 s) 97: BarCode_Plus (0 s) 97: BarCode_Underscore (0 s) 97: NoColonAtTheEnd_Error (0 s) 97: SequenceGetSpotGroupUnderscore (0 s) 97: RetainIlluminaSuffix (0 s) 97: RetainBgiSuffix (0 s) 97: Test_get_next_spot_empty (0 s) 97: Test_get_next_spot (0 s) 97: Test_get_next_spot_multi_2 (0 s) 97: Test_get_next_spot_multi_1 (0 s) 97: Test_get_spot_empty (0 s) 97: Test_get_spot_no_match (0 s) 97: Test_get_spot_no_match2 (0 s) 97: Test_get_spot_match (0 s) 97: Test_get_spot_match_multi (0 s) 97: Test_get_spot_match_multi_skip (0 s) 97: Test_get_spot_match_multi_skip_2 (0 s) 97: IlluminaCasava_1_8 (0 s) 97: IlluminaCasava_1_8_SpotGroupNumber (0 s) 97: IlluminaCasava_1_8_SpotGroup_MoreMadness (0 s) 97: IlluminaCasava_1_8_EmptyTag (0 s) 97: Illumina_Underscore (0 s) 97: SRA192487 (0 s) 97: BgiNew8Digit (0 s) 97: Quality33TooLow (0 s) 97: Quality33Adjusteed (0 s) 97: Quality64TooLow (0 s) 97: Quality64Adjusted (0 s) 97: [2024-08-24 00:18:05.546] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: TextQualityTruncated (0 s) 97: TextQualityAccepted (0 s) 97: TextQualityAdjusted (0 s) 97: [2024-08-24 00:18:05.554] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: QualityTooLongTruncated (0 s) 97: Nanopore1_readno_early (0 s) 97: Nanopore1_readno_late (0 s) 97: Nanopore2 (0 s) 97: Nanopore3 (0 s) 97: Nanopore3_1 (0 s) 97: Nanopore4 (0 s) 97: Nanopore4_WithBarcode (0 s) 97: Nanopore4_WithBarcodeUnclassified (0 s) 97: Nanopore4_EmptyChannel (0 s) 97: Nanopore5 (0 s) 97: Nanopore_DefaultReadno (0 s) 97: Nanopore_ReadNoIsAFile (0 s) 97: Nanopore_ReadFilter_Default (0 s) 97: Nanopore_ReadFilter_Pass (0 s) 97: Nanopore_ReadFilter_Fail (0 s) 97: Nanopore_Barcode_BC (0 s) 97: Nanopore_Barcode_Edit (0 s) 97: 97: *** No errors detected (0 s total) 62/114 Test #97: Test_sharq_parser ............................... Passed 0.37 sec test 98 Start 98: Test_sharq_writer 98: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-sharq-writer 98: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 98: Test timeout computed to be: 1500 98: Running 7 test cases... 98: Construct (0 s) 98: SetAttr (0 s) 98: Destination (0 s) 98: DefaultSchema (0 s) 98: IlluminaSchema (0 s) 98: NanoporeSchema (0 s) 98: NanoporeSpecificColumns (0 s) 98: 98: *** No errors detected (0 s total) 63/114 Test #98: Test_sharq_writer ............................... Passed 0.01 sec test 99 Start 99: Test_001.read.supported 99: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.supported" "0" "0" "--debug" "--no-timestamp" "input/001.R1.fastq" 99: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 99: Test timeout computed to be: 1500 99: running 001.read.supported 99: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/001.R1.fastq 1>./actual/001.read.supported/load.stdout 2>./actual/001.read.supported/load.stderr 64/114 Test #99: Test_001.read.supported ......................... Passed 0.12 sec test 100 Start 100: Test_001.read.unsupported 100: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.unsupported" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.unsupported.fq" 100: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 100: Test timeout computed to be: 1500 100: running 001.read.unsupported 100: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.unsupported.fq 1>./actual/001.read.unsupported/load.stdout 2>./actual/001.read.unsupported/load.stderr 65/114 Test #100: Test_001.read.unsupported ....................... Passed 0.05 sec test 101 Start 101: Test_001.read.no_sequence 101: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_sequence" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_sequence.fq" 101: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 101: Test timeout computed to be: 1500 101: running 001.read.no_sequence 101: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_sequence.fq 1>./actual/001.read.no_sequence/load.stdout 2>./actual/001.read.no_sequence/load.stderr 66/114 Test #101: Test_001.read.no_sequence ....................... Passed 0.05 sec test 102 Start 102: Test_001.read.invalid_sequence 102: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_sequence" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.invalid_sequence.fq" 102: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 102: Test timeout computed to be: 1500 102: running 001.read.invalid_sequence 102: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.invalid_sequence.fq 1>./actual/001.read.invalid_sequence/load.stdout 2>./actual/001.read.invalid_sequence/load.stderr 67/114 Test #102: Test_001.read.invalid_sequence .................. Passed 0.03 sec test 103 Start 103: Test_001.read.no_quality 103: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_quality" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_quality.fq" 103: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 103: Test timeout computed to be: 1500 103: running 001.read.no_quality 103: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality.fq 1>./actual/001.read.no_quality/load.stdout 2>./actual/001.read.no_quality/load.stderr 68/114 Test #103: Test_001.read.no_quality ........................ Passed 0.11 sec test 104 Start 104: Test_001.read.no_quality_2 104: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_quality_2" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_quality_2.fq" 104: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 104: Test timeout computed to be: 1500 104: running 001.read.no_quality_2 104: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality_2.fq 1>./actual/001.read.no_quality_2/load.stdout 2>./actual/001.read.no_quality_2/load.stderr 69/114 Test #104: Test_001.read.no_quality_2 ...................... Passed 0.12 sec test 105 Start 105: Test_001.read.invalid_quality33 105: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality33" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=33 input/001.read.invalid_quality33.fq" 105: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 105: Test timeout computed to be: 1500 105: running 001.read.invalid_quality33 105: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=33 input/001.read.invalid_quality33.fq 1>./actual/001.read.invalid_quality33/load.stdout 2>./actual/001.read.invalid_quality33/load.stderr 70/114 Test #105: Test_001.read.invalid_quality33 ................. Passed 0.13 sec test 106 Start 106: Test_001.read.invalid_quality64 106: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality64" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=64 input/001.read.invalid_quality64.fq" 106: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 106: Test timeout computed to be: 1500 106: running 001.read.invalid_quality64 106: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=64 input/001.read.invalid_quality64.fq 1>./actual/001.read.invalid_quality64/load.stdout 2>./actual/001.read.invalid_quality64/load.stderr 71/114 Test #106: Test_001.read.invalid_quality64 ................. Passed 0.12 sec test 107 Start 107: Test_001.read.invalid_quality0 107: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality0" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=0 input/001.read.invalid_quality0.fq" 107: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 107: Test timeout computed to be: 1500 107: running 001.read.invalid_quality0 107: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=0 input/001.read.invalid_quality0.fq 1>./actual/001.read.invalid_quality0/load.stdout 2>./actual/001.read.invalid_quality0/load.stderr 72/114 Test #107: Test_001.read.invalid_quality0 .................. Passed 0.11 sec test 108 Start 108: Test_001.read.long_quality 108: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.long_quality" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.long_quality.fq" 108: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 108: Test timeout computed to be: 1500 108: running 001.read.long_quality 108: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.long_quality.fq 1>./actual/001.read.long_quality/load.stdout 2>./actual/001.read.long_quality/load.stderr 73/114 Test #108: Test_001.read.long_quality ...................... Passed 0.14 sec test 109 Start 109: Test_001.read.bad_quality0 109: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.bad_quality0" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.bad_quality0.fq" 109: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 109: Test timeout computed to be: 1500 109: running 001.read.bad_quality0 109: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.bad_quality0.fq 1>./actual/001.read.bad_quality0/load.stdout 2>./actual/001.read.bad_quality0/load.stderr 74/114 Test #109: Test_001.read.bad_quality0 ...................... Passed 0.12 sec test 110 Start 110: Test_001.read.bad_quality33 110: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.bad_quality33" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.bad_quality33.fq" 110: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 110: Test timeout computed to be: 1500 110: running 001.read.bad_quality33 110: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.bad_quality33.fq 1>./actual/001.read.bad_quality33/load.stdout 2>./actual/001.read.bad_quality33/load.stderr 75/114 Test #110: Test_001.read.bad_quality33 ..................... Passed 0.13 sec test 111 Start 111: Test_002.readTypes_default 111: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_default" "0" "0" "--debug" "--no-timestamp" "input/002.allBiological_1.fq input/002.allBiological_2.fq" 111: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 111: Test timeout computed to be: 1500 111: running 002.readTypes_default 111: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_default/load.stdout 2>./actual/002.readTypes_default/load.stderr 76/114 Test #111: Test_002.readTypes_default ...................... Passed 0.17 sec test 112 Start 112: Test_002.readTypes_technical 112: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_technical" "0" "0" "--debug" "--no-timestamp" "--readTypes=TT input/002.allBiological_1.fq input/002.allBiological_2.fq" 112: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 112: Test timeout computed to be: 1500 112: running 002.readTypes_technical 112: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TT input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_technical/load.stdout 2>./actual/002.readTypes_technical/load.stderr 77/114 Test #112: Test_002.readTypes_technical .................... Passed 0.16 sec test 113 Start 113: Test_002.readTypes_mixed 113: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_mixed" "0" "0" "--debug" "--no-timestamp" "--readTypes=TB input/002.allBiological_1.fq input/002.allBiological_2.fq" 113: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 113: Test timeout computed to be: 1500 113: running 002.readTypes_mixed 113: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_mixed/load.stdout 2>./actual/002.readTypes_mixed/load.stderr 78/114 Test #113: Test_002.readTypes_mixed ........................ Passed 0.19 sec test 114 Start 114: Test_002.readTypes_missing 114: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_missing" "1" "0" "--debug" "--no-timestamp" "--read1PairFiles=input/001.R1.fastq" 114: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 114: Test timeout computed to be: 1500 114: running 002.readTypes_missing 114: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_missing/load.stdout 2>./actual/002.readTypes_missing/load.stderr 79/114 Test #114: Test_002.readTypes_missing ...................... Passed 0.11 sec test 115 Start 115: Test_002.readTypes_mismatch 115: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_mismatch" "1" "0" "--debug" "--no-timestamp" "--readTypes=TB --read1PairFiles=input/001.R1.fastq" 115: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 115: Test timeout computed to be: 1500 115: running 002.readTypes_mismatch 115: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_mismatch/load.stdout 2>./actual/002.readTypes_mismatch/load.stderr 80/114 Test #115: Test_002.readTypes_mismatch ..................... Passed 0.13 sec test 116 Start 116: Test_002.readTypes_unexpected 116: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_unexpected" "1" "0" "--debug" "--no-timestamp" "--readTypes=X --read1PairFiles=input/002.allBiological_1.fq" 116: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 116: Test timeout computed to be: 1500 116: running 002.readTypes_unexpected 116: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=X --read1PairFiles=input/002.allBiological_1.fq 1>./actual/002.readTypes_unexpected/load.stdout 2>./actual/002.readTypes_unexpected/load.stderr 81/114 Test #116: Test_002.readTypes_unexpected ................... Passed 0.11 sec test 117 Start 117: Test_002.readTypes_interlaved_fail_1 117: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_fail_1" "1" "0" "--debug" "--no-timestamp" "input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 117: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 117: Test timeout computed to be: 1500 117: running 002.readTypes_interlaved_fail_1 117: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_1/load.stdout 2>./actual/002.readTypes_interlaved_fail_1/load.stderr 82/114 Test #117: Test_002.readTypes_interlaved_fail_1 ............ Passed 0.07 sec test 118 Start 118: Test_002.readTypes_interlaved_fail_2 118: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_fail_2" "1" "0" "--debug" "--no-timestamp" "--readTypes=BB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 118: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 118: Test timeout computed to be: 1500 118: running 002.readTypes_interlaved_fail_2 118: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_2/load.stdout 2>./actual/002.readTypes_interlaved_fail_2/load.stderr 83/114 Test #118: Test_002.readTypes_interlaved_fail_2 ............ Passed 0.06 sec test 119 Start 119: Test_002.readTypes_interlaved_pass 119: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_pass" "0" "0" "--debug" "--no-timestamp" "--readTypes=BTB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 119: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 119: Test timeout computed to be: 1500 119: running 002.readTypes_interlaved_pass 119: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BTB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_pass/load.stdout 2>./actual/002.readTypes_interlaved_pass/load.stderr 84/114 Test #119: Test_002.readTypes_interlaved_pass .............. Passed 0.11 sec test 120 Start 120: Test_003.files_not_exists 120: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_not_exists" "1" "0" "--debug" "--no-timestamp" "dummy1.fq" 120: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 120: Test timeout computed to be: 1500 120: running 003.files_not_exists 120: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp dummy1.fq 1>./actual/003.files_not_exists/load.stdout 2>./actual/003.files_not_exists/load.stderr 85/114 Test #120: Test_003.files_not_exists ....................... Passed 0.17 sec test 121 Start 121: Test_003.files_not_valid 121: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_not_valid" "1" "0" "--debug" "--no-timestamp" "input/003.empty.fq" 121: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 121: Test timeout computed to be: 1500 121: running 003.files_not_valid 121: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.empty.fq 1>./actual/003.files_not_valid/load.stdout 2>./actual/003.files_not_valid/load.stderr 86/114 Test #121: Test_003.files_not_valid ........................ Passed 0.18 sec test 122 Start 122: Test_003.files_readpairs 122: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_readpairs" "0" "0" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 122: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 122: Test timeout computed to be: 1500 122: running 003.files_readpairs 122: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.files_readpairs/load.stdout 2>./actual/003.files_readpairs/load.stderr 87/114 Test #122: Test_003.files_readpairs ........................ Passed 0.23 sec test 123 Start 123: Test_003.files_mixed 123: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_mixed" "1" "0" "--debug" "--no-timestamp" "input/005.offset0_1.fq input/001.R1.fastq" 123: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 123: Test timeout computed to be: 1500 123: running 003.files_mixed 123: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/001.R1.fastq 1>./actual/003.files_mixed/load.stdout 2>./actual/003.files_mixed/load.stderr 88/114 Test #123: Test_003.files_mixed ............................ Passed 0.14 sec test 124 Start 124: Test_003.files_mixed_cluster 124: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_mixed_cluster" "1" "0" "--debug" "--no-timestamp" "input/003.t_R1.fastq input/003.t_I1.fastq input/001.R1.fastq" 124: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 124: Test timeout computed to be: 1500 124: running 003.files_mixed_cluster 124: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_R1.fastq input/003.t_I1.fastq input/001.R1.fastq 1>./actual/003.files_mixed_cluster/load.stdout 2>./actual/003.files_mixed_cluster/load.stderr 89/114 Test #124: Test_003.files_mixed_cluster .................... Passed 0.15 sec test 125 Start 125: Test_003.files_10x_mixed 125: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_10x_mixed" "1" "0" "--debug" "--no-timestamp" "input/003.t_I1.fastq input/003.t_R1.fastq input/003.t_R2.fastq input/003._I1.fastq input/003.R1.fastq input/003.R2.fastq" 125: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 125: Test timeout computed to be: 1500 125: running 003.files_10x_mixed 125: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_I1.fastq input/003.t_R1.fastq input/003.t_R2.fastq input/003._I1.fastq input/003.R1.fastq input/003.R2.fastq 1>./actual/003.files_10x_mixed/load.stdout 2>./actual/003.files_10x_mixed/load.stderr 90/114 Test #125: Test_003.files_10x_mixed ........................ Passed 0.27 sec test 126 Start 126: Test_003.readTypes_10x 126: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.readTypes_10x" "0" "0" "--debug" "--no-timestamp" "input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq" 126: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 126: Test timeout computed to be: 1500 126: running 003.readTypes_10x 126: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/003.readTypes_10x/load.stdout 2>./actual/003.readTypes_10x/load.stderr 91/114 Test #126: Test_003.readTypes_10x .......................... Passed 0.20 sec test 127 Start 127: Test_003.wrong_pairing 127: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.wrong_pairing" "1" "0" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 127: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 127: Test timeout computed to be: 1500 127: running 003.wrong_pairing 127: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.wrong_pairing/load.stdout 2>./actual/003.wrong_pairing/load.stderr 92/114 Test #127: Test_003.wrong_pairing .......................... Passed 0.11 sec test 128 Start 128: Test_004.truncated.fail 128: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "004.truncated.fail" "1" "0" "--debug" "--no-timestamp" "input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz" 128: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 128: Test timeout computed to be: 1500 128: running 004.truncated.fail 128: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.fail/load.stdout 2>./actual/004.truncated.fail/load.stderr 93/114 Test #128: Test_004.truncated.fail ......................... Passed 1.67 sec test 129 Start 129: Test_004.truncated.pass 129: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "004.truncated.pass" "0" "0" "--debug" "--no-timestamp" "--allowEarlyFileEnd input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz" 129: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 129: Test timeout computed to be: 1500 129: running 004.truncated.pass 129: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --allowEarlyFileEnd input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.pass/load.stdout 2>./actual/004.truncated.pass/load.stderr 94/114 Test #129: Test_004.truncated.pass ......................... Passed 2.14 sec test 130 Start 130: Test_005.offset0 130: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "005.offset0" "0" "0" "--debug" "--no-timestamp" "input/005.offset0_1.fq input/005.offset0_2.fq" 130: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 130: Test timeout computed to be: 1500 130: running 005.offset0 130: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/005.offset0_2.fq 1>./actual/005.offset0/load.stdout 2>./actual/005.offset0/load.stderr 95/114 Test #130: Test_005.offset0 ................................ Passed 0.11 sec test 131 Start 131: Test_005.offset64 131: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "005.offset64" "0" "0" "--debug" "--no-timestamp" "input/005.offset64_1.fq input/005.offset64_2.fq" 131: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 131: Test timeout computed to be: 1500 131: running 005.offset64 131: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset64_1.fq input/005.offset64_2.fq 1>./actual/005.offset64/load.stdout 2>./actual/005.offset64/load.stderr 96/114 Test #131: Test_005.offset64 ............................... Passed 0.11 sec test 132 Start 132: Test_006.duplicate 132: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "006.duplicate" "1" "0" "--debug" "--no-timestamp" "input/006.duplicate.fq" 132: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 132: Test timeout computed to be: 1500 132: running 006.duplicate 132: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/006.duplicate.fq 1>./actual/006.duplicate/load.stdout 2>./actual/006.duplicate/load.stderr 97/114 Test #132: Test_006.duplicate .............................. Passed 0.11 sec test 133 Start 133: Test_007.digest.udenfined 133: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.udenfined" "0" "0" "--debug" "--no-timestamp" "--digest input/001.read.unsupported.fq" 133: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 133: Test timeout computed to be: 1500 133: running 007.digest.udenfined 133: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/001.read.unsupported.fq 1>./actual/007.digest.udenfined/load.stdout 2>./actual/007.digest.udenfined/load.stderr 98/114 Test #133: Test_007.digest.udenfined ....................... Passed 0.07 sec test 134 Start 134: Test_007.digest.multiple 134: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.multiple" "0" "0" "--debug" "--no-timestamp" "--digest input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq" 134: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 134: Test timeout computed to be: 1500 134: running 007.digest.multiple 134: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/007.digest.multiple/load.stdout 2>./actual/007.digest.multiple/load.stderr 99/114 Test #134: Test_007.digest.multiple ........................ Passed 0.09 sec test 135 Start 135: Test_007.digest.groups 135: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.groups" "0" "0" "--debug" "--no-timestamp" "--digest input/003.t_R1.fastq.gz input/003.t2_R1.fastq input/003.t3_R1.fastq input/003.t_R2.fastq.gz input/003.t2_R2.fastq input/003.t3_R2.fastq input/003.t_I1.fastq.gz input/003.t2_I1.fastq input/003.t3_I1.fastq" 135: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 135: Test timeout computed to be: 1500 135: running 007.digest.groups 135: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq.gz input/003.t2_R1.fastq input/003.t3_R1.fastq input/003.t_R2.fastq.gz input/003.t2_R2.fastq input/003.t3_R2.fastq input/003.t_I1.fastq.gz input/003.t2_I1.fastq input/003.t3_I1.fastq 1>./actual/007.digest.groups/load.stdout 2>./actual/007.digest.groups/load.stderr 100/114 Test #135: Test_007.digest.groups .......................... Passed 0.19 sec test 136 Start 136: Test_007.digest.error 136: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.error" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 --digest input/001.read.invalid_quality0.fq" 136: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 136: Test timeout computed to be: 1500 136: running 007.digest.error 136: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --digest input/001.read.invalid_quality0.fq 1>./actual/007.digest.error/load.stdout 2>./actual/007.digest.error/load.stderr 101/114 Test #136: Test_007.digest.error ........................... Passed 0.10 sec test 137 Start 137: Test_008.telemetry_pass 137: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "008.telemetry_pass" "0" "1" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 137: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 137: Test timeout computed to be: 1500 137: running 008.telemetry_pass 137: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq -t ./actual/008.telemetry_pass/telemetry 1>./actual/008.telemetry_pass/load.stdout 2>./actual/008.telemetry_pass/load.stderr 102/114 Test #137: Test_008.telemetry_pass ......................... Passed 0.25 sec test 138 Start 138: Test_009.more_than_4_per_spot 138: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "009.more_than_4_per_spot" "1" "0" "--debug" "--no-timestamp" "--debug input/009.test_I1_001.fastq input/009.test_R1_001.fastq input/009.test_R2_001.fastq input/009.test_R3_001.fastq" 138: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 138: Test timeout computed to be: 1500 138: running 009.more_than_4_per_spot 138: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --debug input/009.test_I1_001.fastq input/009.test_R1_001.fastq input/009.test_R2_001.fastq input/009.test_R3_001.fastq 1>./actual/009.more_than_4_per_spot/load.stdout 2>./actual/009.more_than_4_per_spot/load.stderr 103/114 Test #138: Test_009.more_than_4_per_spot ................... Passed 0.35 sec test 139 Start 139: Test_010.errors.invalid_seq_pass1 139: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_pass1" "0" "0" "--debug" "--no-timestamp" "input/010.errors.invalid_seq.fq" 139: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 139: Test timeout computed to be: 1500 139: running 010.errors.invalid_seq_pass1 139: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass1/load.stdout 2>./actual/010.errors.invalid_seq_pass1/load.stderr 104/114 Test #139: Test_010.errors.invalid_seq_pass1 ............... Passed 0.11 sec test 140 Start 140: Test_010.errors.invalid_seq_pass2 140: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_pass2" "0" "0" "--debug" "--no-timestamp" "--max-err-count 5 input/010.errors.invalid_seq.fq" 140: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 140: Test timeout computed to be: 1500 140: running 010.errors.invalid_seq_pass2 140: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 5 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass2/load.stdout 2>./actual/010.errors.invalid_seq_pass2/load.stderr 105/114 Test #140: Test_010.errors.invalid_seq_pass2 ............... Passed 0.13 sec test 141 Start 141: Test_010.errors.invalid_seq_fail 141: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_fail" "1" "0" "--debug" "--no-timestamp" "--max-err-count 3 input/010.errors.invalid_seq.fq" 141: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 141: Test timeout computed to be: 1500 141: running 010.errors.invalid_seq_fail 141: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 3 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_fail/load.stdout 2>./actual/010.errors.invalid_seq_fail/load.stderr 106/114 Test #141: Test_010.errors.invalid_seq_fail ................ Passed 0.11 sec test 142 Start 142: Test_011.nanopore.3 142: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "011.nanopore.3" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/011.nanopore.3.fq" 142: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 142: Test timeout computed to be: 1500 142: running 011.nanopore.3 142: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/011.nanopore.3.fq 1>./actual/011.nanopore.3/load.stdout 2>./actual/011.nanopore.3/load.stderr 107/114 Test #142: Test_011.nanopore.3 ............................. Passed 0.16 sec test 143 Start 143: Test_012.qualities 143: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "012.qualities" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/012.test_I1_001.fastq input/012.test_R1_001.fastq input/012.test_R2_001.fastq input/012.test2_I1_001.fastq input/012.test2_R1_001.fastq input/012.test2_R2_001.fastq" 143: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 143: Test timeout computed to be: 1500 143: running 012.qualities 143: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/012.test_I1_001.fastq input/012.test_R1_001.fastq input/012.test_R2_001.fastq input/012.test2_I1_001.fastq input/012.test2_R1_001.fastq input/012.test2_R2_001.fastq 1>./actual/012.qualities/load.stdout 2>./actual/012.qualities/load.stderr 108/114 Test #143: Test_012.qualities .............................. Passed 0.25 sec test 144 Start 144: Test_013.no-reads 144: Test command: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "013.no-reads" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/013.t_I1.fastq input/013.t_I2.fastq input/013.t_R1.fastq input/013.t_R2.fastq" 144: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/loaders/sharq 144: Test timeout computed to be: 1500 144: running 013.no-reads 144: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/013.t_I1.fastq input/013.t_I2.fastq input/013.t_R1.fastq input/013.t_R2.fastq 1>./actual/013.no-reads/load.stdout 2>./actual/013.no-reads/load.stderr 109/114 Test #144: Test_013.no-reads ............................... Passed 16.50 sec test 145 Start 145: Test_Align_samextract 145: Test command: /build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Align_samextract 145: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/internal/align 145: Test timeout computed to be: 1500 145: Running 14 test cases... 145: Test_Qual_Decode (0 s) 145: Fast_Sequence (0 s) 145: Fast_u32toa (0 s) 145: Fast_i32toa (0 s) 145: Fast_strtoi64 (0 s) 145: Decode_Cigar (0 s) 145: Check_Cigar (0 s) 145: In_Range (0 s) 145: Is_MD5 (0 s) 145: Is_floworder (0 s) 145: header1 (0 s) 145: BAMfile (0 s) 145: Filter (0 s) 145: None of below files should hang: 145: fuzz/id000000,sig11,src000036,ophavoc,rep128 145: fuzz/id000000,src000000+000001,opsplice,rep16 145: fuzz/id000000,src000000,oparith8,pos3,val+10 145: fuzz/id000001,src000001,oparith16,pos10,val-6 145: fuzz/id000001,src000001,oparith8,pos10,val+9 145: fuzz/id000001,src000003,ophavoc,rep2 145: fuzz/id000002,src000000+000006,opsplice,rep64 145: fuzz/id000002,src000001,oparith8,pos10,val-31 145: fuzz/id000002,src000001,ophavoc,rep4 145: fuzz/id000003,src000001,ophavoc,rep2 145: fuzz/id000003,src000001,ophavoc,rep8 145: fuzz/id000003,src000007,ophavoc,rep2 145: fuzz/id000004,src000001,ophavoc,rep2 145: fuzz/id000004,src000001,ophavoc,rep32 145: fuzz/id000004,src000012,ophavoc,rep8 145: fuzz/id000005,src000001,ophavoc,rep2 145: fuzz/id000005,src000001,ophavoc,rep8 145: fuzz/id000005,src000013+000012,opsplice,rep4 145: fuzz/id000006,src000001,ophavoc,rep2 145: fuzz/id000006,src000001,ophavoc,rep4 145: fuzz/id000006,src000014,ophavoc,rep2 145: fuzz/id000007,src000002,opflip1,pos4 145: fuzz/id000007,src000023,ophavoc,rep4 145: fuzz/id000008,src000002,opflip1,pos8 145: fuzz/id000008,src000029,ophavoc,rep64 145: fuzz/id000009,src000002,opflip1,pos22 145: fuzz/id000009,src000031,ophavoc,rep2 145: fuzz/id000010,src000002,opflip1,pos25 145: fuzz/id000010,src000037+000017,opsplice,rep2 145: fuzz/id000011,src000002,opflip1,pos33 145: fuzz/id000011,src000046,ophavoc,rep2 145: fuzz/id000012,src000002,opflip4,pos20 145: fuzz/id000012,src000049,ophavoc,rep4 145: fuzz/id000013,src000002,opflip4,pos38 145: fuzz/id000013,src000048,ophavoc,rep2 145: fuzz/id000014,src000002,opflip4,pos76 145: fuzz/id000014,src000021+000026,opsplice,rep2 145: fuzz/id000015,src000002,opflip8,pos25 145: fuzz/id000015,src000056,ophavoc,rep2 145: fuzz/id000016,src000002,opint16,pos77,val-129 145: fuzz/id000016,src000002,opint8,pos14,val-1 145: fuzz/id000017,src000002,ophavoc,rep32 145: fuzz/id000017,src000002,opint16,pos77,val-129 145: fuzz/id000018,src000002,opint32,pos25,val+2147483647 145: fuzz/id000018,src000003,opint16,pos3,val-129 145: fuzz/id000019,src000002,opint32,pos33,valbe-128 145: fuzz/id000019,src000007,opflip16,pos33 145: fuzz/id000020,src000002,ophavoc,rep4 145: fuzz/id000020,src000007,opint16,pos117,val-129 145: fuzz/id000021,src000004,opint16,pos4,val+32767 145: fuzz/id000021,src000011,opflip4,pos76 145: fuzz/id000022,src000004,ophavoc,rep16 145: fuzz/id000022,src000011,opflip4,pos116 145: fuzz/id000023,src000011,opflip4,pos116 145: fuzz/id000023,src000018,opflip1,pos15 145: fuzz/id000024,src000011,opflip16,pos52 145: fuzz/id000024,src000018,opflip1,pos26 145: fuzz/id000025,src000018,opflip1,pos15 145: fuzz/id000025,src000018,opflip4,pos92 145: fuzz/id000026,src000018,opflip1,pos26 145: fuzz/id000026,src000018,opflip4,pos137 145: fuzz/id000027,src000018,opflip4,pos24 145: fuzz/id000028,src000018,opflip4,pos92 145: fuzz/id000029,src000018,opflip4,pos137 145: fuzz/id000030,src000018,opint16,pos138,val-129 145: fuzz/id000031,src000018,ophavoc,rep8 145: 145: Fuzz_Hangs (0 s) 145: 145: *** No errors detected (1 s total) 110/114 Test #145: Test_Align_samextract ........................... Passed 1.05 sec test 147 Start 147: Test_Scripts_prepare-sra-names 147: Test command: /usr/bin/perl "test-prepare-sra-names.pl" 147: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 147: Test timeout computed to be: 1500 111/114 Test #147: Test_Scripts_prepare-sra-names .................. Passed 1.35 sec test 148 Start 148: Test_Scripts_fix-sra-names 148: Test command: /usr/bin/perl "test-fix-sra-names.pl" 148: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 148: Test timeout computed to be: 1500 112/114 Test #148: Test_Scripts_fix-sra-names ...................... Passed 0.57 sec test 149 Start 149: Test_Scripts_prepare-sra-names-py 149: Test command: /usr/bin/perl "test-prepare-sra-names-py.pl" 149: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 149: Test timeout computed to be: 1500 113/114 Test #149: Test_Scripts_prepare-sra-names-py ............... Passed 2.16 sec test 150 Start 150: Test_Scripts_fix-sra-names-py 150: Test command: /usr/bin/perl "test-fix-sra-names-py.pl" 150: Working Directory: /build/sra-sdk-3.0.3+dfsg/test/scripts 150: Test timeout computed to be: 1500 114/114 Test #150: Test_Scripts_fix-sra-names-py ................... Passed 1.31 sec 100% tests passed, 0 tests failed out of 114 Total Test time (real) = 61.72 sec make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake debian/rules override_dh_prep make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg' dh_prep -X debian/tmp make[1]: Leaving directory '/build/sra-sdk-3.0.3+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/sra-sdk-3.0.3+dfsg' dh_auto_install cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/sra-sdk-3.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sra-sdk-3.0.3+dfsg -B/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++-static.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ncbi-vdb/NGS.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/FragTest.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/AlignTest.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/AlignSliceTest.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/PileupTest.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/RefTest.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/DumpReferenceFASTA.cpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/expected.txt -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/Makefile -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/README.txt -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++-static.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-static.a -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/win -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/win/stdbool.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/win/atomic32.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/x86_64 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/x86_64/atomic32.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/i386 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/i386/atomic32.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/fat86 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/fat86/atomic32.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/arm64 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/unix/arm64/atomic32.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/defs.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/VTable.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/VTable.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StringItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StringItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StatisticsItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StatisticsItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceSequenceItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceSequenceItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/Refcount.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/Refcount.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadGroupItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadGroupItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadCollectionItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadCollectionItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupEventItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupEventItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PackageItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/FragmentItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/FragmentItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrorMsg.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrBlock.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrBlock.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/AlignmentItf.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/AlignmentItf.h -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/StringRef.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Statistics.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReferenceSequence.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReferenceIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Reference.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadGroupIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadGroup.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadCollection.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Read.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupEventIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupEvent.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Pileup.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Package.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/FragmentIterator.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Fragment.hpp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/AlignmentIterator.hpp -- Installing: 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/build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rcexplain.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rcexplain -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-search.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-search.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-search -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-sra.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-sra.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-sra -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/cache-mgr.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/cache-mgr.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/cache-mgr -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sratools.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sratools.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sratools -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+ -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+meta.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+meta.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+meta -- Installing: 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/build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/illumina-load.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/illumina-load.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/illumina-load -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/helicos-load.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/helicos-load.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/helicos-load -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-loadxml.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-loadxml.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-loadxml -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-load.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-load.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-load -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/cg-load.3.0.3 -- Installing: 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/build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-read-write-cursor -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/read-filter-redact.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/read-filter-redact.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/read-filter-redact -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/copycat.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/copycat.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/copycat -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-copy.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-copy.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-copy -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-diff.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-diff.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-diff -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/make-read-filter.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/make-read-filter.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/make-read-filter -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-cache.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-cache.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-cache -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats.3.0.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats.3 -- Installing: /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats make[2]: Leaving directory '/build/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' # build/install.sh /usr/include/ncbi-vdb/kfg/ncbi \ # /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy \ debian/sra-toolkit/etc/ncbi /build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu mv /build/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3.0.3 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/sra-sdk-3.0.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/sra-sdk-3.0.3+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 81692 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 abi-dump -> abi-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 abi-dump.3 -> abi-dump.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 267544 Aug 24 00:06 abi-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 abi-load -> abi-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 abi-load.3 -> abi-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 635568 Aug 24 00:07 abi-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 align-cache -> align-cache.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 align-cache.3 -> align-cache.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 244864 Aug 24 00:07 align-cache.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 align-info -> align-info.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 align-info.3 -> align-info.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 95944 Aug 24 00:06 align-info.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 bam-load -> bam-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 bam-load.3 -> bam-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 12579712 Aug 24 00:12 bam-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 cache-mgr -> cache-mgr.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 cache-mgr.3 -> cache-mgr.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 124016 Aug 24 00:06 cache-mgr.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 ccextract -> ccextract.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 ccextract.3 -> ccextract.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 271856 Aug 24 00:07 ccextract.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 cg-load -> cg-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 cg-load.3 -> cg-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 654456 Aug 24 00:07 cg-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 check-corrupt -> check-corrupt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 check-corrupt.3 -> check-corrupt.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 248880 Aug 24 00:06 check-corrupt.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 copycat -> copycat.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 copycat.3 -> copycat.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 462592 Aug 24 00:07 copycat.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 crc32sum -> crc32sum.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 crc32sum.3 -> crc32sum.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 79096 Aug 24 00:07 crc32sum.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 22 Aug 24 00:18 dump-blob-boundaries -> dump-blob-boundaries.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 26 Aug 24 00:18 dump-blob-boundaries.3 -> dump-blob-boundaries.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 31368 Aug 24 00:06 dump-blob-boundaries.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 fastconv -> fastconv.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fastconv.3 -> fastconv.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 4919216 Aug 24 00:11 fastconv.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fasterq-dump -> fasterq-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 822992 Aug 24 00:06 fasterq-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 fasterq-dump.3 -> fasterq-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fasterq-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 fastq-dump -> fastq-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 347056 Aug 24 00:06 fastq-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 fastq-dump.3 -> fastq-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 fastq-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 fastq-load -> fastq-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 fastq-load.3 -> fastq-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 691240 Aug 24 00:07 fastq-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 general-loader -> general-loader.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 general-loader.3 -> general-loader.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 1419528 Aug 24 00:07 general-loader.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 helicos-load -> helicos-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 helicos-load.3 -> helicos-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 602456 Aug 24 00:07 helicos-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 illumina-dump -> illumina-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 illumina-dump.3 -> illumina-dump.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 250040 Aug 24 00:06 illumina-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 illumina-load -> illumina-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 illumina-load.3 -> illumina-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 647480 Aug 24 00:07 illumina-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 5 Aug 24 00:18 kar -> kar.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 6 Aug 24 00:18 kar+ -> kar+.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 kar+.3 -> kar+.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 236680 Aug 24 00:06 kar+.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 kar+meta -> kar+meta.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 kar+meta.3 -> kar+meta.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 158024 Aug 24 00:06 kar+meta.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 kar.3 -> kar.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 190512 Aug 24 00:06 kar.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 kdb-index -> kdb-index.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 kdb-index.3 -> kdb-index.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 78168 Aug 24 00:07 kdb-index.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 kdbmeta -> kdbmeta.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 kdbmeta.3 -> kdbmeta.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 123960 Aug 24 00:06 kdbmeta.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 latf-load -> latf-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 latf-load.3 -> latf-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 504056 Aug 24 00:08 latf-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 make-read-filter -> make-read-filter.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 22 Aug 24 00:18 make-read-filter.3 -> make-read-filter.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 153808 Aug 24 00:07 make-read-filter.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 7 Aug 24 00:18 md5cp -> md5cp.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 md5cp.3 -> md5cp.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 89576 Aug 24 00:07 md5cp.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 meta-cmp -> meta-cmp.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 meta-cmp.3 -> meta-cmp.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 81736 Aug 24 00:07 meta-cmp.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 meta-copy -> meta-copy.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 meta-copy.3 -> meta-copy.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 81696 Aug 24 00:07 meta-copy.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 ngs-pileup -> ngs-pileup.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 ngs-pileup.3 -> ngs-pileup.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 2582160 Aug 24 00:08 ngs-pileup.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 pacbio-correct -> pacbio-correct.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 pacbio-correct.3 -> pacbio-correct.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 75952 Aug 24 00:07 pacbio-correct.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 pacbio-load -> pacbio-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 pacbio-load.3 -> pacbio-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 474872 Aug 24 00:07 pacbio-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 pacbio-loadxml -> pacbio-loadxml.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 pacbio-loadxml.3 -> pacbio-loadxml.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 581984 Aug 24 00:07 pacbio-loadxml.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 pileup-stats -> pileup-stats.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 pileup-stats.3 -> pileup-stats.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 2788008 Aug 24 00:09 pileup-stats.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 prefetch -> prefetch.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 460656 Aug 24 00:08 prefetch-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 prefetch.3 -> prefetch.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 prefetch.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 rcexplain -> rcexplain.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 rcexplain.3 -> rcexplain.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 63288 Aug 24 00:06 rcexplain.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 read-filter-redact -> read-filter-redact.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 24 Aug 24 00:18 read-filter-redact.3 -> read-filter-redact.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 110800 Aug 24 00:07 read-filter-redact.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 ref-variation -> ref-variation.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 ref-variation.3 -> ref-variation.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 2937528 Aug 24 00:09 ref-variation.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 rowwritetest -> rowwritetest.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 rowwritetest.3 -> rowwritetest.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 88120 Aug 24 00:07 rowwritetest.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sam-dump -> sam-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 820032 Aug 24 00:06 sam-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sam-dump.3 -> sam-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sam-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 samview -> samview.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 samview-util -> samview-util.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 samview-util.3 -> samview-util.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 64064 Aug 24 00:07 samview-util.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 samview.3 -> samview.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 301904 Aug 24 00:07 samview.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 schema-replace -> schema-replace.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 20 Aug 24 00:18 schema-replace.3 -> schema-replace.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 82840 Aug 24 00:07 schema-replace.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sff-dump -> sff-dump.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sff-dump.3 -> sff-dump.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 229576 Aug 24 00:06 sff-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sff-load -> sff-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sff-load.3 -> sff-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 645864 Aug 24 00:07 sff-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 7 Aug 24 00:18 sharq -> sharq.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 11 Aug 24 00:18 sharq.3 -> sharq.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 18347328 Aug 24 00:14 sharq.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sortreadtest -> sortreadtest.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 sortreadtest.3 -> sortreadtest.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 79584 Aug 24 00:07 sortreadtest.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 sra-pileup -> sra-pileup.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 439704 Aug 24 00:06 sra-pileup-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 sra-pileup.3 -> sra-pileup.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-pileup.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 sra-search -> sra-search.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 sra-search.3 -> sra-search.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 4015448 Aug 24 00:09 sra-search.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sra-sort -> sra-sort.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 sra-sort-cg -> sra-sort-cg.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 sra-sort-cg.3 -> sra-sort-cg.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 804496 Aug 24 00:07 sra-sort-cg.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-sort.3 -> sra-sort.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 804568 Aug 24 00:07 sra-sort.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sra-stat -> sra-stat.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sra-stat.3 -> sra-stat.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 317000 Aug 24 00:07 sra-stat.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 srapath -> srapath.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 252568 Aug 24 00:06 srapath-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 srapath.3 -> srapath.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 srapath.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 sratools -> sratools.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 sratools.3 -> sratools.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 5112800 Aug 24 00:09 sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 srf-load -> srf-load.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 srf-load.3 -> srf-load.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 824440 Aug 24 00:07 srf-load.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 15 Aug 24 00:18 test-download -> test-download.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 19 Aug 24 00:18 test-download.3 -> test-download.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 88664 Aug 24 00:07 test-download.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 24 Aug 24 00:18 test-read-write-cursor -> test-read-write-cursor.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 28 Aug 24 00:18 test-read-write-cursor.3 -> test-read-write-cursor.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 75216 Aug 24 00:07 test-read-write-cursor.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 test-sra -> test-sra.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 test-sra.3 -> test-sra.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 329568 Aug 24 00:06 test-sra.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 8 Aug 24 00:18 testld -> testld.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 testld.3 -> testld.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 76408 Aug 24 00:07 testld.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 txt2kdb -> txt2kdb.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 txt2kdb.3 -> txt2kdb.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 82720 Aug 24 00:07 txt2kdb.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 var-expand -> var-expand.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 var-expand.3 -> var-expand.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 1988808 Aug 24 00:08 var-expand.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 vdb-config -> vdb-config.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 vdb-config.3 -> vdb-config.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 3392176 Aug 24 00:10 vdb-config.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-copy -> vdb-copy.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-copy.3 -> vdb-copy.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 326936 Aug 24 00:07 vdb-copy.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-decrypt -> vdb-decrypt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 vdb-decrypt.3 -> vdb-decrypt.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 121384 Aug 24 00:06 vdb-decrypt.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-diff -> vdb-diff.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-diff.3 -> vdb-diff.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 150176 Aug 24 00:07 vdb-diff.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-dump -> vdb-dump.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 818504 Aug 24 00:07 vdb-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-dump.3 -> vdb-dump.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-encrypt -> vdb-encrypt.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 17 Aug 24 00:18 vdb-encrypt.3 -> vdb-encrypt.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 119752 Aug 24 00:06 vdb-encrypt.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 10 Aug 24 00:18 vdb-lock -> vdb-lock.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-lock.3 -> vdb-lock.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 68256 Aug 24 00:07 vdb-lock.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 9 Aug 24 00:18 vdb-sql -> vdb-sql.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 13 Aug 24 00:18 vdb-sql.3 -> vdb-sql.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 5170312 Aug 24 00:11 vdb-sql.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 12 Aug 24 00:18 vdb-unlock -> vdb-unlock.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 16 Aug 24 00:18 vdb-unlock.3 -> vdb-unlock.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 68272 Aug 24 00:07 vdb-unlock.3.0.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 14 Aug 24 00:18 vdb-validate -> vdb-validate.3 lrwxrwxrwx 1 pbuilder1 pbuilder1 18 Aug 24 00:18 vdb-validate.3 -> vdb-validate.3.0.3 -rwxr-xr-x 1 pbuilder1 pbuilder1 224008 Aug 24 00:06 vdb-validate.3.0.3 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.3.0.3' -> 'fasterq-dump-orig' 'fasterq-dump.3.0.3' -> 'sratools' renamed 'fastq-dump-orig.3.0.3' -> 'fastq-dump-orig' 'fastq-dump.3.0.3' -> 'sratools' renamed 'prefetch-orig.3.0.3' -> 'prefetch-orig' 'prefetch.3.0.3' -> 'sratools' renamed 'sam-dump-orig.3.0.3' -> 'sam-dump-orig' 'sam-dump.3.0.3' -> 'sratools' renamed 'sra-pileup-orig.3.0.3' -> 'sra-pileup-orig' 'sra-pileup.3.0.3' -> 'sratools' renamed 'srapath-orig.3.0.3' -> 'srapath-orig' 'srapath.3.0.3' -> 'sratools' renamed 'vdb-dump-orig.3.0.3' -> 'vdb-dump-orig' 'vdb-dump.3.0.3' -> 'sratools' removed 'abi-dump.3' renamed 'abi-dump.3.0.3' -> 'abi-dump' removed 'abi-load.3' renamed 'abi-load.3.0.3' -> 'abi-load' removed 'align-cache.3' renamed 'align-cache.3.0.3' -> 'align-cache' removed 'align-info.3' renamed 'align-info.3.0.3' -> 'align-info' removed 'bam-load.3' renamed 'bam-load.3.0.3' -> 'bam-load' removed 'cache-mgr.3' renamed 'cache-mgr.3.0.3' -> 'cache-mgr' removed 'ccextract.3' renamed 'ccextract.3.0.3' -> 'ccextract' removed 'cg-load.3' renamed 'cg-load.3.0.3' -> 'cg-load' removed 'check-corrupt.3' renamed 'check-corrupt.3.0.3' -> 'check-corrupt' removed 'copycat.3' renamed 'copycat.3.0.3' -> 'copycat' removed 'crc32sum.3' renamed 'crc32sum.3.0.3' -> 'crc32sum' removed 'dump-blob-boundaries.3' renamed 'dump-blob-boundaries.3.0.3' -> 'dump-blob-boundaries' removed 'fastconv.3' renamed 'fastconv.3.0.3' -> 'fastconv' removed 'fasterq-dump.3' renamed 'fasterq-dump.3.0.3' -> 'fasterq-dump' removed 'fastq-dump.3' renamed 'fastq-dump.3.0.3' -> 'fastq-dump' removed 'fastq-load.3' renamed 'fastq-load.3.0.3' -> 'fastq-load' removed 'general-loader.3' renamed 'general-loader.3.0.3' -> 'general-loader' removed 'helicos-load.3' renamed 'helicos-load.3.0.3' -> 'helicos-load' removed 'illumina-dump.3' renamed 'illumina-dump.3.0.3' -> 'illumina-dump' removed 'illumina-load.3' renamed 'illumina-load.3.0.3' -> 'illumina-load' removed 'kar.3' renamed 'kar.3.0.3' -> 'kar' removed 'kar+.3' renamed 'kar+.3.0.3' -> 'kar+' removed 'kar+meta.3' renamed 'kar+meta.3.0.3' -> 'kar+meta' removed 'kdb-index.3' renamed 'kdb-index.3.0.3' -> 'kdb-index' removed 'kdbmeta.3' renamed 'kdbmeta.3.0.3' -> 'kdbmeta' removed 'latf-load.3' renamed 'latf-load.3.0.3' -> 'latf-load' removed 'make-read-filter.3' renamed 'make-read-filter.3.0.3' -> 'make-read-filter' removed 'md5cp.3' renamed 'md5cp.3.0.3' -> 'md5cp' removed 'meta-cmp.3' renamed 'meta-cmp.3.0.3' -> 'meta-cmp' removed 'meta-copy.3' renamed 'meta-copy.3.0.3' -> 'meta-copy' removed 'ngs-pileup.3' renamed 'ngs-pileup.3.0.3' -> 'ngs-pileup' removed 'pacbio-correct.3' renamed 'pacbio-correct.3.0.3' -> 'pacbio-correct' removed 'pacbio-load.3' renamed 'pacbio-load.3.0.3' -> 'pacbio-load' removed 'pacbio-loadxml.3' renamed 'pacbio-loadxml.3.0.3' -> 'pacbio-loadxml' removed 'pileup-stats.3' renamed 'pileup-stats.3.0.3' -> 'pileup-stats' removed 'prefetch.3' renamed 'prefetch.3.0.3' -> 'prefetch' removed 'rcexplain.3' renamed 'rcexplain.3.0.3' -> 'rcexplain' removed 'read-filter-redact.3' renamed 'read-filter-redact.3.0.3' -> 'read-filter-redact' removed 'ref-variation.3' renamed 'ref-variation.3.0.3' -> 'ref-variation' removed 'rowwritetest.3' renamed 'rowwritetest.3.0.3' -> 'rowwritetest' removed 'sam-dump.3' renamed 'sam-dump.3.0.3' -> 'sam-dump' removed 'samview.3' renamed 'samview.3.0.3' -> 'samview' removed 'samview-util.3' renamed 'samview-util.3.0.3' -> 'samview-util' removed 'schema-replace.3' renamed 'schema-replace.3.0.3' -> 'schema-replace' removed 'sff-dump.3' renamed 'sff-dump.3.0.3' -> 'sff-dump' removed 'sff-load.3' renamed 'sff-load.3.0.3' -> 'sff-load' removed 'sharq.3' renamed 'sharq.3.0.3' -> 'sharq' removed 'sortreadtest.3' renamed 'sortreadtest.3.0.3' -> 'sortreadtest' removed 'sra-pileup.3' renamed 'sra-pileup.3.0.3' -> 'sra-pileup' removed 'sra-search.3' renamed 'sra-search.3.0.3' -> 'sra-search' removed 'sra-sort.3' renamed 'sra-sort.3.0.3' -> 'sra-sort' removed 'sra-sort-cg.3' renamed 'sra-sort-cg.3.0.3' -> 'sra-sort-cg' removed 'sra-stat.3' renamed 'sra-stat.3.0.3' -> 'sra-stat' removed 'srapath.3' renamed 'srapath.3.0.3' -> 'srapath' removed 'sratools.3' renamed 'sratools.3.0.3' -> 'sratools' removed 'srf-load.3' renamed 'srf-load.3.0.3' -> 'srf-load' removed 'test-download.3' renamed 'test-download.3.0.3' -> 'test-download' removed 'test-read-write-cursor.3' renamed 'test-read-write-cursor.3.0.3' -> 'test-read-write-cursor' removed 'test-sra.3' renamed 'test-sra.3.0.3' -> 'test-sra' removed 'testld.3' renamed 'testld.3.0.3' -> 'testld' removed 'txt2kdb.3' renamed 'txt2kdb.3.0.3' -> 'txt2kdb' removed 'var-expand.3' renamed 'var-expand.3.0.3' -> 'var-expand' removed 'vdb-config.3' renamed 'vdb-config.3.0.3' -> 'vdb-config' removed 'vdb-copy.3' renamed 'vdb-copy.3.0.3' -> 'vdb-copy' removed 'vdb-decrypt.3' renamed 'vdb-decrypt.3.0.3' -> 'vdb-decrypt' removed 'vdb-diff.3' renamed 'vdb-diff.3.0.3' -> 'vdb-diff' removed 'vdb-dump.3' renamed 'vdb-dump.3.0.3' -> 'vdb-dump' removed 'vdb-encrypt.3' renamed 'vdb-encrypt.3.0.3' -> 'vdb-encrypt' removed 'vdb-lock.3' renamed 'vdb-lock.3.0.3' -> 'vdb-lock' removed 'vdb-sql.3' renamed 'vdb-sql.3.0.3' -> 'vdb-sql' removed 'vdb-unlock.3' renamed 'vdb-unlock.3.0.3' -> 'vdb-unlock' removed 'vdb-validate.3' renamed 'vdb-validate.3.0.3' -> '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 ${x%-orig} ; \ done renamed 'debian/tmp/usr/bin/fasterq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fasterq-dump-orig' 'debian/tmp/usr/bin/fasterq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/fastq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fastq-dump-orig' 'debian/tmp/usr/bin/fastq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/prefetch-orig' -> 'debian/tmp/usr/lib/sra-toolkit/prefetch-orig' 'debian/tmp/usr/bin/prefetch' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sam-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sam-dump-orig' 'debian/tmp/usr/bin/sam-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sra-pileup-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sra-pileup-orig' 'debian/tmp/usr/bin/sra-pileup' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/srapath-orig' -> 'debian/tmp/usr/lib/sra-toolkit/srapath-orig' 'debian/tmp/usr/bin/srapath' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/vdb-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/vdb-dump-orig' 'debian/tmp/usr/bin/vdb-dump' -> '../lib/sra-toolkit/sratools' dh_install # remove susipcious file which is not executable and conflicts with package magic rm -f debian/*/usr/bin/magic # Formally supply a standard installation ID to satisfy sratools echo '/LIBS/GUID = "806b5c3b-0088-4732-8359-51630950d723"' >debian/sra-toolkit/etc/ncbi/debian.kfg set -e && for i in 3.11; do \ cd ngs/ngs-python; \ python$i ./setup.py install --install-layout=deb \ --root /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs; \ cd ../..; \ done /build/sra-sdk-3.0.3+dfsg/ngs/ngs-python/./setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup running install running build running build_py running install_lib creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3 creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages creating /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Alignment.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/AlignmentIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ErrorMsg.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Fragment.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/FragmentIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/LibChecker.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Package.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Pileup.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupEvent.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupEventIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Read.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadCollection.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadGroup.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadGroupIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Refcount.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Reference.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReferenceIterator.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReferenceSequence.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Statistics.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/String.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/__init__.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/LibManager.py -> /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Alignment.py to Alignment.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/AlignmentIterator.py to AlignmentIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ErrorMsg.py to ErrorMsg.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Fragment.py to Fragment.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/FragmentIterator.py to FragmentIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibChecker.py to LibChecker.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Package.py to Package.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Pileup.py to Pileup.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEvent.py to PileupEvent.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEventIterator.py to PileupEventIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupIterator.py to PileupIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Read.py to Read.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadCollection.py to ReadCollection.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroup.py to ReadGroup.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroupIterator.py to ReadGroupIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadIterator.py to ReadIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Refcount.py to Refcount.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Reference.py to Reference.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceIterator.py to ReferenceIterator.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceSequence.py to ReferenceSequence.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Statistics.py to Statistics.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/String.py to String.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/__init__.py to __init__.cpython-311.pyc byte-compiling /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibManager.py to LibManager.cpython-311.pyc running install_egg_info Writing /build/sra-sdk-3.0.3+dfsg/debian/python3-ngs/usr/lib/python3/dist-packages/ngs-1.0.egg-info find debian -name "*.pyc" -delete find debian -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg' dh_installexamples find debian/*/ -name .gitignore -delete make[1]: Leaving directory '/build/sra-sdk-3.0.3+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/sra-sdk-3.0.3+dfsg' # Putting the upstream version number (without the dfsg part) at the end of # symlink source in the -jni package. sed -e 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\13.0.3+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/sra-sdk-3.0.3+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 KVectorRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VBlobSize used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol KVectorGetFirstBool used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol DLListPopHead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol xcCursorExhausted used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VCursorCloseRow used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol PageMapIteratorDataOffset_Ext used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol xcIntegerOutOfBounds used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol xcParamNull used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol KNSManagerMake used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 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: package libncbi-ngs-dev: substitution variable ${devlibs:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package libngs-jni: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libngs-c++3' in '../libngs-c++3_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-c++3-dbgsym' in '../libngs-c++3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'python3-ngs' in '../python3-ngs_3.0.3+dfsg-6~deb12u1_all.deb'. dpkg-deb: building package 'libncbi-ngs-dev' in '../libncbi-ngs-dev_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-java-doc' in '../libngs-java-doc_3.0.3+dfsg-6~deb12u1_all.deb'. dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'sra-toolkit-dbgsym' in '../sra-toolkit-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-java' in '../libngs-java_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3-dbgsym' in '../libncbi-ngs3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-jni' in '../libngs-jni_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3' in '../libncbi-ngs3_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-deb: building package 'libngs-c++-dev' in '../libngs-c++-dev_3.0.3+dfsg-6~deb12u1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sra-sdk_3.0.3+dfsg-6~deb12u1_amd64.buildinfo dpkg-genchanges --build=binary -O../sra-sdk_3.0.3+dfsg-6~deb12u1_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/428083 and its subdirectories I: Current time: Sat Aug 24 00:20:55 -12 2024 I: pbuilder-time-stamp: 1724502055