sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | kissplice 2.5.3-2 (amd64) Sun, 20 Sep 2020 06:23:41 +0000 | +==============================================================================+ Package: kissplice Version: 2.5.3-2 Source Version: 2.5.3-2 Distribution: perl-5.32-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.32-amd64-debomatic-d9868c7d-c31d-4aa8-9a94-863f9c589a22' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kissplice_2.5.3-2 perl-5.32-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup kissplice_2.5.3-2 perl-5.32-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/kissplice-SZX2nP/resolver-YXOSk7' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.32 InRelease [2871 B] Hit:2 http://localhost:3142/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.32 InRelease [2871 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/kissplice_2.5.3-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/kissplice-SZX2nP/kissplice-2.5.3' with '<>' I: NOTICE: Log filtering will replace 'build/kissplice-SZX2nP' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, libpython3-stdlib, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, libpython3-stdlib, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [403 B] Get:5 copy:/<>/apt_archive ./ Packages [487 B] Fetched 1847 B in 0s (144 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcroco3 libcurl4 libdebhelper-perl libelf1 libexpat1 libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db mime-support po-debconf procps python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support Recommended packages: curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libcroco3 libcurl4 libdebhelper-perl libelf1 libexpat1 libexpat1-dev libfakeroot libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db mime-support po-debconf procps python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 76 newly installed, 0 to remove and 0 not upgraded. Need to get 43.0 MB of archives. After this operation, 165 MB of additional disk space will be used. 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http://localhost:3142/debian unstable/main amd64 python3-dev amd64 3.8.2-3 [1164 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 43.0 MB in 0s (159 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up libpsl5:amd64 (0.21.0-1.1) ... Setting up mime-support (3.64) ... Setting up bsdextrautils (2.36-3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-4) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.0-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.2.1) ... Setting up libbrotli1:amd64 (1.0.9-2) ... Setting up libnghttp2-14:amd64 (1.41.0-3) ... Setting up libmagic1:amd64 (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-5) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up libkrb5support0:amd64 (1.17-10) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.39.0-1) ... Setting up libexpat1-dev:amd64 (2.2.9-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20200912-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... Setting up libk5crypto3:amd64 (1.17-10) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up librhash0:amd64 (1.4.0-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.18.2-1) ... Setting up libkrb5-3:amd64 (1.17-10) ... Setting up libpython3.8-stdlib:amd64 (3.8.6~rc1-2) ... Setting up python3.8 (3.8.6~rc1-2) ... Setting up libelf1:amd64 (0.181-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6) ... Setting up libprocps8:amd64 (2:3.3.16-5) ... Setting up libjsoncpp1:amd64 (1.7.4-3.1) ... Setting up libpython3-stdlib:amd64 (3.8.2-3) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libtool (2.4.6-14) ... Setting up libarchive13:amd64 (3.4.3-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-3) ... Setting up libpython3.8:amd64 (3.8.6~rc1-2) ... Setting up libgssapi-krb5-2:amd64 (1.17-10) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up procps (2:3.3.16-5) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcurl4:amd64 (7.72.0-1) ... Setting up python3-lib2to3 (3.8.5-1) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.5-1) ... Setting up dh-python (4.20200804) ... Setting up gettext (0.19.8.1-10) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.8-dev:amd64 (3.8.6~rc1-2) ... Setting up python3.8-dev (3.8.6~rc1-2) ... Setting up cmake (3.18.2-1) ... Setting up libpython3-dev:amd64 (3.8.2-3) ... Setting up po-debconf (1.0.21) ... Setting up python3-dev (3.8.2-3) ... Setting up debhelper (13.2.1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64 any-ppc64el any-sparc64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35-3 dpkg-dev_1.20.5 g++-10_10.2.0-9 g++-9_9.3.0-18 gcc-10_10.2.0-9 gcc-9_9.3.0-18 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-9 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-9 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-3 binutils-common_2.35-3 binutils-x86-64-linux-gnu_2.35-3 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.2-1 cmake-data_3.18.2-1 coreutils_8.32-3 cpp_4:10.2.0-1 cpp-10_10.2.0-9 cpp-9_9.3.0-18 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.1 dh-autoreconf_19 dh-python_4.20200804 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 eatmydata_105-9 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1 g++-10_10.2.0-9 g++-9_9.3.0-18 gcc_4:10.2.0-1 gcc-10_10.2.0-9 gcc-10-base_10.2.0-9 gcc-9_9.3.0-18 gcc-9-base_9.3.0-18 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 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libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-9 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed5_3.5.1+really3.5.1-2 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10.2.0-9 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1+b1 libldap-common_2.4.53+dfsg-1 liblsan0_10.2.0-9 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200912-1 libncursesw6_6.2+20200912-1 libnettle7_3.5.1+really3.5.1-2 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-3 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 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Source: kissplice Binary: kissplice Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64 any-ppc64el any-sparc64 Version: 2.5.3-2 Maintainer: Debian Med Packaging Team Uploaders: David Parsons , Andreas Tille Homepage: http://kissplice.prabi.fr/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kissplice Vcs-Git: https://salsa.debian.org/med-team/kissplice.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, libpython3-stdlib, zlib1g-dev Package-List: kissplice deb science optional arch=any-amd64,any-arm64,any-mips64,any-mips64el,any-ia64,any-ppc64,any-ppc64el,any-sparc64 Checksums-Sha1: f00233e1e020c635db38f6c0948070a9f5e21b8b 10183268 kissplice_2.5.3.orig.tar.gz 925e44d2e04a04b095ab778428f5caaef0e784d3 12512 kissplice_2.5.3-2.debian.tar.xz Checksums-Sha256: 6d0314e40815246043895cb05ef508d537ca9f3eadc31869006c10a0aafa4191 10183268 kissplice_2.5.3.orig.tar.gz 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atd4tB6d3RP+CsaWDKNSM9v8UX6mEZ10g/S5JV3ZuTUwPLyF79ZG1BoNyK/Bf2Li z+SORC2l+Cc= =YMxw -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.v4Y8eSiQ/trustedkeys.kbx': General error gpgv: Signature made Thu Jun 25 18:35:53 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kissplice_2.5.3-2.dsc dpkg-source: info: extracting kissplice in /<> dpkg-source: info: unpacking kissplice_2.5.3.orig.tar.gz dpkg-source: info: unpacking kissplice_2.5.3-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-bcalm-install.patch dpkg-source: info: applying tests-2to3.patch dpkg-source: info: applying spelling.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kissplice_2.5.3-2 perl-5.32-throwaway amd64 ------------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network kissplice_2.5.3-2 perl-5.32-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.32-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.32-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.32-amd64-debomatic-d9868c7d-c31d-4aa8-9a94-863f9c589a22 SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c1422599 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package kissplice dpkg-buildpackage: info: source version 2.5.3-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by David Parsons dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -rf bcalm/README.md tests/functional_tests/__pycache__/ tests/integration_tests/__pycache__/ make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building kissplice using existing ./kissplice_2.5.3.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building kissplice in kissplice_2.5.3-2.debian.tar.xz dpkg-source: info: building kissplice in kissplice_2.5.3-2.dsc debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DCMAKE_INSTALL_LIBEXECDIR=lib/ 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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_INSTALL_LIBEXECDIR=lib/ .. -- The CXX compiler identification is GNU 10.2.0 -- The C compiler identification is GNU 10.2.0 -- 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 -- 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 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- gatb-core is here '/<>/bcalm/gatb-core/gatb-core' -- CppUnit NOT FOUND -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of __uint128 -- Check size of __uint128 - failed -- Check size of __uint128_t -- Check size of __uint128_t - done -- SSE 4.2 detected -- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof -- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 96 128 <-- max supported kmer size without recompilation -- SOVERSION: 10.2.1 -- SOVERSION_TOOLS: 10.0.4 -- SOVERSION_CXX: 13.0.0 -- SOVERSION_F: 10.0.4 -- SOVERSION_HL: 10.1.1 -- SOVERSION_HL_CXX: 11.1.0 -- SOVERSION_HL_F: 10.0.3 -- Check for STD namespace -- Check for STD namespace - found -- Looking for ceil in m; -- Looking for ceil in m; - found -- Looking for dlopen in dl;m -- Looking for dlopen in dl;m - found -- Looking for WSAStartup in ws2_32;m;dl -- Looking for WSAStartup in ws2_32;m;dl - not found -- Looking for gethostbyname in wsock32;m;dl -- Looking for gethostbyname in wsock32;m;dl - not found -- Looking for gethostname in ucb;m;dl -- Looking for gethostname in ucb;m;dl - not found -- Check if the system is big endian -- Searching 16 bit integer -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Performing Other Test STDC_HEADERS - Success CMake Warning (dev) at /usr/share/cmake-3.18/Modules/CheckIncludeFiles.cmake:120 (message): Policy CMP0075 is not set: Include file check macros honor CMAKE_REQUIRED_LIBRARIES. Run "cmake --help-policy CMP0075" for policy details. Use the cmake_policy command to set the policy and suppress this warning. CMAKE_REQUIRED_LIBRARIES is set to: m;dl For compatibility with CMake 3.11 and below this check is ignoring it. Call Stack (most recent call first): bcalm/gatb-core/gatb-core/thirdparty/hdf5/config/cmake_ext_mod/ConfigureChecks.cmake:192 (CHECK_INCLUDE_FILES) bcalm/gatb-core/gatb-core/thirdparty/hdf5/config/cmake_ext_mod/ConfigureChecks.cmake:201 (CHECK_INCLUDE_FILE_CONCAT) bcalm/gatb-core/gatb-core/thirdparty/hdf5/config/cmake/ConfigureChecks.cmake:5 (include) bcalm/gatb-core/gatb-core/thirdparty/hdf5/CMakeLists.txt:383 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for include file sys/resource.h -- Looking for include file sys/resource.h - found -- Looking for include files sys/resource.h, sys/time.h -- Looking for include files sys/resource.h, sys/time.h - found -- Looking for 3 include files sys/resource.h, ..., unistd.h -- Looking for 3 include files sys/resource.h, ..., unistd.h - found -- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h -- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h - found -- Looking for 5 include files sys/resource.h, ..., sys/stat.h -- Looking for 5 include files sys/resource.h, ..., sys/stat.h - found -- Looking for 6 include files sys/resource.h, ..., sys/socket.h -- Looking for 6 include files sys/resource.h, ..., sys/socket.h - found -- Looking for 7 include files sys/resource.h, ..., sys/types.h -- Looking for 7 include files sys/resource.h, ..., sys/types.h - found -- Looking for 8 include files sys/resource.h, ..., stddef.h -- Looking for 8 include files sys/resource.h, ..., stddef.h - found -- Looking for 9 include files sys/resource.h, ..., setjmp.h -- Looking for 9 include files sys/resource.h, ..., setjmp.h - found -- Looking for 10 include files sys/resource.h, ..., features.h -- Looking for 10 include files sys/resource.h, ..., features.h - found -- Looking for 11 include files sys/resource.h, ..., dirent.h -- Looking for 11 include files sys/resource.h, ..., dirent.h - found -- Looking for 12 include files sys/resource.h, ..., stdint.h -- Looking for 12 include files sys/resource.h, ..., stdint.h - found -- Looking for C++ include stdint.h -- Looking for C++ include stdint.h - found -- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h -- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h - not found -- Looking for 13 include files sys/resource.h, ..., io.h -- Looking for 13 include files sys/resource.h, ..., io.h - not found -- Looking for 13 include files sys/resource.h, ..., winsock2.h -- Looking for 13 include files sys/resource.h, ..., winsock2.h - not found -- Looking for 13 include files sys/resource.h, ..., sys/timeb.h -- Looking for 13 include files sys/resource.h, ..., sys/timeb.h - found -- Looking for 14 include files sys/resource.h, ..., globus/common.h -- Looking for 14 include files sys/resource.h, ..., globus/common.h - not found -- Looking for 14 include files sys/resource.h, ..., pdb.h -- Looking for 14 include files sys/resource.h, ..., pdb.h - not found -- Looking for 14 include files sys/resource.h, ..., pthread.h -- Looking for 14 include files sys/resource.h, ..., pthread.h - found -- Looking for 15 include files sys/resource.h, ..., srbclient.h -- Looking for 15 include files sys/resource.h, ..., srbclient.h - not found -- Looking for 15 include files sys/resource.h, ..., string.h -- Looking for 15 include files sys/resource.h, ..., string.h - found -- Looking for 16 include files sys/resource.h, ..., strings.h -- Looking for 16 include files sys/resource.h, ..., strings.h - found -- Looking for 17 include files sys/resource.h, ..., stdlib.h -- Looking for 17 include files sys/resource.h, ..., stdlib.h - found -- Looking for 18 include files sys/resource.h, ..., memory.h -- Looking for 18 include files sys/resource.h, ..., memory.h - found -- Looking for 19 include files sys/resource.h, ..., dlfcn.h -- Looking for 19 include files sys/resource.h, ..., dlfcn.h - found -- Looking for 20 include files sys/resource.h, ..., inttypes.h -- Looking for 20 include files sys/resource.h, ..., inttypes.h - found -- Looking for 21 include files sys/resource.h, ..., netinet/in.h -- Looking for 21 include files sys/resource.h, ..., netinet/in.h - found -- Performing TEST_LFS_WORKS... yes -- Performing Other Test HAVE_OFF64_T - Success -- Looking for lseek64 -- Looking for lseek64 - found -- Looking for fseeko64 -- Looking for fseeko64 - found -- Looking for ftello64 -- Looking for ftello64 - found -- Looking for ftruncate64 -- Looking for ftruncate64 - found -- Looking for fseeko -- Looking for fseeko - found -- Looking for ftello -- Looking for ftello - found -- Performing Other Test HAVE_STAT64_STRUCT - Success -- Looking for fstat64 -- Looking for fstat64 - found -- Looking for stat64 -- Looking for stat64 - found -- Check size of char -- Check size of char - done -- Check size of short -- Check size of short - done -- Check size of int -- Check size of int - done -- Check size of unsigned -- Check size of unsigned - done -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of __int64 -- Check size of __int64 - failed -- Check size of float -- Check size of float - done -- Check size of double -- Check size of double - done -- Check size of long double -- Check size of long double - done -- Check size of int8_t -- Check size of int8_t - done -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int_least8_t -- Check size of int_least8_t - done -- Check size of uint_least8_t -- Check size of uint_least8_t - done -- Check size of int_fast8_t -- Check size of int_fast8_t - done -- Check size of uint_fast8_t -- Check size of uint_fast8_t - done -- Check size of int16_t -- Check size of int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of int_least16_t -- Check size of int_least16_t - done -- Check size of uint_least16_t -- Check size of uint_least16_t - done -- Check size of int_fast16_t -- Check size of int_fast16_t - done -- Check size of uint_fast16_t -- Check size of uint_fast16_t - done -- Check size of int32_t -- Check size of int32_t - done -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of int_least32_t -- Check size of int_least32_t - done -- Check size of uint_least32_t -- Check size of uint_least32_t - done -- Check size of int_fast32_t -- Check size of int_fast32_t - done -- Check size of uint_fast32_t -- Check size of uint_fast32_t - done -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Check size of int_least64_t -- Check size of int_least64_t - done -- Check size of uint_least64_t -- Check size of uint_least64_t - done -- Check size of int_fast64_t -- Check size of int_fast64_t - done -- Check size of uint_fast64_t -- Check size of uint_fast64_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - done -- Looking for 22 include files sys/resource.h, ..., stdbool.h -- Looking for 22 include files sys/resource.h, ..., stdbool.h - found -- Check size of _Bool -- Check size of _Bool - done -- Performing Other Test DEV_T_IS_SCALAR - Success -- Looking for CLOCK_MONOTONIC -- Looking for CLOCK_MONOTONIC - not found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Performing Other Test HAVE_TM_GMTOFF - Success -- Performing Other Test HAVE___TM_GMTOFF - Failed -- Performing Other Test HAVE_STRUCT_TIMEZONE - Success -- Performing Other Test GETTIMEOFDAY_GIVES_TZ - Success -- Performing Other Test TIME_WITH_SYS_TIME - Success -- Performing Other Test HAVE_TM_ZONE - Failed -- Performing Other Test HAVE_STRUCT_TM_TM_ZONE - Failed -- Performing Other Test HAVE_TIMEZONE - Success -- Performing Other Test HAVE_STAT_ST_BLOCKS - Success -- Looking for ioctl -- Looking for ioctl - found -- Performing Other Test HAVE_STRUCT_VIDEOCONFIG - Failed -- Performing Other Test HAVE_STRUCT_TEXT_INFO - Failed -- Looking for _getvideoconfig -- Looking for _getvideoconfig - not found -- Looking for gettextinfo -- Looking for gettextinfo - not found -- Looking for _scrsize -- Looking for _scrsize - not found -- Looking for GetConsoleScreenBufferInfo -- Looking for GetConsoleScreenBufferInfo - not found -- Looking for TIOCGWINSZ -- Looking for TIOCGWINSZ - found -- Looking for TIOCGETD -- Looking for TIOCGETD - found -- Looking for getpwuid -- Looking for getpwuid - found -- Looking for alarm -- Looking for alarm - found -- Looking for fork -- Looking for fork - found -- Looking for frexpf -- Looking for frexpf - found -- Looking for frexpl -- Looking for frexpl - found -- Looking for gethostname -- Looking for gethostname - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for lstat -- Looking for lstat - found -- Looking for rand_r -- Looking for rand_r - found -- Looking for random -- Looking for random - found -- Looking for setsysinfo -- Looking for setsysinfo - not found -- Looking for signal -- Looking for signal - found -- Looking for longjmp -- Looking for longjmp - found -- Looking for setjmp -- Looking for setjmp - found -- Looking for siglongjmp -- Looking for siglongjmp - found -- Looking for sigsetjmp -- Looking for sigsetjmp - not found -- Looking for sigprocmask -- Looking for sigprocmask - found -- Looking for snprintf -- Looking for snprintf - found -- Looking for srandom -- Looking for srandom - found -- Looking for strdup -- Looking for strdup - found -- Looking for symlink -- Looking for symlink - found -- Looking for system -- Looking for system - found -- Looking for tmpfile -- Looking for tmpfile - found -- Looking for asprintf -- Looking for asprintf - found -- Looking for vasprintf -- Looking for vasprintf - found -- Looking for waitpid -- Looking for waitpid - found -- Looking for vsnprintf -- Looking for vsnprintf - found -- Performing Other Test VSNPRINTF_WORKS - Success -- Looking for sigsetjmp -- Looking for sigsetjmp - found -- Performing Other Test HAVE_ATTRIBUTE - Success -- Performing Other Test HAVE_C99_FUNC - Success -- Performing Other Test HAVE_FUNCTION - Success -- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success -- Performing Other Test SYSTEM_SCOPE_THREADS - Success -- Performing Other Test HAVE_SOCKLEN_T - Success -- Performing Other Test CXX_HAVE_OFFSETOF - Success -- Performing CXX Test OLD_HEADER_FILENAME - Failed -- Performing CXX Test H5_NO_NAMESPACE - Failed -- Performing CXX Test H5_NO_STD - Failed -- Performing CXX Test BOOL_NOTDEFINED - Failed -- Performing CXX Test NO_STATIC_CAST - Failed -- Performing Other Test HAVE_INLINE - Success -- Performing Other Test HAVE___INLINE__ - Success -- Performing Other Test HAVE___INLINE - Success -- Checking for appropriate format for 64 bit long: -- Checking for appropriate format for 64 bit long: found "l" -- Looking for difftime -- Looking for difftime - found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for clock_gettime in posix4 -- Looking for clock_gettime in posix4 - not found -- Performing Other Test HAVE_DIRECT - Success -- Checking IF your system converts long double to (unsigned) long values with special algorithm... no -- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no -- Checking IF correctly converting long double to (unsigned) long long values... yes -- Checking IF correctly converting (unsigned) long long to long double values... yes -- Checking IF alignment restrictions are strictly enforced... yes -- Could NOT find ZLIB (missing: ZLIB_DIR) -- Filter ZLIB is ON CMake Warning (dev) at bcalm/gatb-core/gatb-core/thirdparty/hdf5/CMakeLists.txt:668 (set): implicitly converting 'INTEGER' to 'STRING' type. This warning is for project developers. Use -Wno-dev to suppress it. DYNAMIC BINARIES for gatb-h5dump -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/build.make bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/depend make -f bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/build.make bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/depend make -f bcalm/ext/gatb-core/thirdparty/CMakeFiles/hdf5_postbuild.dir/build.make bcalm/ext/gatb-core/thirdparty/CMakeFiles/hdf5_postbuild.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/DependInfo.cmake --color= make -f bcalm/ext/gatb-core/thirdparty/CMakeFiles/thirdparty_copy.dir/build.make bcalm/ext/gatb-core/thirdparty/CMakeFiles/thirdparty_copy.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/bcalm/gatb-core/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/CMakeFiles/hdf5_postbuild.dir/DependInfo.cmake --color= Scanning dependencies of target H5detect make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/build.make bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/bcalm/gatb-core/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/CMakeFiles/thirdparty_copy.dir/DependInfo.cmake --color= Scanning dependencies of target hdf5_postbuild make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f bcalm/ext/gatb-core/thirdparty/CMakeFiles/hdf5_postbuild.dir/build.make bcalm/ext/gatb-core/thirdparty/CMakeFiles/hdf5_postbuild.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target H5make_libsettings make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/build.make bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' Scanning dependencies of target thirdparty_copy make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f bcalm/ext/gatb-core/thirdparty/CMakeFiles/thirdparty_copy.dir/build.make bcalm/ext/gatb-core/thirdparty/CMakeFiles/thirdparty_copy.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/json [ 0%] Building C object bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src && /usr/bin/cc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5 -I/<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src -I/<>/obj-x86_64-linux-gnu/lib/kissplice -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -msse2 -msse4.2 -mpopcnt -std=c99 -fstdarg-opt -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -fmessage-length=0 -fPIE -w -o CMakeFiles/H5detect.dir/H5detect.c.o -c /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5detect.c [ 0%] Building C object bcalm/ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src && /usr/bin/cc -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5 -I/<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src -I/<>/obj-x86_64-linux-gnu/lib/kissplice -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -msse2 -msse4.2 -mpopcnt -std=c99 -fstdarg-opt -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -fmessage-length=0 -fPIE -w -o CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o -c /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5make_libsettings.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5ACpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E make_directory /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/BooPHF cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/BooPHF/BooPHF.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/BooPHF/ cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5ACprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/json/json.hpp /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/json/ cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5ACpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Apkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Built target thirdparty_copy make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/depend cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Aprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/thirdparty/kissreads/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/DependInfo.cmake --color= Scanning dependencies of target ks_kissreadsSplice make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Apublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/commons.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/commons.c.o -c /<>/thirdparty/kissreads/src/commons.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5B2pkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5B2private.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5B2public.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Linking C executable ../../../../../../lib/kissplice/H5make_libsettings cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/H5make_libsettings.dir/link.txt --verbose=1 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Bpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -msse2 -msse4.2 -mpopcnt -std=c99 -fstdarg-opt -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -fmessage-length=0 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o -o ../../../../../../lib/kissplice/H5make_libsettings cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Bprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/extension_algorithm.c.o -c /<>/thirdparty/kissreads/src/extension_algorithm.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Bpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5CSprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Built target H5make_libsettings make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/thirdparty/kissreads/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/DependInfo.cmake --color= cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Cpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 Scanning dependencies of target ks_kissreadsSNPS make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build.make thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/build cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Cprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Cpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/commons.c.o -c /<>/thirdparty/kissreads/src/commons.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Dpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/interface_libchash.c.o -c /<>/thirdparty/kissreads/src/interface_libchash.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Edefin.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Einit.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Epkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Eprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Epubgen.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Epublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Eterm.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDcore.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDdirect.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/extension_algorithm.c.o -c /<>/thirdparty/kissreads/src/extension_algorithm.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDfamily.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/libchash.c.o -c /<>/thirdparty/kissreads/src/libchash.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDlog.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDmpi.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDmpio.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDmulti.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 0%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/interface_libchash.c.o -c /<>/thirdparty/kissreads/src/interface_libchash.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDsec2.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDstdio.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FDwindows.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FLprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FOprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 1%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/libchash.c.o -c /<>/thirdparty/kissreads/src/libchash.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FSpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FSprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5FSpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Fpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Fprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Fpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Gpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Gprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Gpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HFpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HFprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HFpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HGpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HGprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HGpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HLpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HLprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HLpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5HPprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Ipkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Iprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Ipublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 2%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/outputs.c.o -c /<>/thirdparty/kissreads/src/outputs.c [ 2%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/outputs.c.o -c /<>/thirdparty/kissreads/src/outputs.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Lpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Lprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Lpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MFpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MFprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MMprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MMpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MPpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5MPprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 2%] Linking C executable ../../../../../../lib/kissplice/H5detect cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/H5detect.dir/link.txt --verbose=1 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Opkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 /usr/bin/cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -msse2 -msse4.2 -mpopcnt -std=c99 -fstdarg-opt -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -fmessage-length=0 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/H5detect.dir/H5detect.c.o -o ../../../../../../lib/kissplice/H5detect cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Oprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target H5detect make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/modules /<>/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_clean_duplicates.dir/DependInfo.cmake --color= cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Opublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 Scanning dependencies of target ks_clean_duplicates make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_clean_duplicates.dir/build.make modules/CMakeFiles/ks_clean_duplicates.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Oshared.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5PLextern.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5PLprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 3%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o -c /<>/modules/CleanDuplicates.cpp cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5PLpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Ppkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Pprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Ppublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5RCprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5RSprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Rpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Rprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Rpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5SLprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5SMpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5SMprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5STprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Spkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Sprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Spublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5TSprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 3%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/coherent_algorithm.c.o -c /<>/thirdparty/kissreads/src/coherent_algorithm.c [ 3%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/coherent_algorithm.c.o -c /<>/thirdparty/kissreads/src/coherent_algorithm.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Tpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Tprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Tpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5VMprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5WBprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 3%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/couple.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/couple.c.o -c /<>/thirdparty/kissreads/src/couple.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Zpkg.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Zprivate.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 3%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/couple.c.o -c /<>/thirdparty/kissreads/src/couple.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5Zpublic.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5api_adpt.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5overflow.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5private.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 3%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o [ 4%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/fragment_index.c.o -c /<>/thirdparty/kissreads/src/fragment_index.c cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/fragment_index.c.o -c /<>/thirdparty/kissreads/src/fragment_index.c cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5public.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5version.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/H5win32defs.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/bcalm/gatb-core/gatb-core/thirdparty/hdf5/src/hdf5.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 cd /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty && /usr/bin/cmake -E copy_if_different /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/thirdparty/hdf5/H5pubconf.h /<>/obj-x86_64-linux-gnu/bcalm/ext/gatb-core/include/None/hdf5 [ 4%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/kissReads.c.o -c /<>/thirdparty/kissreads/src/kissReads.c make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/kissReads.c.o -c /<>/thirdparty/kissreads/src/kissReads.c [ 5%] Built target hdf5_postbuild make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/modules /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/modules /<>/obj-x86_64-linux-gnu/modules/CMakeFiles/ks_bubble_enumeration.dir/DependInfo.cmake --color= Scanning dependencies of target ks_bubble_enumeration make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f modules/CMakeFiles/ks_bubble_enumeration.dir/build.make modules/CMakeFiles/ks_bubble_enumeration.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o -c /<>/modules/BubbleEnumeration.cpp [ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/list.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/list.c.o -c /<>/thirdparty/kissreads/src/list.c [ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/list.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -DINPUT_FROM_KISSPLICE -o CMakeFiles/ks_kissreadsSplice.dir/list.c.o -c /<>/thirdparty/kissreads/src/list.c [ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && /usr/bin/cc -I/<>/thirdparty/kissreads/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -DCLASSICAL_SPANNING -o CMakeFiles/ks_kissreadsSNPS.dir/tree.c.o -c /<>/thirdparty/kissreads/src/tree.c [ 5%] Building C object thirdparty/kissreads/src/CMakeFiles/ks_kissreadsSplice.dir/tree.c.o cd /<>/obj-x86_64-linux-gnu/thirdparty/kissreads/src && 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Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o -c /<>/modules/LabelledCEdge.cpp [ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o -c /<>/modules/NNode.cpp [ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o -c /<>/modules/NEdge.cpp [ 8%] Building CXX object modules/CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -c /<>/modules/Utils.cpp [ 8%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result 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Linking CXX executable ../lib/kissplice/ks_bubble_enumeration cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_bubble_enumeration.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_bubble_enumeration.dir/BubbleEnumeration.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CycleCompression.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CGraph.cpp.o CMakeFiles/ks_bubble_enumeration.dir/CEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/LabelledCEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NNode.cpp.o CMakeFiles/ks_bubble_enumeration.dir/NEdge.cpp.o CMakeFiles/ks_bubble_enumeration.dir/Utils.cpp.o -o ../lib/kissplice/ks_bubble_enumeration [ 9%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o -c /<>/modules/NNode.cpp [ 9%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o -c /<>/modules/NEdge.cpp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 9%] Built target ks_bubble_enumeration [ 9%] Building CXX object modules/CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/c++ -I/<>/modules -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -std=c++11 -o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -c /<>/modules/Utils.cpp [ 10%] Linking CXX executable ../lib/kissplice/ks_clean_duplicates cd /<>/obj-x86_64-linux-gnu/modules && /usr/bin/cmake -E cmake_link_script CMakeFiles/ks_clean_duplicates.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-result -Wno-parentheses -Wno-error=format-security -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ks_clean_duplicates.dir/CleanDuplicates.cpp.o CMakeFiles/ks_clean_duplicates.dir/CycleCompression.cpp.o CMakeFiles/ks_clean_duplicates.dir/NGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CGraph.cpp.o CMakeFiles/ks_clean_duplicates.dir/CEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/LabelledCEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/NNode.cpp.o CMakeFiles/ks_clean_duplicates.dir/NEdge.cpp.o CMakeFiles/ks_clean_duplicates.dir/Utils.cpp.o -o ../lib/kissplice/ks_clean_duplicates make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 10%] Built target ks_clean_duplicates make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:185: all] Error 2 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:36: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-09-20T06:24:19Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 87268 Build-Time: 25 Distribution: perl-5.32-throwaway Fail-Stage: build Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/kissplice_2.5.3-2.dsc Machine Architecture: amd64 Package: kissplice Package-Time: 38 Source-Version: 2.5.3-2 Space: 87268 Status: attempted Version: 2.5.3-2 -------------------------------------------------------------------------------- Finished at 2020-09-20T06:24:19Z Build needed 00:00:38, 87268k disk space