sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | prime-phylo 1.0.11-11 (amd64) Sun, 04 Aug 2024 22:57:36 +0000 | +==============================================================================+ Package: prime-phylo Version: 1.0.11-11 Source Version: 1.0.11-11 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-69059a2e-7c3e-475e-8559-d8c811976e65' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-11 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup prime-phylo_1.0.11-11 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/prime-phylo-hMYLm1/resolver-Q2yRIa' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://localhost:3142/debian sid InRelease [198 kB] Get:3 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [21.8 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [21.8 kB] Get:5 http://deb.debian.org/debian unstable InRelease [198 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [23.4 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [23.4 kB] Fetched 569 kB in 6s (103 kB/s) 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/prime-phylo_1.0.11-11.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/prime-phylo-hMYLm1/prime-phylo-1.0.11' with '<>' I: NOTICE: Log filtering will replace 'build/prime-phylo-hMYLm1' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [787 B] Get:5 copy:/<>/apt_archive ./ Packages [819 B] Fetched 2215 B in 0s (0 B/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 bison bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file flex gengetopt gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libcbor0.10 libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librhash0 librtmp1 libssh2-1t64 libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 libz3-4 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make flex-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-14-multilib gfortran-14-doc libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost-graph1.83-dev libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc liblzma-doc openmpi-doc pciutils gcj-jdk pkgconf m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: libfl-dev curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common krb5-locales libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: autoconf automake autopoint autotools-dev bison bsdextrautils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file flex gengetopt gettext gettext-base gfortran gfortran-14 gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu groff-base ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libarchive13t64 libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.83-dev libboost-mpi1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libcbor0.10 libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libexpat1 libfabric1 libfakeroot libfido2-1 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu72 libjs-jquery libjs-jquery-ui libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm17t64 libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1t64 libmunge2 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3t64 libpciaccess0 libpipeline1 libpmix-dev libpmix2t64 libproc2-0 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librhash0 librtmp1 libssh2-1t64 libtool libuchardet0 libucx0 libuv1t64 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-dev libxnvctrl0 libz3-4 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf procps sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 138 newly installed, 0 to remove and 0 not upgraded. Need to get 154 MB of archives. After this operation, 756 MB of additional disk space will be used. 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amd64 1.6.3-3 [8952 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.8p1-2 [964 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 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http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.30.2-1 [2268 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.30.2-1 [11.4 MB] Get:46 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:52 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 gengetopt amd64 2.23+dfsg1-1 [173 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-1 [837 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-1 [880 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-1 [11.7 MB] Get:64 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-1 [11.6 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2 [1284 B] Get:66 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.1.0-2 [1436 B] Get:67 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2 [61.6 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2 [343 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5 [207 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-15 [23.6 MB] Get:74 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get:75 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.122-1 [7992 B] Get:76 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.122-1 [38.7 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [22.2 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-4 [8770 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3.1 [10.6 MB] Get:85 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:86 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0.5.15-4 [19.8 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.0-2 [17.9 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.3-2 [658 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2 [27.7 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2 [43.3 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83.0 amd64 1.83.0-3.1 [271 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2 [647 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.0-2 [251 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.3-2 [3954 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get:131 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83-dev amd64 1.83.0-3.1 [290 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get:133 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get:134 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5 [10.4 MB] Get:135 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg-3+b1 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 154 MB in 1s (182 MB/s) Selecting previously unselected package m4. 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Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up fakeroot (1.35.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libboost-serialization1.83.0:amd64 (1.83.0-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmunge2:amd64 (0.5.15-4) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up libhwloc15:amd64 (2.11.0-2) ... Setting up autopoint (0.22.5-2) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up icu-devtools (72.1-5) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libltdl7:amd64 (2.4.7-7+b1) ... Setting up libgfortran5:amd64 (14.2.0-1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnuma1:amd64 (2.0.18-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b1) ... Setting up librhash0:amd64 (1.4.3-3+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up libnl-3-200:amd64 (3.7.0-0.3) ... 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 libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (4.1.6-13.3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up cmake-data (3.30.2-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.15.0-1) ... Setting up libdrm-common (2.4.122-1) ... Setting up libicu-dev:amd64 (72.1-5) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 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 libgfortran-14-dev:amd64 (14.2.0-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up flex (2.6.4-8.2+b2) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-3.1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.18-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-7+b1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg-3+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-15) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libboost-serialization-dev:amd64 (1.83.0.2+b2) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.122-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-5) ... Setting up libhwloc-dev:amd64 (2.11.0-2) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up gfortran-14 (14.2.0-1) ... Setting up libarchive13t64:amd64 (3.7.2-2.1) ... Setting up libdrm-amdgpu1:amd64 (2.4.122-1) ... Setting up libibverbs1:amd64 (52.0-2) ... Setting up libcurl4t64:amd64 (8.9.1-1) ... Setting up ibverbs-providers:amd64 (52.0-2) ... Setting up openssh-client (1:9.8p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhwloc-plugins:amd64 (2.11.0-2) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.1.0-2) ... Setting up gfortran (4:14.1.0-2) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up libpmix2t64:amd64 (5.0.3-2) ... Setting up cmake (3.30.2-1) ... Setting up librdmacm1t64:amd64 (52.0-2) ... Setting up libpmix-dev:amd64 (5.0.3-2) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up debhelper (13.16) ... Setting up libibverbs-dev:amd64 (52.0-2) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libamdhip64-5 (5.7.1-4) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up libboost-mpi1.83.0 (1.83.0-3.1) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.17) ... Setting up libboost-mpi1.83-dev (1.83.0-3.1) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bison_2:3.8.2+dfsg-1+b1 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 cmake_3.30.2-1 cmake-data_3.30.2-1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 flex_2.6.4-8.2+b2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 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libevent-pthreads-2.1-7t64_2.1.12-stable-10 libexpat1_2.6.2-1 libfabric1_1.17.0-3+b1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfido2-1_1.15.0-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgfortran-14-dev_14.2.0-1 libgfortran5_14.2.0-1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhsa-runtime64-1_5.7.1-2 libhsakmt1_5.7.0-1 libhwasan0_14.2.0-1 libhwloc-dev_2.11.0-2 libhwloc-plugins_2.11.0-2 libhwloc15_2.11.0-2 libibmad5_52.0-2 libibumad3_52.0-2 libibverbs-dev_52.0-2 libibverbs1_52.0-2 libicu-dev_72.1-5 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-ui_1.13.2+dfsg-1 libjsoncpp25_1.9.5-6+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 liblapack-dev_3.12.0-3 liblapack3_3.12.0-3 libldap-2.5-0_2.5.18+dfsg-2+b1 libllvm17t64_1:17.0.6-15 liblsan0_14.2.0-1 libltdl-dev_2.4.7-7+b1 libltdl7_2.4.7-7+b1 liblz4-1_1.9.4-3 liblzma-dev_5.6.2-2 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libmunge2_0.5.15-4 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-2 libnl-3-200_3.7.0-0.3 libnl-3-dev_3.7.0-0.3 libnl-route-3-200_3.7.0-0.3 libnl-route-3-dev_3.7.0-0.3 libnpth0t64_1.6-3.1 libnuma-dev_2.0.18-1 libnuma1_2.0.18-1 libopenmpi-dev_4.1.6-13.3 libopenmpi3t64_4.1.6-13.3 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpciaccess0_0.17-3+b1 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-1 libpipeline1_1.5.7-2 libpmix-dev_5.0.3-2 libpmix2t64_5.0.3-2 libproc2-0_2:4.0.4-5 libpsl5t64_0.21.2-1.1 libpsm-infinipath1_3.3+20.604758e7-6.3 libpsm2-2_11.2.185-2.1 libquadmath0_14.2.0-1 librdmacm1t64_52.0-2 libreadline8t64_8.2-4 librhash0_1.4.3-3+b1 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssh2-1t64_1.11.0-7 libssl3t64_3.3.1-2 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libucx0_1.17.0+ds-3 libudev1_256.4-2 libunistring5_1.2-1 libuuid1_2.40.2-1 libuv1t64_1.48.0-5 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b1 libxml2_2.12.7+dfsg-3+b1 libxml2-dev_2.12.7+dfsg-3+b1 libxnvctrl0_535.171.04-1 libxxhash0_0.8.2-2+b1 libz3-4_4.8.12-3.1+b2 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 mpi-default-dev_1.17 ncurses-base_6.5-2 ncurses-bin_6.5-2 ocl-icd-libopencl1_2.3.2-1+b1 openmpi-bin_4.1.6-13.3 openmpi-common_4.1.6-13.3 openssh-client_1:9.8p1-2 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-5 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: prime-phylo Binary: prime-phylo Architecture: any Version: 1.0.11-11 Maintainer: Debian Med Packaging Team Uploaders: Erik Sjolund , Andreas Tille Homepage: http://prime.sbc.su.se Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/prime-phylo Vcs-Git: https://salsa.debian.org/med-team/prime-phylo.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev Package-List: prime-phylo deb science optional arch=any Checksums-Sha1: 1dd3b086599e29f6a17319f8ebe294cd6eed0c07 750651 prime-phylo_1.0.11.orig.tar.gz 4b4d37421b0bada8f13c5d0f5171b84cd7d63f26 9072 prime-phylo_1.0.11-11.debian.tar.xz Checksums-Sha256: 5d46b4e528417bb4a0be56756069f255f86ab58b28b55fa6a96983f10585bd8d 750651 prime-phylo_1.0.11.orig.tar.gz c6efedce9ab0d79d8bb5619b859c0af34c505dbbac4442b266b79b0a75ca314a 9072 prime-phylo_1.0.11-11.debian.tar.xz Files: 0356071434de01edf92a1b9182ed6ef1 750651 prime-phylo_1.0.11.orig.tar.gz 072ed1ec4c5b69b37b5e87d68141c646 9072 prime-phylo_1.0.11-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYZGCQACgkQPCZ2P2xn 5uI8sg//QyIrmizClvLu9dIH3QvhVxZeMsXascshFHYuwu8Z16jiAgxE5y/XQ6uG 4bSbQkoF4vOJRhppMTDdnXPDz1JTrlu9X/wuxzn2EAo5m/1HiVi/Vs+Lxz4kN8RQ j+ngp6T8vwnGkt/zjVTkPXjK5CqIvyDznNTPtNyJjDNfrwDIV7xG5ptaPr2XYiQf MXexFAG5RS4WNPJhu+1orcqXRfm5XKhz7NTXcKq3qV83S/UAGAWoqQWU5lVmFSPV xeWhYVU1ijEiE1bA4LZiSsfOFwlTricjaye47egdbIZ+CloNYRsdsXJsWzJJp98a lpCnlw2gP7rtksf3Bnkeolc5NC8B8UX+CG9YQIcA1W+gPn37u4Jye1BQuhR39lwh rLa6X1Z5ZiIZvgj5yIdE7sBMykej8qCVf0o4HunB++kYzyWIYC7ZWdW0xz6WNE5d +RJNf2GNPtG7ZTNQnYv67pg3VskimV7Ie+772nhxDcUsf4MSR3q9aJ/rWKVPmG+L XzT3XqLV7jDHPp3dFGvD7DnpRG5rKJtO3N/HbHUKJs4AmVHh1XYTvODNMVArIc3i KXNQzhdDt/+PCiX3/6uWbbkawt7hbsIUiOPPYRmDuLkdmQb7MbPnuCHVMxJ/EzNX r1Ue3Id8N+peoDyfBEYub0hmALo9Lz+9xSj5XS3fEG/fMBQSkuM= =Eki9 -----END PGP SIGNATURE----- gpgv: Signature made Fri Apr 12 11:16:52 2024 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./prime-phylo_1.0.11-11.dsc: no acceptable signature found dpkg-source: info: extracting prime-phylo in /<> dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: unpacking prime-phylo_1.0.11-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-Boost160.patch dpkg-source: info: applying fix-gcc-8.patch dpkg-source: info: applying 0003-Fix-build-with-Boost-1.67.patch dpkg-source: info: applying 0004-fix-gcc10-build.patch dpkg-source: info: applying fix-ftbfs-with-gcc13.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-11 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network prime-phylo_1.0.11-11 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en 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-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-69059a2e-7c3e-475e-8559-d8c811976e65 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building prime-phylo using existing ./prime-phylo_1.0.11.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building prime-phylo in prime-phylo_1.0.11-11.debian.tar.xz dpkg-source: info: building prime-phylo in prime-phylo_1.0.11-11.dsc debian/rules binary dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ -Dofficial_binary_packaging=on \ -Dprime_dynamic=on \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. CMake Deprecation Warning at CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 14.2.0 -- 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 -- The Fortran compiler identification is GNU 14.2.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- The C compiler identification is GNU 14.2.0 -- 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 -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so hittade /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/libmpi_usempif08.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") CMake Warning (dev) at src/cxx/CMakeLists.txt:92 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.40.0") found components: mpi serialization -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.12.7") mpilib is /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi included path is CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDTLSR". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDTLSR/CMakeLists.txt:30 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "primeDLRS". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/applications/primeDLRS/CMakeLists.txt:27 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/cxx/CMakeLists.txt:366 (get_target_property): Policy CMP0026 is not set: Disallow use of the LOCATION target property. Run "cmake --help-policy CMP0026" for policy details. Use the cmake_policy command to set the policy and suppress this warning. The LOCATION property should not be read from target "showtree". Use the target name directly with add_custom_command, or use the generator expression $, as appropriate. Call Stack (most recent call first): src/cxx/tools/showtree/CMakeLists.txt:12 (prime_add_tests) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:120 (if): Policy CMP0053 is not set: Simplify variable reference and escape sequence evaluation. Run "cmake --help-policy CMP0053" for policy details. Use the cmake_policy command to set the policy and suppress this warning. For input: '@CMAKE_SOURCE_DIR@/excluded_from_release' the old evaluation rules produce: '/<>/excluded_from_release' but the new evaluation rules produce: '@CMAKE_SOURCE_DIR@/excluded_from_release' Using the old result for compatibility since the policy is not set. This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (5.4s) CMake Warning (dev) at src/cxx/tools/tree2leafnames/CMakeLists.txt:4 (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: /<>/src/cxx/tools/tree2leafnames/tree2leafnames.cc This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 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 src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 0%] [BISON][MyParser2] Building parser with bison 3.8.2 cd /<>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] gb.y:259.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother] 259 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} | ^~~~~~~~~~~~ [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /<>/src/cxx/libraries/sfile && /usr/bin/flex -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/sfile /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gbread.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /<>/src/cxx/libraries/sfile/gbread.c [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<>/src/cxx/libraries/sfile/sfile.c /<>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’: /<>/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 265 | printf("%9d", char_counter + 1); | ^~~~~ ~~~~~~~~~~~~~~~~ | | | long int /<>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c /<>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_add_comment’: /<>/src/cxx/libraries/sfile/sfile.c:303:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 303 | tmp->text = strdup(s); | ^~ /<>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’ 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/cxx/libraries/sfile/sfile.c:304:20: warning: array subscript ‘struct comment[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 304 | tmp->next = NULL; | ^~ /<>/src/cxx/libraries/sfile/sfile.c:301:38: note: object of size 8 allocated by ‘malloc’ 301 | tmp = (struct comment *) malloc(sizeof(struct comment *)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ seqreader.l: In function ‘seq_read’: seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable] /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function] 1864 | static int input (void) | ^~~~~ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function] 1821 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries/prime -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y: In function ‘add_to_seq’: gb.y:403:9: warning: unused variable ‘new_buf’ [-Wunused-variable] [ 4%] Linking C shared library libprime-phylo-sfile.so cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so "CMakeFiles/prime-phylo-sfile.dir/gbread.c.o" "CMakeFiles/prime-phylo-sfile.dir/sfile.c.o" "CMakeFiles/prime-phylo-sfile.dir/lexer.c.o" "CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o" -Wl,-rpath,:::::::::::::::::::: make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 [ 5%] [BISON][MyParser] Building parser with bison 3.8.2 cd /<>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l cd /<>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 108 | %expect 4 | ^~~~~~~ cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src/cxx/libraries/prime /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o [ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /<>/src/cxx/libraries/prime/NHXnode.c cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /<>/src/cxx/libraries/prime/NHXtree.c /<>/src/cxx/libraries/prime/NHXnode.c: In function ‘NHX_debug_print’: /<>/src/cxx/libraries/prime/NHXnode.c:155:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=] 155 | fprintf(stderr, "BW:\t%d\n", l->arg.t); | ~^ ~~~~~~~~ | | | | int double | %f [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -MF CMakeFiles/prime-phylo.dir/NHXannotation.c.o.d -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /<>/src/cxx/libraries/prime/NHXannotation.c [ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c /<>/src/cxx/libraries/prime/NHXannotation.c: In function ‘new_annotation’: /<>/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: ‘__builtin_strncpy’ specified bound 5 equals destination size [-Wstringop-truncation] 80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH); | ^ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: ‘input’ defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: ‘yyunput’ defined but not used [-Wunused-function] 1554 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/<>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /<>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y: In function ‘read_tree’: NHXparse.y:354:11: error: passing argument 1 of ‘close’ makes integer from pointer without a cast [-Wint-conversion] In file included from NHXparse.y:5: /usr/include/unistd.h:358:23: note: expected ‘int’ but argument is of type ‘FILE *’ 358 | extern int close (int __fd); | ~~~~^~~~ NHXparse.y: In function ‘read_tree_string’: NHXparse.y:402:20: warning: passing argument 1 of ‘read_from_string’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] NHXparse.y:19:36: note: expected ‘char *’ but argument is of type ‘const char *’ make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:147: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:314: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[1]: *** [Makefile:159: all] Error 2 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:12: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-08-04T22:58:10Z 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: 8384 Build-Time: 8 Distribution: perl-5.40-throwaway Fail-Stage: build Host Architecture: amd64 Install-Time: 17 Job: /srv/debomatic/incoming/prime-phylo_1.0.11-11.dsc Machine Architecture: amd64 Package: prime-phylo Package-Time: 34 Source-Version: 1.0.11-11 Space: 8384 Status: attempted Version: 1.0.11-11 -------------------------------------------------------------------------------- Finished at 2024-08-04T22:58:10Z Build needed 00:00:34, 8384k disk space