sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | phyml 3:3.3.20190909-1 (armel) Thu, 07 Nov 2019 18:23:12 +0000 | +==============================================================================+ Package: phyml Version: 3:3.3.20190909-1 Source Version: 3:3.3.20190909-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-198b5c2e-60c8-4879-badf-d6a3f7ee1e61' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-6FZNVF/resolver-U8AEbw' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [139 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-07-0813.42.pdiff [3590 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-07-1413.06.pdiff [10.5 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-11-07-1413.06.pdiff [10.5 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-07-0813.42.pdiff [2693 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-07-1413.06.pdiff [11.7 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-11-07-1413.06.pdiff [11.7 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main armel Packages [7893 kB] Fetched 8116 kB in 2s (4041 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 | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phyml.git Please use: git clone https://salsa.debian.org/med-team/phyml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2257 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190909-1 (dsc) [2098 B] Get:2 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190909-1 (tar) [2238 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190909-1 (diff) [17.2 kB] Fetched 2257 kB in 0s (40.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phyml-6FZNVF/phyml-3.3.20190909' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-6FZNVF' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [425 B] Get:5 copy:/<>/apt_archive ./ Packages [512 B] Fetched 1894 B in 0s (90.9 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 binutils-arm-linux-gnueabi bsdmainutils chrpath cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base ibverbs-providers:armel intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libedit2 libelf1 libevent-2.1-6:armel libevent-core-2.1-6:armel libevent-pthreads-2.1-6:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel libgcc1-armel-cross libgfortran5:armel libglib2.0-0 libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2 libhwloc-dev:armel libhwloc-plugins:armel libhwloc5:armel libibverbs-dev:armel libibverbs1:armel libicu63 libicu63:armel libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev:armel libltdl7:armel liblzma5:armel libmagic-mgc libmagic1 libncurses6 libnl-3-200:armel libnl-3-dev:armel libnl-route-3-200:armel libnl-route-3-dev:armel libopenmpi-dev:armel libopenmpi3:armel libpciaccess0:armel libpipeline1 libpmix2:armel libsigsegv2 libssl1.1 libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:armel libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db ocl-icd-libopencl1:armel openmpi-bin:armel openmpi-common openssh-client pkg-config po-debconf sensible-utils ucf zlib1g:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch gcc-9-doc libstdc++6-9-dbg-armel-cross libgcc1-dbg-armel-cross libgomp1-dbg-armel-cross libitm1-dbg-armel-cross libatomic1-dbg-armel-cross libasan5-dbg-armel-cross liblsan0-dbg-armel-cross libtsan0-dbg-armel-cross libubsan1-dbg-armel-cross libquadmath0-dbg-armel-cross manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel manpages-dev:armel krb5-doc krb5-user libhwloc-contrib-plugins:armel libtool-doc:armel openmpi-doc:armel pciutils:armel libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser opencl-icd:armel gfortran:armel | fortran-compiler:armel keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils chrpath cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base ibverbs-providers:armel intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libdebhelper-perl libdebian-dpkgcross-perl libedit2 libelf1 libevent-2.1-6:armel libevent-core-2.1-6:armel libevent-pthreads-2.1-6:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc1:armel libgcc1-armel-cross libgfortran5:armel libglib2.0-0 libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2 libhwloc-dev:armel libhwloc-plugins:armel libhwloc5:armel libibverbs-dev:armel libibverbs1:armel libicu63 libicu63:armel libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libltdl-dev:armel libltdl7:armel liblzma5:armel libmagic-mgc libmagic1 libncurses6 libnl-3-200:armel libnl-3-dev:armel libnl-route-3-200:armel libnl-route-3-dev:armel libopenmpi-dev:armel libopenmpi3:armel libpciaccess0:armel libpipeline1 libpmix2:armel libsigsegv2 libssl1.1 libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:armel libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db ocl-icd-libopencl1:armel openmpi-bin:armel openmpi-common openssh-client pkg-config po-debconf sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 79.5 MB of archives. After this operation, 310 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-1 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-17 [194 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-6 [253 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-6 [119 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-6 [67.2 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libedit2 amd64 3.1-20191025-1 [95.1 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 openssh-client amd64 1:8.1p1-1 [830 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.33.1-2 [2721 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-15cross1 [194 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-15cross1 [6811 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-15cross1 [189 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-1cross7 [1139 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armel-cross all 1:9.2.1-15cross1 [39.1 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 9.2.1-15cross1 [74.8 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 9.2.1-15cross1 [8936 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-15cross1 [340 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 9.2.1-15cross1 [376 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 9.2.1-15cross1 [110 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-15cross1 [646 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-15cross1 [7153 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.2.9-2cross7 [1312 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-1cross7 [2155 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-15cross1 [1708 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-15cross1 [7388 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-11 [547 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.7.1 [173 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.2-1 [23.6 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.2-1 [14.6 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-1 [81.8 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.2-3 [1318 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.7.1 [997 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armel libgcc1 armel 1:9.2.1-17 [39.0 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-3 [2348 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armel libnl-3-200 armel 3.4.0-1+b1 [55.7 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main armel libnl-route-3-200 armel 3.4.0-1+b1 [134 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armel libibverbs1 armel 26.0-2 [47.0 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armel ibverbs-providers armel 26.0-2 [24.6 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-17 [346 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 9.2.1-17 [9092 B] Get:92 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.3.7-1 [977 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-3 [2195 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armel libevent-2.1-6 armel 2.1.8-stable-4 [159 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armel libevent-core-2.1-6 armel 2.1.8-stable-4 [118 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armel libevent-pthreads-2.1-6 armel 2.1.8-stable-4 [47.6 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 9.2.1-17 [76.7 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 9.2.1-17 [415 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 9.2.1-17 [111 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-17 [642 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libgfortran5 armel 9.2.1-17 [246 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libltdl7 armel 2.4.6-11 [387 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel libhwloc5 armel 1.11.13-1 [88.6 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libltdl-dev armel 2.4.6-11 [160 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libhwloc-dev armel 1.11.13-1 [153 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-1+b1 [84.7 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libpciaccess0 armel 0.14-1 [50.9 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libicu63 armel 63.2-2 [7979 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel liblzma5 armel 5.2.4-1+b1 [144 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libxml2 armel 2.9.4+dfsg1-7+b3 [572 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel ocl-icd-libopencl1 armel 2.2.12-2 [36.3 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main armel libhwloc-plugins armel 1.11.13-1 [17.3 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libnl-3-dev armel 3.4.0-1+b1 [97.1 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libnl-route-3-dev armel 3.4.0-1+b1 [158 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libibverbs-dev armel 26.0-2 [167 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel libpmix2 armel 3.1.4-1 [440 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel libopenmpi3 armel 3.1.3-11 [1828 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel openmpi-bin armel 3.1.3-11 [200 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libopenmpi-dev armel 3.1.3-11 [963 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-17 [1738 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main amd64 pkg-config amd64 0.29-6 [63.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.5 MB in 1s (56.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 14998 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.0-1_amd64.deb ... Unpacking man-db (2.9.0-1) ... 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Selecting previously unselected package libc6-dev:armel. Preparing to unpack .../091-libc6-dev_2.29-3_armel.deb ... Unpacking libc6-dev:armel (2.29-3) ... Selecting previously unselected package libevent-2.1-6:armel. Preparing to unpack .../092-libevent-2.1-6_2.1.8-stable-4_armel.deb ... Unpacking libevent-2.1-6:armel (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:armel. Preparing to unpack .../093-libevent-core-2.1-6_2.1.8-stable-4_armel.deb ... Unpacking libevent-core-2.1-6:armel (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:armel. Preparing to unpack .../094-libevent-pthreads-2.1-6_2.1.8-stable-4_armel.deb ... Unpacking libevent-pthreads-2.1-6:armel (2.1.8-stable-4) ... Selecting previously unselected package libgomp1:armel. Preparing to unpack .../095-libgomp1_9.2.1-17_armel.deb ... Unpacking libgomp1:armel (9.2.1-17) ... Selecting previously unselected package libstdc++6:armel. 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Preparing to unpack .../102-libltdl-dev_2.4.6-11_armel.deb ... Unpacking libltdl-dev:armel (2.4.6-11) ... Selecting previously unselected package libhwloc-dev:armel. Preparing to unpack .../103-libhwloc-dev_1.11.13-1_armel.deb ... Unpacking libhwloc-dev:armel (1.11.13-1) ... Selecting previously unselected package zlib1g:armel. Preparing to unpack .../104-zlib1g_1%3a1.2.11.dfsg-1+b1_armel.deb ... Unpacking zlib1g:armel (1:1.2.11.dfsg-1+b1) ... Selecting previously unselected package libpciaccess0:armel. Preparing to unpack .../105-libpciaccess0_0.14-1_armel.deb ... Unpacking libpciaccess0:armel (0.14-1) ... Selecting previously unselected package libicu63:armel. Preparing to unpack .../106-libicu63_63.2-2_armel.deb ... Unpacking libicu63:armel (63.2-2) ... Selecting previously unselected package liblzma5:armel. Preparing to unpack .../107-liblzma5_5.2.4-1+b1_armel.deb ... Unpacking liblzma5:armel (5.2.4-1+b1) ... Selecting previously unselected package libxml2:armel. Preparing to unpack .../108-libxml2_2.9.4+dfsg1-7+b3_armel.deb ... Unpacking libxml2:armel (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package ocl-icd-libopencl1:armel. Preparing to unpack .../109-ocl-icd-libopencl1_2.2.12-2_armel.deb ... Unpacking ocl-icd-libopencl1:armel (2.2.12-2) ... Selecting previously unselected package libhwloc-plugins:armel. Preparing to unpack .../110-libhwloc-plugins_1.11.13-1_armel.deb ... Unpacking libhwloc-plugins:armel (1.11.13-1) ... Selecting previously unselected package libnl-3-dev:armel. Preparing to unpack .../111-libnl-3-dev_3.4.0-1+b1_armel.deb ... Unpacking libnl-3-dev:armel (3.4.0-1+b1) ... Selecting previously unselected package libnl-route-3-dev:armel. Preparing to unpack .../112-libnl-route-3-dev_3.4.0-1+b1_armel.deb ... Unpacking libnl-route-3-dev:armel (3.4.0-1+b1) ... Selecting previously unselected package libibverbs-dev:armel. Preparing to unpack .../113-libibverbs-dev_26.0-2_armel.deb ... Unpacking libibverbs-dev:armel (26.0-2) ... Selecting previously unselected package libpmix2:armel. Preparing to unpack .../114-libpmix2_3.1.4-1_armel.deb ... Unpacking libpmix2:armel (3.1.4-1) ... Selecting previously unselected package libopenmpi3:armel. Preparing to unpack .../115-libopenmpi3_3.1.3-11_armel.deb ... Unpacking libopenmpi3:armel (3.1.3-11) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../116-openmpi-common_3.1.3-11_all.deb ... Unpacking openmpi-common (3.1.3-11) ... Selecting previously unselected package openmpi-bin:armel. Preparing to unpack .../117-openmpi-bin_3.1.3-11_armel.deb ... Unpacking openmpi-bin:armel (3.1.3-11) ... Selecting previously unselected package libopenmpi-dev:armel. Preparing to unpack .../118-libopenmpi-dev_3.1.3-11_armel.deb ... Unpacking libopenmpi-dev:armel (3.1.3-11) ... Selecting previously unselected package libstdc++-9-dev:armel. Preparing to unpack .../119-libstdc++-9-dev_9.2.1-17_armel.deb ... Unpacking libstdc++-9-dev:armel (9.2.1-17) ... Selecting previously unselected package pkg-config. Preparing to unpack .../120-pkg-config_0.29-6_amd64.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package sbuild-build-depends-main-dummy:armel. Preparing to unpack .../121-sbuild-build-depends-main-dummy_0.invalid.0_armel.deb ... Unpacking sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libfile-which-perl (1.23-1) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up binutils-arm-linux-gnueabi (2.33.1-2) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.2-3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-2) ... Setting up libdebhelper-perl (12.7.1) ... Setting up libmagic1:amd64 (1:5.37-6) ... Setting up linux-libc-dev:armel (5.3.7-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-6) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up linux-libc-dev-armel-cross (5.2.9-2cross7) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-15cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libncurses6:amd64 (6.1+20191019-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.2.1-15cross1) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up gcc-9-cross-base (9.2.1-15cross1) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up libc6-armel-cross (2.29-1cross7) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up openmpi-common (3.1.3-11) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libc6-dev-armel-cross (2.29-1cross7) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up chrpath (0.16-2+b1) ... Setting up gcc-9-base:armel (9.2.1-17) ... Setting up libfile-stripnondeterminism-perl (1.6.2-1) ... Setting up libgomp1-armel-cross (9.2.1-15cross1) ... Setting up libtool (2.4.6-11) ... Setting up libedit2:amd64 (3.1-20191025-1) ... Setting up m4 (1.4.18-4) ... Setting up libatomic1-armel-cross (9.2.1-15cross1) ... Setting up libgcc1-armel-cross (1:9.2.1-15cross1) ... Setting up libasan5-armel-cross (9.2.1-15cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dh-strip-nondeterminism (1.6.2-1) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up openssh-client (1:8.1p1-1) ... Setting up libstdc++6-armel-cross (9.2.1-15cross1) ... Setting up man-db (2.9.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libubsan1-armel-cross (9.2.1-15cross1) ... Setting up libgcc-9-dev-armel-cross (9.2.1-15cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up po-debconf (1.0.21) ... Setting up libstdc++-9-dev-armel-cross (9.2.1-15cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.2.1-15cross1) ... Setting up g++-9-arm-linux-gnueabi (9.2.1-15cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libgcc1:armel (1:9.2.1-17) ... Setting up dh-autoreconf (19) ... Setting up libc6:armel (2.29-3) ... Setting up ocl-icd-libopencl1:armel (2.2.12-2) ... Setting up libnl-3-200:armel (3.4.0-1+b1) ... Setting up libc6-dev:armel (2.29-3) ... Setting up libstdc++6:armel (9.2.1-17) ... Setting up liblzma5:armel (5.2.4-1+b1) ... Setting up debhelper (12.7.1) ... Setting up zlib1g:armel (1:1.2.11.dfsg-1+b1) ... Setting up libgomp1:armel (9.2.1-17) ... Setting up libicu63:armel (63.2-2) ... Setting up libnl-route-3-200:armel (3.4.0-1+b1) ... Setting up libasan5:armel (9.2.1-17) ... Setting up libatomic1:armel (9.2.1-17) ... Setting up libltdl7:armel (2.4.6-11) ... Setting up libevent-core-2.1-6:armel (2.1.8-stable-4) ... Setting up libgfortran5:armel (9.2.1-17) ... Setting up libevent-2.1-6:armel (2.1.8-stable-4) ... Setting up libubsan1:armel (9.2.1-17) ... Setting up libnl-3-dev:armel (3.4.0-1+b1) ... Setting up libxml2:armel (2.9.4+dfsg1-7+b3) ... Setting up libevent-pthreads-2.1-6:armel (2.1.8-stable-4) ... Setting up libpciaccess0:armel (0.14-1) ... Setting up libibverbs1:armel (26.0-2) ... Setting up ibverbs-providers:armel (26.0-2) ... Setting up libhwloc5:armel (1.11.13-1) ... Setting up libhwloc-plugins:armel (1.11.13-1) ... Setting up libgcc-9-dev:armel (9.2.1-17) ... Setting up libnl-route-3-dev:armel (3.4.0-1+b1) ... Setting up libltdl-dev:armel (2.4.6-11) ... Setting up libhwloc-dev:armel (1.11.13-1) ... Setting up libstdc++-9-dev:armel (9.2.1-17) ... Setting up libpmix2:armel (3.1.4-1) ... Setting up libopenmpi3:armel (3.1.3-11) ... Setting up libibverbs-dev:armel (26.0-2) ... Setting up openmpi-bin:armel (3.1.3-11) ... 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:armel (3.1.3-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/openmpi/include to provide /usr/include/arm-linux-gnueabi/mpi (mpi-arm-linux-gnueabi) in auto mode Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.29-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.33.1-2 dpkg-dev_1.19.7 g++-8_8.3.0-23 g++-9_9.2.1-17 gcc-8_8.3.0-23 gcc-9_9.2.1-17 libc6-dev_2.29-3 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-17 libstdc++-9-dev-armel-cross_9.2.1-15cross1 libstdc++6_9.2.1-17 libstdc++6-armel-cross_9.2.1-15cross1 linux-libc-dev_5.3.7-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.33.1-2 binutils-arm-linux-gnueabi_2.33.1-2 binutils-common_2.33.1-2 binutils-x86-64-linux-gnu_2.33.1-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 chrpath_0.16-2+b1 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-23 cpp-9_9.2.1-17 cpp-9-arm-linux-gnueabi_9.2.1-15cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debian-archive-keyring_2019.1 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.2-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-8_8.3.0-23 g++-9_9.2.1-17 g++-9-arm-linux-gnueabi_9.2.1-15cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-8_8.3.0-23 gcc-8-base_8.3.0-23 gcc-9_9.2.1-17 gcc-9-arm-linux-gnueabi_9.2.1-15cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-15cross1 gcc-9-base_9.2.1-17 gcc-9-cross-base_9.2.1-15cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3+b1 hostname_3.22+b1 ibverbs-providers_26.0-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-17 libasan5-armel-cross_9.2.1-15cross1 libatomic1_9.2.1-17 libatomic1-armel-cross_9.2.1-15cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3 libc-dev-bin_2.29-3 libc6_2.29-3 libc6-armel-cross_2.29-1cross7 libc6-dev_2.29-3 libc6-dev-armel-cross_2.29-1cross7 libcap-ng0_0.7.9-2.1 libcc1-0_9.2.1-17 libcom-err2_1.45.4-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libedit2_3.1-20191025-1 libelf1_0.176-1.1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.2-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-23 libgcc-9-dev_9.2.1-17 libgcc-9-dev-armel-cross_9.2.1-15cross1 libgcc1_1:9.2.1-17 libgcc1-armel-cross_1:9.2.1-15cross1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-17 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-17 libgomp1-armel-cross_9.2.1-15cross1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_1.11.13-1 libhwloc-plugins_1.11.13-1 libhwloc5_1.11.13-1 libibverbs-dev_26.0-2 libibverbs1_26.0-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl21_0.21-2 libitm1_9.2.1-17 libk5crypto3_1.17-6 libkeyutils1_1.6-6 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblocale-gettext-perl_1.07-4 liblsan0_9.2.1-17 libltdl-dev_2.4.6-11 libltdl7_2.4.6-11 liblz4-1_1.9.2-1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-23 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnl-3-200_3.4.0-1+b1 libnl-3-dev_3.4.0-1+b1 libnl-route-3-200_3.4.0-1+b1 libnl-route-3-dev_3.4.0-1+b1 libopenmpi-dev_3.1.3-11 libopenmpi3_3.1.3-11 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpmix2_3.1.4-1 libquadmath0_9.2.1-17 libseccomp2_2.4.1-2 libselinux1_2.9-2+b2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2+b2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libstdc++-8-dev_8.3.0-23 libstdc++-9-dev_9.2.1-17 libstdc++-9-dev-armel-cross_9.2.1-15cross1 libstdc++6_9.2.1-17 libstdc++6-armel-cross_9.2.1-15cross1 libsub-override-perl_0.09-2 libsystemd0_242-7 libtasn1-6_4.14-3 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libtsan0_9.2.1-17 libubsan1_9.2.1-17 libubsan1-armel-cross_9.2.1-15cross1 libuchardet0_0.0.6-3 libudev1_242-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1+b1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.3.7-1 linux-libc-dev-armel-cross_5.2.9-2cross7 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-11 openmpi-common_3.1.3-11 openssh-client_1:8.1p1-1 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-9 pkg-config_0.29-6 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20190909-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/phyml Vcs-Git: https://salsa.debian.org/med-team/phyml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: ced3abf09a2371b75d846be555c499d980358ffe 2237651 phyml_3.3.20190909.orig.tar.gz b7b5cb0a37499a9d962fbcba7dfd074292d9ef0e 17200 phyml_3.3.20190909-1.debian.tar.xz Checksums-Sha256: f3afd6d5332cd98298736b3c6df63d751fa74388a0e972ec08f63a032d5e6a9c 2237651 phyml_3.3.20190909.orig.tar.gz cf31d9cd6b8d8492a10ee5680485c1acac275a12ddc4c6d7363c95a8f847fb5d 17200 phyml_3.3.20190909-1.debian.tar.xz Files: 35698ff61c1db57b238f5b2d2cc784b3 2237651 phyml_3.3.20190909.orig.tar.gz e845c58f69514eb093e8a46c34887398 17200 phyml_3.3.20190909-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl3DPQITHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0Qe8EACs5PjkZRGZTGDSFIsVuMjrS6pyzmkS kH+eJ16ozXN/M3AHvIHYQl8pP0TxKuxYfxAFm/9zbgcEoVX1+nyiD7FYN61UN4j1 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signature on ./phyml_3.3.20190909-1.dsc dpkg-source: info: extracting phyml in /<> dpkg-source: info: unpacking phyml_3.3.20190909.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20190909-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-stdc++.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-198b5c2e-60c8-4879-badf-d6a3f7ee1e61 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20190909-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin rm -rf doc/Makefile make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' dh_autoreconf --as-needed configure.ac:16: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armel checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabi-strip... arm-linux-gnueabi-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabi checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabi-gcc accepts -g... yes checking for arm-linux-gnueabi-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabi-gcc... none checking dependency style of arm-linux-gnueabi-gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabi" checking for log in -lm... yes checking how to run the C preprocessor... arm-linux-gnueabi-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... (cached) yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for arm-linux-gnueabi-pkg-config... /usr/bin/arm-linux-gnueabi-pkg-config checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j1 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' .: Building [phyml]. Version 3.3.3:3.3.20190909-1 :. arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o main.o main.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o utilities.o utilities.c utilities.c: In function ‘Assign_State_With_Ambiguity’: utilities.c:3048:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3048 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3048:26: note: directive argument in the range [0, 2147483647] 3048 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utilities.c: In function ‘Are_Compatible’: utilities.c:4880:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4880 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:4880:26: note: directive argument in the range [0, 2147483647] 4880 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o optimiz.o optimiz.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o lk.o lk.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o bionj.o bionj.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o models.o models.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o free.o free.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o help.o help.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o simu.o simu.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o eigen.o eigen.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o pars.o pars.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o alrt.o alrt.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o interface.o interface.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o cl.o cl.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o spr.o spr.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o draw.o draw.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o stats.o stats.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o rates.o rates.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mcmc.o mcmc.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o times.o times.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tiporder.o tiporder.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o m4.o m4.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o io.o io.c io.c: In function ‘Print_Fp_Out’: io.c:2629:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2629 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2629:43: note: directive argument in the range [1, 2147483647] 2629 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from io.h:18, from io.c:13: /usr/arm-linux-gnueabi/include/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 5 and 14 bytes into a destination of size 8 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o make.o make.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o nexus.o nexus.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o init.o init.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o xml.o xml.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o date.o date.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o sse.o sse.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o avx.o avx.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o tbe.o tbe.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o ancestral.o ancestral.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o mixt.o mixt.c arm-linux-gnueabi-gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o m4.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # move phyml binary to temporary dir inside debian/ mkdir -p /<>/debian/bin mv src/phyml /<>/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/<>' Making distclean in src make[3]: Entering directory '/<>/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/beagle_utils.Po rm -f ./.deps/bionj.Po rm -f ./.deps/checkpoint.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/geo.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/invitee.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/m4.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-date.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-m4.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mcmc.Po rm -f ./.deps/phyml_mpi-mg.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-rates.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-times.Po rm -f ./.deps/phyml_mpi-tiporder.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/simu.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/tiporder.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/<>' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/<>' dh_auto_configure -- --enable-mpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi --enable-mpi configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armel checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabi-strip... arm-linux-gnueabi-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabi checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabi-gcc accepts -g... yes checking for arm-linux-gnueabi-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabi-gcc... none checking dependency style of arm-linux-gnueabi-gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabi" checking for log in -lm... yes checking how to run the C preprocessor... arm-linux-gnueabi-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... (cached) yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for arm-linux-gnueabi-pkg-config... /usr/bin/arm-linux-gnueabi-pkg-config checking pkg-config is at least version 0.9.0... yes checking for MPI_C... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j1 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20190909-1 :. arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c utilities.c: In function ‘Assign_State_With_Ambiguity’: utilities.c:3048:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3048 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3048:26: note: directive argument in the range [0, 2147483647] 3048 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utilities.c: In function ‘Are_Compatible’: utilities.c:4880:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4880 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:4880:26: note: directive argument in the range [0, 2147483647] 4880 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabi/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 6 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-m4.o `test -f 'm4.c' || echo './'`m4.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c io.c: In function ‘Print_Fp_Out’: io.c:2629:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2629 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2629:43: note: directive argument in the range [1, 2147483647] 2629 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/stdio.h:867, from utilities.h:19, from io.h:18, from io.c:13: /usr/arm-linux-gnueabi/include/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 5 and 14 bytes into a destination of size 8 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c arm-linux-gnueabi-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c arm-linux-gnueabi-gcc -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabi/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # move phyml binary to temporary dir inside debian/ # mkdir -p /<>/debian/bin mv src/phyml-mpi /<>/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install make -j1 install DESTDIR=/<>/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in src make[3]: Entering directory '/<>/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20190909-1 :. arm-linux-gnueabi-gcc -pthread -I/usr/lib/arm-linux-gnueabi/openmpi/include -I/usr/lib/arm-linux-gnueabi/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabi/openmpi/lib -lmpi -lm Done. make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/<>/debian/phyml/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # install phyml binary we have kept safe above mkdir -p /<>/debian/phyml/usr/lib/phyml/bin mv /<>/debian/bin/* /<>/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/<>' dh_install -a debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs mv /<>/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<>/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/<>' dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_perl: /usr/lib/arm-linux-gnueabi/perl/cross-config-5.30.0/Config.pm does not exist (missing build dependency on perl-xs-dev?) dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a debian/rules override_dh_dwz make[1]: Entering directory '/<>' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/<>' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phyml' in '../phyml_3.3.20190909-1_armel.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20190909-1_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phyml_3.3.20190909-1_armel.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-11-07T18:26:08Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyml_3.3.20190909-1_armel.changes: ----------------------------------- Format: 1.8 Date: Wed, 06 Nov 2019 21:46:04 +0100 Source: phyml Binary: phyml phyml-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 3:3.3.20190909-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (3:3.3.20190909-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.4.1 * Reported autogenerated files in archive to upstream (https://github.com/stephaneguindon/phyml/issues/113) Checksums-Sha1: deb1f486bf0128ac8dc92634fda944cf9331c3b3 42656 phyml-dbgsym_3.3.20190909-1_armel.deb 5949d850ed978e7093c7d82ab1bcc5f9adac585b 5783 phyml_3.3.20190909-1_armel.buildinfo 3534e95dc1fef385b9c3fa052fad1967f9325de3 1639672 phyml_3.3.20190909-1_armel.deb Checksums-Sha256: d288497774b09f158911cdd72cd0716a395b7672f7503a40c738b281f08b89ae 42656 phyml-dbgsym_3.3.20190909-1_armel.deb 41337989192500543f34731c5f6379118feb264be0d9401311d22e9b61397720 5783 phyml_3.3.20190909-1_armel.buildinfo e54ee504eb37b84ae0088bd3bf520d04cf8fa99612d0999f98701536321ca8a4 1639672 phyml_3.3.20190909-1_armel.deb Files: e9ed89759d7283a286cac74d2bf3a959 42656 debug optional phyml-dbgsym_3.3.20190909-1_armel.deb 55a2a58ad52492e8c5727fb4ebb36848 5783 science optional phyml_3.3.20190909-1_armel.buildinfo 1161995721fae203d334bca04fe7957c 1639672 science optional phyml_3.3.20190909-1_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phyml Binary: phyml Architecture: armel Version: 3:3.3.20190909-1 Checksums-Md5: e9ed89759d7283a286cac74d2bf3a959 42656 phyml-dbgsym_3.3.20190909-1_armel.deb 1161995721fae203d334bca04fe7957c 1639672 phyml_3.3.20190909-1_armel.deb Checksums-Sha1: deb1f486bf0128ac8dc92634fda944cf9331c3b3 42656 phyml-dbgsym_3.3.20190909-1_armel.deb 3534e95dc1fef385b9c3fa052fad1967f9325de3 1639672 phyml_3.3.20190909-1_armel.deb Checksums-Sha256: d288497774b09f158911cdd72cd0716a395b7672f7503a40c738b281f08b89ae 42656 phyml-dbgsym_3.3.20190909-1_armel.deb e54ee504eb37b84ae0088bd3bf520d04cf8fa99612d0999f98701536321ca8a4 1639672 phyml_3.3.20190909-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 07 Nov 2019 18:26:08 +0000 Build-Path: /<> Installed-Build-Depends: adduser (= 3.118), autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.33.1-2), binutils-common (= 2.33.1-2), binutils-x86-64-linux-gnu (= 2.33.1-2), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.8), bzip2 (= 1.0.8-2), chrpath (= 0.16-2+b1), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-8 (= 8.3.0-23), cpp-9 (= 9.2.1-17), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.7.1), debianutils (= 4.9), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.2-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-1), fdisk (= 2.34-0.1), file (= 1:5.37-6), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.2.1-17), gcc (= 4:9.2.1-3.1), gcc-8 (= 8.3.0-23), gcc-8-base (= 8.3.0-23), gcc-9 (= 9.2.1-17), gcc-9-base (= 9.2.1-17), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3+b1), hostname (= 3.22+b1), ibverbs-providers (= 26.0-2), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-5), libarchive-zip-perl (= 1.67-1), libasan5 (= 9.2.1-17), libatomic1 (= 9.2.1-17), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.33.1-2), libblkid1 (= 2.34-0.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.29-3), libc-dev-bin (= 2.29-3), libc6 (= 2.29-3), libc6-dev (= 2.29-3), libcap-ng0 (= 0.7.9-2.1), libcc1-0 (= 9.2.1-17), libcom-err2 (= 1.45.4-1), libcroco3 (= 0.6.13-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.250), libdebhelper-perl (= 12.7.1), libdpkg-perl (= 1.19.7), libedit2 (= 3.1-20191025-1), libelf1 (= 0.176-1.1), libevent-2.1-6 (= 2.1.8-stable-4), libevent-core-2.1-6 (= 2.1.8-stable-4), libevent-pthreads-2.1-6 (= 2.1.8-stable-4), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.6.2-1), libgcc-8-dev (= 8.3.0-23), libgcc-9-dev (= 9.2.1-17), libgcc1 (= 1:9.2.1-17), libgcrypt20 (= 1.8.5-3), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libgfortran5 (= 9.2.1-17), libglib2.0-0 (= 2.62.2-3), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.2.1-17), libgpg-error0 (= 1.36-7), libgssapi-krb5-2 (= 1.17-6), libhwloc-dev (= 1.11.13-1), libhwloc-plugins (= 1.11.13-1), libhwloc5 (= 1.11.13-1), libibverbs-dev (= 26.0-2), libibverbs1 (= 26.0-2), libicu63 (= 63.2-2), libisl21 (= 0.21-2), libitm1 (= 9.2.1-17), libk5crypto3 (= 1.17-6), libkeyutils1 (= 1.6-6), libkrb5-3 (= 1.17-6), libkrb5support0 (= 1.17-6), liblsan0 (= 9.2.1-17), libltdl-dev (= 2.4.6-11), libltdl7 (= 2.4.6-11), liblz4-1 (= 1.9.2-1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.37-6), libmagic1 (= 1:5.37-6), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-23), libncurses6 (= 6.1+20191019-1), libncursesw6 (= 6.1+20191019-1), libnl-3-200 (= 3.4.0-1+b1), libnl-3-dev (= 3.4.0-1+b1), libnl-route-3-200 (= 3.4.0-1+b1), libnl-route-3-dev (= 3.4.0-1+b1), libopenmpi-dev (= 3.1.3-11), libopenmpi3 (= 3.1.3-11), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpciaccess0 (= 0.14-1), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-9), libpipeline1 (= 1.5.1-2), libpmix2 (= 3.1.4-1), libquadmath0 (= 9.2.1-17), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2+b2), libsemanage-common (= 2.9-3), libsemanage1 (= 2.9-3), libsepol1 (= 2.9-2+b2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libssl1.1 (= 1.1.1d-2), libstdc++-9-dev (= 9.2.1-17), libstdc++6 (= 9.2.1-17), libsub-override-perl (= 0.09-2), libsystemd0 (= 242-7), libtinfo6 (= 6.1+20191019-1), libtool (= 2.4.6-11), libtsan0 (= 9.2.1-17), libubsan1 (= 9.2.1-17), libuchardet0 (= 0.0.6-3), libudev1 (= 242-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.3.7-1), login (= 1:4.7-2), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.0-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20191019-1), ncurses-bin (= 6.1+20191019-1), ocl-icd-libopencl1 (= 2.2.12-2), openmpi-bin (= 3.1.3-11), openmpi-common (= 3.1.3-11), openssh-client (= 1:8.1p1-1), passwd (= 1:4.7-2), patch (= 2.7.6-6), perl (= 5.30.0-9), perl-base (= 5.30.0-9), perl-modules-5.30 (= 5.30.0-9), pkg-config (= 0.29-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.96-1), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1573073164" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyml-dbgsym_3.3.20190909-1_armel.deb ------------------------------------- new Debian package, version 2.0. size 42656 bytes: control archive=660 bytes. 462 bytes, 12 lines control 318 bytes, 3 lines md5sums Package: phyml-dbgsym Source: phyml Version: 3:3.3.20190909-1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 287 Depends: phyml (= 3:3.3.20190909-1) Section: debug Priority: optional Description: debug symbols for phyml Build-Ids: acc0b78a546d8b85d1086492e20f107d8a5b8aa8 d843389f343124480b7fbc24867a2719682859ea ee2f4ea9b99302d44291f42ab7c51cf3aefd007f drwxr-xr-x root/root 0 2019-11-06 20:46 ./ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/debug/.build-id/ac/ -rw-r--r-- root/root 93496 2019-11-06 20:46 ./usr/lib/debug/.build-id/ac/c0b78a546d8b85d1086492e20f107d8a5b8aa8.debug drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/debug/.build-id/d8/ -rw-r--r-- root/root 93496 2019-11-06 20:46 ./usr/lib/debug/.build-id/d8/43389f343124480b7fbc24867a2719682859ea.debug drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/debug/.build-id/ee/ -rw-r--r-- root/root 92696 2019-11-06 20:46 ./usr/lib/debug/.build-id/ee/2f4ea9b99302d44291f42ab7c51cf3aefd007f.debug drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-11-06 20:46 ./usr/share/doc/phyml-dbgsym -> phyml phyml_3.3.20190909-1_armel.deb ------------------------------ new Debian package, version 2.0. size 1639672 bytes: control archive=1912 bytes. 1667 bytes, 31 lines control 1773 bytes, 25 lines md5sums Package: phyml Version: 3:3.3.20190909-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 5677 Depends: libc6 (>= 2.29), libopenmpi3, openmpi-bin Section: science Priority: optional Homepage: http://www.atgc-montpellier.fr/phyml Description: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. . This package also includes PhyTime. drwxr-xr-x root/root 0 2019-11-06 20:46 ./ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/bin/ -rwxr-xr-x root/root 579 2019-11-06 20:45 ./usr/bin/phyml -rwxr-xr-x root/root 1502628 2019-11-06 20:46 ./usr/bin/phyml-mpi drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/phyml/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/lib/phyml/bin/ -rwxr-xr-x root/root 1493984 2019-11-06 20:46 ./usr/lib/phyml/bin/phyml -rwxr-xr-x root/root 1502176 2019-11-06 20:46 ./usr/lib/phyml/bin/phyml-mpi drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/doc-base/ -rw-r--r-- root/root 202 2019-11-06 20:45 ./usr/share/doc-base/phyml drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/doc/phyml/ -rw-r--r-- root/root 2446 2019-11-06 20:45 ./usr/share/doc/phyml/README.Debian -rw-r--r-- root/root 3168 2019-11-06 20:46 ./usr/share/doc/phyml/changelog.Debian.gz -rw-r--r-- root/root 1490 2019-11-06 20:45 ./usr/share/doc/phyml/copyright drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/doc/phyml/examples/ -rw-r--r-- root/root 20905 2019-11-06 20:45 ./usr/share/doc/phyml/examples/example.nex drwxr-xr-x root/root 0 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/ -rw-r--r-- root/root 1900 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/X1.mat -rw-r--r-- root/root 1899 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/X2.mat -rw-r--r-- root/root 1893 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/X3.mat -rw-r--r-- root/root 1895 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/X4.mat -rw-r--r-- root/root 1994 2019-09-09 06:55 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml -rw-r--r-- root/root 2175 2019-09-09 06:55 ./usr/share/doc/phyml/examples/nexus_example.nxs -rwxr-xr-x root/root 60771 2019-09-09 06:55 ./usr/share/doc/phyml/examples/nucleic drwxr-xr-x root/root 0 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phyrex/ -rw-r--r-- root/root 9007 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phyrex/flu.xml -rw-r--r-- root/root 70310 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs -rw-r--r-- root/root 1784 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt drwxr-xr-x root/root 0 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phytime/ -rw-r--r-- root/root 2248 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phytime/dating_example.xml -rw-r--r-- root/root 100171 2019-09-09 06:55 ./usr/share/doc/phyml/examples/phytime/seq.txt -rwxr-xr-x root/root 25990 2019-09-09 06:55 ./usr/share/doc/phyml/examples/proteic -rw-r--r-- root/root 971010 2019-09-09 06:55 ./usr/share/doc/phyml/phyml_manual.pdf -rw-r--r-- root/root 1257 2019-11-06 20:45 ./usr/share/doc/phyml/run-unit-test drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/man/ drwxr-xr-x root/root 0 2019-11-06 20:46 ./usr/share/man/man1/ -rw-r--r-- root/root 2899 2019-11-06 20:46 ./usr/share/man/man1/phyml.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [556 B] Get:5 copy:/<>/apt_archive ./ Packages [641 B] Fetched 2160 B in 0s (96.0 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libfreezethaw-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libpackage-stash-xs-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libdevel-callchecker-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armel t1utils 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 7317 kB of archives. After this operation, 20.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.30.1-1 [649 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b2 [71.3 kB] Get:11 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0.62-1+b2 [46.0 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.24-1 [18.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libberkeleydb-perl amd64 0.62-1+b1 [124 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b4 [105 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:29 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http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.41-1 [79.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b2 [16.9 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b6 [33.6 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-2 [101 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003006-1 [58.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.80+repack-2+b1 [34.8 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.33.0 [1278 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7317 kB in 0s (34.0 MB/s) Selecting previously unselected package readline-common. (Reading database ... 22706 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-3_all.deb ... Unpacking readline-common (8.0-3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-3_amd64.deb ... Unpacking libreadline8:amd64 (8.0-3) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libclass-accessor-perl (0.51-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-3) ... Setting up liburi-perl (1.76-1) ... Setting up libnet-ssleay-perl (1.88-1+b1) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libtype-tiny-perl (1.004004-1) ... Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-3+b4) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up gpg (2.2.17-3) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003006-1) ... Setting up libb-hooks-endofscope-perl (0.24-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.33.0) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for man-db (2.9.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.29-3) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 19036 Build-Time: 142 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 21 Job: phyml_3:3.3.20190909-1 Lintian: pass Machine Architecture: amd64 Package: phyml Package-Time: 176 Source-Version: 3:3.3.20190909-1 Space: 19036 Status: successful Version: 3:3.3.20190909-1 -------------------------------------------------------------------------------- Finished at 2019-11-07T18:26:08Z Build needed 00:02:56, 19036k disk space