https://launchpad.net/ubuntu/+source/phyml/3:3.3.20200621-1/+build/19626924 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-065 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 23 Jul 05:12:09 ntpdate[976557]: adjust time server 10.211.37.1 offset 0.000299 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 --image-type chroot /home/buildd/filecache-default/a310bc38fff7ff850d9523076a2a133474f10c4a Creating target for build PACKAGEBUILD-19626924 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 Starting target for build PACKAGEBUILD-19626924 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19626924 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 Updating target for build PACKAGEBUILD-19626924 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main riscv64 Packages [891 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe riscv64 Packages [8199 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5232 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 Packages [34.8 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [35.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe riscv64 Packages [456 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [238 kB] Fetched 16.2 MB in 32s (509 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. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19626924 riscv64 groovy-proposed -c chroot:build-PACKAGEBUILD-19626924 --arch=riscv64 --dist=groovy-proposed --nolog phyml_3.3.20200621-1.dsc Initiating build PACKAGEBUILD-19626924 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-065.buildd +==============================================================================+ | phyml 3:3.3.20200621-1 (riscv64) Thu, 23 Jul 2020 05:13:57 +0000 | +==============================================================================+ Package: phyml Version: 3:3.3.20200621-1 Source Version: 3:3.3.20200621-1 Distribution: groovy-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19626924/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-rUbJUP/resolver-FkjiRP' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phyml_3.3.20200621-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phyml-rUbJUP/phyml-3.3.20200621' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-rUbJUP' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [393 B] Get:5 copy:/<>/apt_archive ./ Packages [476 B] Fetched 1826 B in 0s (4146 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev chrpath debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcbor0.6 libcroco3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfido2-1 libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu66 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-9-doc libcoarrays-dev groff krb5-doc krb5-user libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libcoarrays-openmpi-dev xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev chrpath debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-9 groff-base ibverbs-providers intltool-debian libarchive-zip-perl libbsd0 libcbor0.6 libcroco3 libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfido2-1 libfile-stripnondeterminism-perl libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu66 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf sbuild-build-depends-main-dummy tzdata zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 32.5 MB of archives. After this operation, 145 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main riscv64 libuchardet0 riscv64 0.0.7-1 [67.7 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main riscv64 groff-base riscv64 1.22.4-5 [815 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main riscv64 man-db riscv64 2.9.3-2 [1081 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main riscv64 libmagic-mgc riscv64 1:5.38-5 [218 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main riscv64 libmagic1 riscv64 1:5.38-5 [70.6 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main riscv64 file riscv64 1:5.38-5 [22.5 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main riscv64 libelf1 riscv64 0.180-0ubuntu1 [41.6 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main riscv64 libglib2.0-0 riscv64 2.64.4-1 [1123 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main riscv64 tzdata all 2020a-0ubuntu1 [293 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main riscv64 libicu66 riscv64 66.1-2ubuntu3 [8401 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main riscv64 libxml2 riscv64 2.9.10+dfsg-5 [559 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main riscv64 libcbor0.6 riscv64 0.6.0-0ubuntu2 [18.0 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main riscv64 libedit2 riscv64 3.1-20191231-1 [74.8 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main riscv64 libfido2-1 riscv64 1.4.0-2 [43.3 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main riscv64 libkrb5support0 riscv64 1.17-10 [28.3 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main riscv64 libk5crypto3 riscv64 1.17-10 [91.8 kB] Get:21 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[233 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main riscv64 debhelper all 13.2ubuntu1 [878 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main riscv64 libgfortran5 riscv64 10.1.0-6ubuntu1 [332 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main riscv64 libgfortran-9-dev riscv64 9.3.0-13ubuntu1 [887 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main riscv64 gfortran-9 riscv64 9.3.0-13ubuntu1 [6472 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main riscv64 libnl-3-200 riscv64 3.4.0-1 [46.5 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main riscv64 libnl-route-3-200 riscv64 3.4.0-1 [130 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main riscv64 libibverbs1 riscv64 29.0-1build1 [48.0 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main riscv64 ibverbs-providers riscv64 29.0-1build1 [21.7 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main riscv64 libevent-2.1-7 riscv64 2.1.12-stable-1 [119 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main 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3.4.0-1 [359 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main riscv64 libpciaccess0 riscv64 0.16-0ubuntu1 [15.5 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main riscv64 libxnvctrl0 riscv64 440.82-0ubuntu1 [10.3 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main riscv64 ocl-icd-libopencl1 riscv64 2.2.12-4 [29.2 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/universe riscv64 libhwloc-plugins riscv64 2.2.0+dfsg-3 [12.6 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/universe riscv64 libpmix2 riscv64 3.1.5-1 [389 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/universe riscv64 libopenmpi3 riscv64 4.0.3-6ubuntu2 [1707 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/universe riscv64 openmpi-common all 4.0.3-6ubuntu2 [151 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/universe riscv64 openmpi-bin riscv64 4.0.3-6ubuntu2 [65.3 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main riscv64 pkg-config riscv64 0.29.2-1ubuntu1 [43.7 kB] Get:79 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(Reading database ... 9854 files and directories currently installed.) Preparing to unpack .../00-libuchardet0_0.0.7-1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../01-groff-base_1.22.4-5_riscv64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../02-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.9.3-2_riscv64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.38-5_riscv64.deb ... Unpacking libmagic-mgc (1:5.38-5) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../05-libmagic1_1%3a5.38-5_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.38-5) ... 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Unpacking gfortran-9 (9.3.0-13ubuntu1) ... Selecting previously unselected package libnl-3-200:riscv64. Preparing to unpack .../53-libnl-3-200_3.4.0-1_riscv64.deb ... Unpacking libnl-3-200:riscv64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-200:riscv64. Preparing to unpack .../54-libnl-route-3-200_3.4.0-1_riscv64.deb ... Unpacking libnl-route-3-200:riscv64 (3.4.0-1) ... Selecting previously unselected package libibverbs1:riscv64. Preparing to unpack .../55-libibverbs1_29.0-1build1_riscv64.deb ... Unpacking libibverbs1:riscv64 (29.0-1build1) ... Selecting previously unselected package ibverbs-providers:riscv64. Preparing to unpack .../56-ibverbs-providers_29.0-1build1_riscv64.deb ... Unpacking ibverbs-providers:riscv64 (29.0-1build1) ... Selecting previously unselected package libevent-2.1-7:riscv64. Preparing to unpack .../57-libevent-2.1-7_2.1.12-stable-1_riscv64.deb ... Unpacking libevent-2.1-7:riscv64 (2.1.12-stable-1) ... 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Unpacking libevent-dev (2.1.12-stable-1) ... Selecting previously unselected package libhwloc15:riscv64. Preparing to unpack .../63-libhwloc15_2.2.0+dfsg-3_riscv64.deb ... Unpacking libhwloc15:riscv64 (2.2.0+dfsg-3) ... Selecting previously unselected package libltdl7:riscv64. Preparing to unpack .../64-libltdl7_2.4.6-14_riscv64.deb ... Unpacking libltdl7:riscv64 (2.4.6-14) ... Selecting previously unselected package libltdl-dev:riscv64. Preparing to unpack .../65-libltdl-dev_2.4.6-14_riscv64.deb ... Unpacking libltdl-dev:riscv64 (2.4.6-14) ... Selecting previously unselected package libnl-3-dev:riscv64. Preparing to unpack .../66-libnl-3-dev_3.4.0-1_riscv64.deb ... Unpacking libnl-3-dev:riscv64 (3.4.0-1) ... Selecting previously unselected package libnl-route-3-dev:riscv64. Preparing to unpack .../67-libnl-route-3-dev_3.4.0-1_riscv64.deb ... Unpacking libnl-route-3-dev:riscv64 (3.4.0-1) ... Selecting previously unselected package libpciaccess0:riscv64. 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Preparing to unpack .../79-libhwloc-dev_2.2.0+dfsg-3_riscv64.deb ... Unpacking libhwloc-dev:riscv64 (2.2.0+dfsg-3) ... Selecting previously unselected package libibverbs-dev:riscv64. Preparing to unpack .../80-libibverbs-dev_29.0-1build1_riscv64.deb ... Unpacking libibverbs-dev:riscv64 (29.0-1build1) ... Selecting previously unselected package libopenmpi-dev:riscv64. Preparing to unpack .../81-libopenmpi-dev_4.0.3-6ubuntu2_riscv64.deb ... Unpacking libopenmpi-dev:riscv64 (4.0.3-6ubuntu2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../82-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.2-2build1) ... Setting up libpciaccess0:riscv64 (0.16-0ubuntu1) ... Setting up libxau6:riscv64 (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:riscv64 (1.6.1-2ubuntu1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:riscv64 (2.64.4-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.2ubuntu1) ... Setting up libmagic1:riscv64 (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libcbor0.6:riscv64 (0.6.0-0ubuntu2) ... Setting up libkrb5support0:riscv64 (1.17-10) ... Setting up tzdata (2020a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jul 23 05:17:02 UTC 2020. Universal Time is now: Thu Jul 23 05:17:02 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libx11-data (2:1.6.9-2ubuntu1) ... Setting up libsigsegv2:riscv64 (2.12-2build1) ... Setting up libhwloc15:riscv64 (2.2.0+dfsg-3) ... Setting up libevent-core-2.1-7:riscv64 (2.1.12-stable-1) ... Setting up libevent-2.1-7:riscv64 (2.1.12-stable-1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libk5crypto3:riscv64 (1.17-10) ... Setting up libltdl7:riscv64 (2.4.6-14) ... Setting up libgfortran5:riscv64 (10.1.0-6ubuntu1) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up libnuma1:riscv64 (2.0.12-1build1) ... Setting up ocl-icd-libopencl1:riscv64 (2.2.12-4) ... Setting up libuchardet0:riscv64 (0.0.7-1) ... Setting up libnl-3-200:riscv64 (3.4.0-1) ... Setting up openmpi-common (4.0.3-6ubuntu2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:riscv64 (1.17-10) ... Setting up libfido2-1:riscv64 (1.4.0-2) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.180-0ubuntu1) ... Setting up chrpath (0.16-2) ... Setting up libevent-pthreads-2.1-7:riscv64 (2.1.12-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libxdmcp6:riscv64 (1:1.1.3-0ubuntu1) ... Setting up libevent-extra-2.1-7:riscv64 (2.1.12-stable-1) ... Setting up libxcb1:riscv64 (1.14-2) ... Setting up libtool (2.4.6-14) ... Setting up libicu66:riscv64 (66.1-2ubuntu3) ... Setting up libedit2:riscv64 (3.1-20191231-1) ... Setting up libgfortran-9-dev:riscv64 (9.3.0-13ubuntu1) ... Setting up libevent-openssl-2.1-7:riscv64 (2.1.12-stable-1) ... Setting up m4 (1.4.18-4) ... Setting up libnuma-dev:riscv64 (2.0.12-1build1) ... Setting up libnl-route-3-200:riscv64 (3.4.0-1) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up libgssapi-krb5-2:riscv64 (1.17-10) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:riscv64 (3.4.0-1) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:riscv64 (2:1.6.9-2ubuntu1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-5) ... Setting up automake (1:1.16.2-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:riscv64 (29.0-1build1) ... Setting up gfortran-9 (9.3.0-13ubuntu1) ... Setting up ibverbs-providers:riscv64 (29.0-1build1) ... Setting up openssh-client (1:8.3p1-1) ... Setting up libxext6:riscv64 (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:riscv64 (440.82-0ubuntu1) ... Setting up libnl-route-3-dev:riscv64 (3.4.0-1) ... Setting up libltdl-dev:riscv64 (2.4.6-14) ... Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up libhwloc-dev:riscv64 (2.2.0+dfsg-3) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libibverbs-dev:riscv64 (29.0-1build1) ... Setting up libhwloc-plugins:riscv64 (2.2.0+dfsg-3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpmix2:riscv64 (3.1.5-1) ... Setting up po-debconf (1.0.21) ... Setting up libopenmpi3:riscv64 (4.0.3-6ubuntu2) ... Setting up openmpi-bin (4.0.3-6ubuntu2) ... 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:riscv64 (4.0.3-6ubuntu2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/openmpi/include to provide /usr/include/riscv64-linux-gnu/mpi (mpi-riscv64-linux-gnu) in auto mode Setting up dh-autoreconf (19) ... Setting up debhelper (13.2ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.34.90.20200716-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-6ubuntu1 linux-libc-dev_5.4.0-30.34 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu9 base-passwd_3.5.47 bash_5.0-6ubuntu2 binutils_2.34.90.20200716-1ubuntu1 binutils-common_2.34.90.20200716-1ubuntu1 binutils-riscv64-linux-gnu_2.34.90.20200716-1ubuntu1 bsdextrautils_2.35.2-9ubuntu1 bsdutils_1:2.35.2-9ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 chrpath_0.16-2 coreutils_8.30-3ubuntu3 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-6ubuntu1 gcc-8-base_8.4.0-4ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gfortran-9_9.3.0-13ubuntu1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 ibverbs-providers_29.0-1build1 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-6ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34.90.20200716-1ubuntu1 libblkid1_2.35.2-9ubuntu1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcbor0.6_0.6.0-0ubuntu2 libcc1-0_10.1.0-6ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libctf-nobfd0_2.34.90.20200716-1ubuntu1 libctf0_2.34.90.20200716-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.2ubuntu1 libdpkg-perl_1.19.7ubuntu4 libedit2_3.1-20191231-1 libelf1_0.180-0ubuntu1 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libkrb5support0_1.17-10 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-9ubuntu1 libmpc3_1.1.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnettle8_3.6-2 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-2 libnuma-dev_2.0.12-1build1 libnuma1_2.0.12-1build1 libopenmpi-dev_4.0.3-6ubuntu2 libopenmpi3_4.0.3-6ubuntu2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpciaccess0_0.16-0ubuntu1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpmix2_3.1.5-1 libpng16-16_1.6.37-2 libreadline8_8.0-4 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.2-9ubuntu1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-6ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libuchardet0_0.0.7-1 libudev1_245.6-3ubuntu3 libunistring2_0.9.10-4 libuuid1_2.35.2-9ubuntu1 libx11-6_2:1.6.9-2ubuntu1 libx11-data_2:1.6.9-2ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxml2_2.9.10+dfsg-5 libxnvctrl0_440.82-0ubuntu1 libzstd1_1.4.5+dfsg-3 linux-libc-dev_5.4.0-30.34 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-9ubuntu1 ncurses-base_6.2-1 ncurses-bin_6.2-1 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.3-6ubuntu2 openmpi-common_4.0.3-6ubuntu2 openssh-client_1:8.3p1-1 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.2-9ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20200621-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.5.0 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 (= 13), pkg-config, libopenmpi-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: df6cc658a1733806b9c467e82f152b2fff6cd5bd 2235154 phyml_3.3.20200621.orig.tar.gz 5c941bc6c685697b7bb553250de3781f20437df5 17296 phyml_3.3.20200621-1.debian.tar.xz Checksums-Sha256: a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867 2235154 phyml_3.3.20200621.orig.tar.gz 4a634ce483f68a707ddbc8a215cf5b2701e3671dbf7bf8f6dcff3b9376e6b2a7 17296 phyml_3.3.20200621-1.debian.tar.xz Files: 12622e111c388bcb16696660033143b5 2235154 phyml_3.3.20200621.orig.tar.gz 877a070edeb3e61e0eab3a92afdeff3c 17296 phyml_3.3.20200621-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8YmFsRHHRpbGxlQGRl 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./phyml_3.3.20200621-1.dsc dpkg-source: info: extracting phyml in /<> dpkg-source: info: unpacking phyml_3.3.20200621.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20200621-1.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 DEB_BUILD_OPTIONS=parallel=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19626924 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19626924 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19626924 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20200621-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 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 binary-arch dh binary-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=riscv64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/riscv64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes 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... riscv64-unknown-linux-gnu checking host system type... riscv64-unknown-linux-gnu checking for gcc... 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... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking dependency style of gcc... (cached) none configure: "Do not use MSSE = because not available on arch riscv64-unknown-linux-gnu" checking for log in -lm... yes checking how to run the C preprocessor... 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... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... 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 pkg-config... /usr/bin/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 dh_auto_build -- LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make -j8 "LDFLAGS=-Wl,-Bsymbolic-functions -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' 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 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 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 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 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 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 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 .: Building [phyml]. Version 3.3.3:3.3.20200621-1 :. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 utilities.c: In function ‘Assign_State_With_Ambiguity’: utilities.c:3073:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3073 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3073:26: note: directive argument in the range [0, 2147483647] 3073 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from io.h:18, from io.c:13: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 utilities.c: In function ‘Are_Compatible’: utilities.c:4899:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4899 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:4899:26: note: directive argument in the range [0, 2147483647] 4899 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 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 gcc -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-Bsymbolic-functions -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 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/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-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/rrw.Po rm -f ./.deps/rw.Po rm -f ./.deps/simu.Po rm -f ./.deps/slfv.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=riscv64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/riscv64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-mpi checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes 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... riscv64-unknown-linux-gnu checking host system type... riscv64-unknown-linux-gnu checking for gcc... 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... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking dependency style of gcc... (cached) none configure: "Do not use MSSE = because not available on arch riscv64-unknown-linux-gnu" checking for log in -lm... yes checking how to run the C preprocessor... 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... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... 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 pkg-config... /usr/bin/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 dh_auto_build -- LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now" make -j8 "LDFLAGS=-Wl,-Bsymbolic-functions -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' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 In file included from lk.h:18, from lk.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from lk.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 In file included from cl.h:21, from cl.c:13: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/unistd.h:25, from cl.h:19, from cl.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 utilities.c: In function ‘Assign_State_With_Ambiguity’: utilities.c:3073:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 3073 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:3073:26: note: directive argument in the range [0, 2147483647] 3073 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 io.c: In function ‘Print_Fp_Out’: io.c:2315:47: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~ io.c:2315:43: note: directive argument in the range [1, 2147483647] 2315 | if (precision > 0) snprintf (format, 8, "%%.%df", precision); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from io.h:18, from io.c:13: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 utilities.c: In function ‘Are_Compatible’: utilities.c:4899:29: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 4899 | sprintf(format,"%%%dd",stepsize); | ^~ utilities.c:4899:26: note: directive argument in the range [0, 2147483647] 4899 | sprintf(format,"%%%dd",stepsize); | ^~~~~~~ In file included from /usr/include/stdio.h:867, from utilities.h:21, from utilities.c:12: /usr/include/riscv64-linux-gnu/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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 In file included from sse.h:18, from sse.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from sse.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 In file included from avx.h:18, from avx.c:14: utilities.h:18: warning: "_POSIX_C_SOURCE" redefined 18 | #define _POSIX_C_SOURCE 200112L | In file included from /usr/include/assert.h:35, from avx.c:13: /usr/include/features.h:310: note: this is the location of the previous definition 310 | # define _POSIX_C_SOURCE 199506L | gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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 gcc -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline -Wl,-Bsymbolic-functions -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-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/riscv64-linux-gnu/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 make -j8 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' gcc -pthread -I/usr/lib/riscv64-linux-gnu/openmpi/include -I/usr/lib/riscv64-linux-gnu/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-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/riscv64-linux-gnu/openmpi/lib -lmpi -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. Done. make[2]: Leaving directory '/<>/src' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install make -j8 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 3.3.3:3.3.20200621-1 :. Done. make[4]: Entering directory '/<>/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/<>/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/<>/debian/phyml/usr/bin' 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_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 -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing phyml (in debian/phyml); do_strip: , oemstrip: pkgstriptranslations: processing phyml-dbgsym (in debian/.debhelper/phyml/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/phyml/DEBIAN/control, package phyml, directory debian/phyml pkgstripfiles: Truncating usr/share/doc/phyml/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/phyml/dbgsym-root/DEBIAN/control, package phyml-dbgsym, directory debian/.debhelper/phyml/dbgsym-root dpkg-deb: building package 'phyml-dbgsym' in 'debian/.debhelper/scratch-space/build-phyml/phyml-dbgsym_3.3.20200621-1_riscv64.deb'. pkgstripfiles: Running PNG optimization (using 8 cpus) for package phyml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phyml' in '../phyml_3.3.20200621-1_riscv64.deb'. Renaming phyml-dbgsym_3.3.20200621-1_riscv64.deb to phyml-dbgsym_3.3.20200621-1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../phyml_3.3.20200621-1_riscv64.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 2020-07-23T05:29:04Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyml_3.3.20200621-1_riscv64.changes: ------------------------------------- Format: 1.8 Date: Wed, 22 Jul 2020 16:25:36 +0000 Source: phyml Binary: phyml Architecture: riscv64 Version: 3:3.3.20200621-1 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Shayan Doust Description: phyml - Phylogenetic estimation using Maximum Likelihood Closes: 957679 Changes: phyml (3:3.3.20200621-1) unstable; urgency=medium . * Team upload * New upstream version 3.3.20200621 (Closes: #957679) * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. 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/<>/phyml_3.3.20200621-1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phyml Binary: phyml Architecture: riscv64 Version: 3:3.3.20200621-1 Checksums-Md5: a2c01ffe1295215a87572a425b00bac1 35032 phyml-dbgsym_3.3.20200621-1_riscv64.ddeb f4380ecb63e8d9380e5cd638d3b98f3c 1750936 phyml_3.3.20200621-1_riscv64.deb Checksums-Sha1: 4fbdd0fe5eb0e12d622dcc7a56e37b49af09f849 35032 phyml-dbgsym_3.3.20200621-1_riscv64.ddeb b683f5f9f786d88667687efe86abbf27ced0cd1a 1750936 phyml_3.3.20200621-1_riscv64.deb Checksums-Sha256: 41aa1bace19ac545f8bc22cfd146da415eee05c14dfcad0f78ace868632331dd 35032 phyml-dbgsym_3.3.20200621-1_riscv64.ddeb e0e1f43ddf40c73b7a5441904d28fa77082631b62caa8000f86aca3cb1d90ea7 1750936 phyml_3.3.20200621-1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Thu, 23 Jul 2020 05:28:57 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu2), autoconf (= 2.69-11.1), automake (= 1:1.16.2-3ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu9), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu2), binutils (= 2.34.90.20200716-1ubuntu1), binutils-common (= 2.34.90.20200716-1ubuntu1), binutils-riscv64-linux-gnu (= 2.34.90.20200716-1ubuntu1), bsdextrautils (= 2.35.2-9ubuntu1), bsdutils (= 1:2.35.2-9ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), chrpath (= 0.16-2), coreutils (= 8.30-3ubuntu3), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-13ubuntu1), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2ubuntu1), debianutils (= 4.11), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3build1), dpkg (= 1.19.7ubuntu4), dpkg-dev (= 1.19.7ubuntu4), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-13ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10.1.0-6ubuntu1), gcc-9 (= 9.3.0-13ubuntu1), gcc-9-base (= 9.3.0-13ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), gfortran-9 (= 9.3.0-13ubuntu1), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), ibverbs-providers (= 29.0-1build1), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libatomic1 (= 10.1.0-6ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34.90.20200716-1ubuntu1), libblkid1 (= 2.35.2-9ubuntu1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.31-0ubuntu10), libc-dev-bin (= 2.31-0ubuntu10), libc6 (= 2.31-0ubuntu10), libc6-dev (= 2.31-0ubuntu10), libcap-ng0 (= 0.7.9-2.2), libcbor0.6 (= 0.6.0-0ubuntu2), libcc1-0 (= 10.1.0-6ubuntu1), libcom-err2 (= 1.45.6-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1ubuntu1), libcrypt1 (= 1:4.4.16-1ubuntu1), libctf-nobfd0 (= 2.34.90.20200716-1ubuntu1), libctf0 (= 2.34.90.20200716-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.252ubuntu1), libdebhelper-perl (= 13.2ubuntu1), libdpkg-perl (= 1.19.7ubuntu4), libedit2 (= 3.1-20191231-1), libelf1 (= 0.180-0ubuntu1), libevent-2.1-7 (= 2.1.12-stable-1), libevent-core-2.1-7 (= 2.1.12-stable-1), libevent-dev (= 2.1.12-stable-1), libevent-extra-2.1-7 (= 2.1.12-stable-1), libevent-openssl-2.1-7 (= 2.1.12-stable-1), libevent-pthreads-2.1-7 (= 2.1.12-stable-1), libffi7 (= 3.3-4), libfido2-1 (= 1.4.0-2), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-9-dev (= 9.3.0-13ubuntu1), libgcc-s1 (= 10.1.0-6ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu2), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libgfortran-9-dev (= 9.3.0-13ubuntu1), libgfortran5 (= 10.1.0-6ubuntu1), libglib2.0-0 (= 2.64.4-1), libgmp10 (= 2:6.2.0+dfsg-6), libgomp1 (= 10.1.0-6ubuntu1), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10), libhwloc-dev (= 2.2.0+dfsg-3), libhwloc-plugins (= 2.2.0+dfsg-3), libhwloc15 (= 2.2.0+dfsg-3), libibverbs-dev (= 29.0-1build1), libibverbs1 (= 29.0-1build1), libicu66 (= 66.1-2ubuntu3), libisl22 (= 0.22.1-1), libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), libltdl-dev (= 2.4.6-14), libltdl7 (= 2.4.6-14), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.35.2-9ubuntu1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.1.0-3), libnl-3-200 (= 3.4.0-1), libnl-3-dev (= 3.4.0-1), libnl-route-3-200 (= 3.4.0-1), libnl-route-3-dev (= 3.4.0-1), libnuma-dev (= 2.0.12-1build1), libnuma1 (= 2.0.12-1build1), libopenmpi-dev (= 4.0.3-6ubuntu2), libopenmpi3 (= 4.0.3-6ubuntu2), libpam-modules (= 1.3.1-5ubuntu5), libpam-modules-bin (= 1.3.1-5ubuntu5), libpam-runtime (= 1.3.1-5ubuntu5), libpam0g (= 1.3.1-5ubuntu5), libpciaccess0 (= 0.16-0ubuntu1), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.2-2build1), libpmix2 (= 3.1.5-1), libselinux1 (= 3.1-2), libsemanage-common (= 3.1-1), libsemanage1 (= 3.1-1), libsepol1 (= 3.1-1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.35.2-9ubuntu1), libssl1.1 (= 1.1.1f-1ubuntu3), libstdc++-9-dev (= 9.3.0-13ubuntu1), libstdc++6 (= 10.1.0-6ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.6-3ubuntu3), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libuchardet0 (= 0.0.7-1), libudev1 (= 245.6-3ubuntu3), libunistring2 (= 0.9.10-4), libuuid1 (= 2.35.2-9ubuntu1), libx11-6 (= 2:1.6.9-2ubuntu1), libx11-data (= 2:1.6.9-2ubuntu1), libxau6 (= 1:1.0.9-0ubuntu1), libxcb1 (= 1.14-2), libxdmcp6 (= 1:1.1.3-0ubuntu1), libxext6 (= 2:1.3.4-0ubuntu1), libxml2 (= 2.9.10+dfsg-5), libxnvctrl0 (= 440.82-0ubuntu1), libzstd1 (= 1.4.5+dfsg-3), linux-libc-dev (= 5.4.0-30.34), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), ocl-icd-libopencl1 (= 2.2.12-4), openmpi-bin (= 4.0.3-6ubuntu2), openmpi-common (= 4.0.3-6ubuntu2), openssh-client (= 1:8.3p1-1), passwd (= 1:4.8.1-1ubuntu6), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), pkg-config (= 0.29.2-1ubuntu1), po-debconf (= 1.0.21), sed (= 4.7-1build1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-3ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2020a-0ubuntu1), util-linux (= 2.35.2-9ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=8" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1595435136" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyml_3.3.20200621-1_riscv64.deb -------------------------------- new Debian package, version 2.0. size 1750936 bytes: control archive=1932 bytes. 1759 bytes, 32 lines control 1773 bytes, 25 lines md5sums Package: phyml Version: 3:3.3.20200621-1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4838 Depends: libc6 (>= 2.27), libopenmpi3 (>= 4.0.3), 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 2020-07-22 16:25 ./ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/bin/ -rwxr-xr-x root/root 579 2020-07-22 16:25 ./usr/bin/phyml -rwxr-xr-x root/root 1214328 2020-07-22 16:25 ./usr/bin/phyml-mpi drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/lib/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/lib/phyml/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/lib/phyml/bin/ -rwxr-xr-x root/root 1206000 2020-07-22 16:25 ./usr/lib/phyml/bin/phyml -rwxr-xr-x root/root 1214328 2020-07-22 16:25 ./usr/lib/phyml/bin/phyml-mpi drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/doc-base/ -rw-r--r-- root/root 202 2020-07-22 16:25 ./usr/share/doc-base/phyml drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/doc/phyml/ -rw-r--r-- root/root 2446 2020-07-22 16:25 ./usr/share/doc/phyml/README.Debian -rw-r--r-- root/root 1207 2020-07-22 16:25 ./usr/share/doc/phyml/changelog.Debian.gz -rw-r--r-- root/root 1490 2020-07-22 16:25 ./usr/share/doc/phyml/copyright drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/doc/phyml/examples/ -rw-r--r-- root/root 20905 2020-07-22 16:25 ./usr/share/doc/phyml/examples/example.nex drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/ -rw-r--r-- root/root 1900 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X1.mat -rw-r--r-- root/root 1899 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X2.mat -rw-r--r-- root/root 1893 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X3.mat -rw-r--r-- root/root 1895 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/X4.mat -rw-r--r-- root/root 1994 2020-07-14 09:31 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml -rw-r--r-- root/root 2175 2020-07-14 09:31 ./usr/share/doc/phyml/examples/nexus_example.nxs -rwxr-xr-x root/root 60771 2020-07-14 09:31 ./usr/share/doc/phyml/examples/nucleic drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/ -rw-r--r-- root/root 9115 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/flu.xml -rw-r--r-- root/root 70310 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs -rw-r--r-- root/root 1784 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt drwxr-xr-x root/root 0 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/ -rw-r--r-- root/root 2248 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/dating_example.xml -rw-r--r-- root/root 100171 2020-07-14 09:31 ./usr/share/doc/phyml/examples/phytime/seq.txt -rwxr-xr-x root/root 25990 2020-07-14 09:31 ./usr/share/doc/phyml/examples/proteic -rw-r--r-- root/root 976126 2020-07-14 09:31 ./usr/share/doc/phyml/phyml_manual.pdf -rw-r--r-- root/root 1257 2020-07-22 16:25 ./usr/share/doc/phyml/run-unit-test drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/man/ drwxr-xr-x root/root 0 2020-07-22 16:25 ./usr/share/man/man1/ -rw-r--r-- root/root 2899 2020-07-22 16:25 ./usr/share/man/man1/phyml.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 21704 Build-Time: 685 Distribution: groovy-proposed Host Architecture: riscv64 Install-Time: 191 Job: phyml_3.3.20200621-1.dsc Machine Architecture: riscv64 Package: phyml Package-Time: 907 Source-Version: 3:3.3.20200621-1 Space: 21704 Status: successful Version: 3:3.3.20200621-1 -------------------------------------------------------------------------------- Finished at 2020-07-23T05:29:04Z Build needed 00:15:07, 21704k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 Scanning for processes to kill in build PACKAGEBUILD-19626924 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 Stopping target for build PACKAGEBUILD-19626924 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=groovy --arch=riscv64 PACKAGEBUILD-19626924 Removing build PACKAGEBUILD-19626924