https://launchpad.net/ubuntu/+source/phyml/3:3.3.20200621-1/+build/19626925 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-016 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:15:38 UTC 2020 s390x Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 23 Jul 05:12:21 ntpdate[1860]: adjust time server 10.211.37.1 offset -0.013469 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19626925 --image-type chroot /home/buildd/filecache-default/0c27a67c210d6cb13869ddd14c37f7dc742e8ea2 Creating target for build PACKAGEBUILD-19626925 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19626925 Starting target for build PACKAGEBUILD-19626925 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19626925 '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-19626925 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19626925 Updating target for build PACKAGEBUILD-19626925 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 s390x Packages [931 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe s390x Packages [8403 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5232 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x Packages [58.5 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [35.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe s390x Packages [505 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [238 kB] Fetched 16.5 MB in 3s (5352 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed6 libnettle8 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-s390x-linux-gnu bsdutils build-essential bzip2 ca-certificates coreutils cpp-9 dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan5 libassuan0 libatomic1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libidn2-0 libitm1 libjson-c4 libkmod2 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libnpth0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.30 libprocps8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin openssl passwd perl perl-base perl-modules-5.30 pinentry-curses pkgbinarymangler procps sed systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata ubuntu-keyring util-linux xz-utils 125 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 62.0 MB of archives. After this operation, 2036 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main s390x libcrypt-dev s390x 1:4.4.16-1ubuntu1 [107 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main s390x libc6-dev s390x 2.31-0ubuntu10 [2028 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main s390x libc-dev-bin s390x 2.31-0ubuntu10 [63.9 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main s390x libcrypt1 s390x 1:4.4.16-1ubuntu1 [80.7 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x linux-libc-dev s390x 5.4.0-42.46 [1109 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main s390x libatomic1 s390x 10.1.0-6ubuntu1 [8384 B] Get:7 http://ftpmaster.internal/ubuntu groovy/main s390x libubsan1 s390x 10.1.0-6ubuntu1 [155 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main s390x libitm1 s390x 10.1.0-6ubuntu1 [28.6 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main s390x libgomp1 s390x 10.1.0-6ubuntu1 [115 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main s390x gcc-10-base s390x 10.1.0-6ubuntu1 [19.6 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main s390x libgcc-s1 s390x 10.1.0-6ubuntu1 [30.4 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main s390x libcc1-0 s390x 10.1.0-6ubuntu1 [39.4 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main s390x libstdc++6 s390x 10.1.0-6ubuntu1 [517 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main s390x libc6 s390x 2.31-0ubuntu10 [2275 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main s390x base-files s390x 11ubuntu9 [60.1 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main s390x debianutils s390x 4.11 [85.6 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main s390x bash s390x 5.0-6ubuntu2 [621 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x bsdutils s390x 1:2.35.2-9ubuntu1 [82.5 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main s390x coreutils s390x 8.30-3ubuntu3 [1227 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main s390x dpkg s390x 1.19.7ubuntu4 [1113 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main s390x perl-modules-5.30 all 5.30.3-4 [2740 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main s390x libperl5.30 s390x 5.30.3-4 [3778 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main s390x perl s390x 5.30.3-4 [223 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main s390x perl-base s390x 5.30.3-4 [1424 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main s390x bzip2 s390x 1.0.8-4ubuntu2 [33.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main s390x libbz2-1.0 s390x 1.0.8-4ubuntu2 [32.4 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main s390x debconf all 1.5.74 [121 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main s390x dash s390x 0.5.10.2-7 [86.0 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main s390x diffutils s390x 1:3.7-3build1 [195 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main s390x gzip s390x 1.10-2ubuntu1 [96.0 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main s390x login s390x 1:4.8.1-1ubuntu6 [218 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main s390x ncurses-bin s390x 6.2-1 [170 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main s390x sed s390x 4.7-1build1 [188 kB] Get:34 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libselinux1 s390x 3.1-2 [65.7 kB] Get:35 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libblkid1 s390x 2.35.2-9ubuntu1 [124 kB] Get:36 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libuuid1 s390x 2.35.2-9ubuntu1 [22.0 kB] Get:37 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libfdisk1 s390x 2.35.2-9ubuntu1 [156 kB] Get:38 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libmount1 s390x 2.35.2-9ubuntu1 [135 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main s390x libncurses6 s390x 6.2-1 [94.9 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main s390x libncursesw6 s390x 6.2-1 [122 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main s390x libtinfo6 s390x 6.2-1 [84.6 kB] Get:42 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libsmartcols1 s390x 2.35.2-9ubuntu1 [89.3 kB] Get:43 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x fdisk s390x 2.35.2-9ubuntu1 [118 kB] Get:44 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x util-linux s390x 2.35.2-9ubuntu1 [1010 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main s390x init-system-helpers all 1.58 [38.4 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main s390x libc-bin s390x 2.31-0ubuntu10 [523 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main s390x ncurses-base all 6.2-1 [18.7 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main s390x sysvinit-utils s390x 2.96-3ubuntu1 [20.6 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main s390x libgpg-error0 s390x 1.38-2 [60.0 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main s390x libgcrypt20 s390x 1.8.5-5ubuntu2 [352 kB] Get:51 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x liblzma5 s390x 5.2.4-1ubuntu1 [90.5 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main s390x systemd-sysv s390x 245.6-3ubuntu3 [10.3 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main s390x systemd-timesyncd s390x 245.6-3ubuntu3 [26.0 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main s390x libacl1 s390x 2.2.53-8 [18.5 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main s390x libapparmor1 s390x 2.13.3-7ubuntu6 [32.9 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main s390x libcap2 s390x 1:2.36-1 [17.0 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main s390x libargon2-1 s390x 0~20171227-0.2build20.10.0 [44.4 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main s390x libudev1 s390x 245.6-3ubuntu3 [69.5 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main s390x libdevmapper1.02.1 s390x 2:1.02.167-1ubuntu3 [122 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main s390x libjson-c4 s390x 0.13.1+dfsg-9 [28.1 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main s390x libssl1.1 s390x 1.1.1f-1ubuntu3 [987 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main s390x libcryptsetup12 s390x 2:2.3.3-1ubuntu3 [170 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main s390x libnettle8 s390x 3.6-2 [130 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main s390x libgmp10 s390x 2:6.2.0+dfsg-6 [248 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main s390x libhogweed6 s390x 3.6-2 [193 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main s390x libunistring2 s390x 0.9.10-4 [357 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main s390x libidn2-0 s390x 2.3.0-1 [51.7 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main s390x libgnutls30 s390x 3.6.13-4ubuntu4 [655 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main s390x libkmod2 s390x 27+20200310-2ubuntu1 [41.4 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main s390x libpam0g s390x 1.3.1-5ubuntu5 [52.9 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main s390x libseccomp2 s390x 2.4.3-1ubuntu4 [44.2 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x mount s390x 2.35.2-9ubuntu1 [113 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main s390x systemd s390x 245.6-3ubuntu3 [3440 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main s390x libsystemd0 s390x 245.6-3ubuntu3 [245 kB] Get:75 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libzstd1 s390x 1.4.5+dfsg-3 [340 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main s390x libapt-pkg6.0 s390x 2.1.7 [786 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main s390x gpgv s390x 2.2.20-1ubuntu1 [186 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main s390x ubuntu-keyring all 2020.06.17.1 [22.2 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main s390x apt s390x 2.1.7 [1249 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu5 [36.5 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main s390x libpam-modules s390x 1.3.1-5ubuntu5 [242 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main s390x logsave s390x 1.45.6-1ubuntu1 [10.1 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main s390x libext2fs2 s390x 1.45.6-1ubuntu1 [178 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main s390x e2fsprogs s390x 1.45.6-1ubuntu1 [508 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main s390x init s390x 1.58 [6172 B] Get:86 http://ftpmaster.internal/ubuntu groovy/main s390x libcap-ng0 s390x 0.7.9-2.2 [10.9 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main s390x libdebconfclient0 s390x 0.252ubuntu1 [6104 B] Get:88 http://ftpmaster.internal/ubuntu groovy/main s390x libpam-runtime all 1.3.1-5ubuntu5 [37.3 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/main s390x libpcre3 s390x 2:8.39-13 [157 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main s390x libsepol1 s390x 3.1-1 [230 kB] Get:91 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libsemanage-common all 3.1-1 [10.2 kB] Get:92 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libsemanage1 s390x 3.1-1 [80.7 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main s390x passwd s390x 1:4.8.1-1ubuntu6 [778 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main s390x libcom-err2 s390x 1.45.6-1ubuntu1 [9512 B] Get:95 http://ftpmaster.internal/ubuntu groovy/main s390x libprocps8 s390x 2:3.3.16-5ubuntu1 [30.7 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main s390x libss2 s390x 1.45.6-1ubuntu1 [11.0 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main s390x procps s390x 2:3.3.16-5ubuntu1 [225 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main s390x openssl s390x 1.1.1f-1ubuntu3 [609 kB] Get:99 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x ca-certificates all 20200601 [147 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main s390x libsqlite3-0 s390x 3.32.3-1 [514 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main s390x tzdata all 2020a-0ubuntu1 [293 kB] Get:102 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x xz-utils s390x 5.2.4-1ubuntu1 [80.5 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main s390x libctf0 s390x 2.34.90.20200716-1ubuntu1 [43.7 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/main s390x binutils-s390x-linux-gnu s390x 2.34.90.20200716-1ubuntu1 [1455 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/main s390x libbinutils s390x 2.34.90.20200716-1ubuntu1 [308 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main s390x binutils s390x 2.34.90.20200716-1ubuntu1 [3348 B] Get:107 http://ftpmaster.internal/ubuntu groovy/main s390x binutils-common s390x 2.34.90.20200716-1ubuntu1 [212 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/main s390x libctf-nobfd0 s390x 2.34.90.20200716-1ubuntu1 [44.4 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/main s390x make s390x 4.3-4ubuntu1 [165 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/main s390x dpkg-dev all 1.19.7ubuntu4 [679 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/main s390x libdpkg-perl all 1.19.7ubuntu4 [230 kB] Get:112 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x build-essential s390x 12.8ubuntu3 [4636 B] Get:113 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libasan5 s390x 9.3.0-16ubuntu1 [361 kB] Get:114 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x g++-9 s390x 9.3.0-16ubuntu1 [6610 kB] Get:115 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gcc-9 s390x 9.3.0-16ubuntu1 [6474 kB] Get:116 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libstdc++-9-dev s390x 9.3.0-16ubuntu1 [1678 kB] Get:117 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgcc-9-dev s390x 9.3.0-16ubuntu1 [706 kB] Get:118 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x cpp-9 s390x 9.3.0-16ubuntu1 [5731 kB] Get:119 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gcc-9-base s390x 9.3.0-16ubuntu1 [19.3 kB] Get:120 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libmpfr6 s390x 4.1.0-3 [254 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main s390x libassuan0 s390x 2.5.3-7.1 [32.8 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main s390x pinentry-curses s390x 1.1.0-4build1 [35.3 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main s390x libnpth0 s390x 1.6-2 [7592 B] Get:124 http://ftpmaster.internal/ubuntu groovy/main s390x gpg s390x 2.2.20-1ubuntu1 [448 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main s390x gpgconf s390x 2.2.20-1ubuntu1 [119 kB] Get:126 http://ftpmaster.internal/ubuntu groovy/main s390x gpg-agent s390x 2.2.20-1ubuntu1 [218 kB] Get:127 http://ftpmaster.internal/ubuntu groovy/main s390x pkgbinarymangler all 146 [31.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 62.0 MB in 1s (67.1 MB/s) (Reading database ... 12607 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.16-1ubuntu1_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.16-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Preparing to unpack .../libc6-dev_2.31-0ubuntu10_s390x.deb ... Unpacking libc6-dev:s390x (2.31-0ubuntu10) over (2.31-0ubuntu9) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu10_s390x.deb ... Unpacking libc-dev-bin (2.31-0ubuntu10) over (2.31-0ubuntu9) ... Preparing to unpack .../libcrypt1_1%3a4.4.16-1ubuntu1_s390x.deb ... Unpacking libcrypt1:s390x (1:4.4.16-1ubuntu1) over (1:4.4.10-10ubuntu4) ... Setting up libcrypt1:s390x (1:4.4.16-1ubuntu1) ... (Reading database ... 12606 files and directories currently installed.) Preparing to unpack .../0-linux-libc-dev_5.4.0-42.46_s390x.deb ... Unpacking linux-libc-dev:s390x (5.4.0-42.46) over (5.4.0-26.30) ... Preparing to unpack .../1-libatomic1_10.1.0-6ubuntu1_s390x.deb ... Unpacking libatomic1:s390x (10.1.0-6ubuntu1) over (10-20200411-0ubuntu1) ... 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Setting up libassuan0:s390x (2.5.3-7.1) ... Setting up libgomp1:s390x (10.1.0-6ubuntu1) ... Setting up bzip2 (1.0.8-4ubuntu2) ... Setting up tzdata (2020a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jul 23 05:12:40 UTC 2020. Universal Time is now: Thu Jul 23 05:12:40 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.3-4ubuntu1) ... Setting up libmpfr6:s390x (4.1.0-3) ... Setting up libncurses6:s390x (6.2-1) ... Setting up xz-utils (5.2.4-1ubuntu1) ... Setting up libatomic1:s390x (10.1.0-6ubuntu1) ... Setting up libss2:s390x (1.45.6-1ubuntu1) ... Setting up libncursesw6:s390x (6.2-1) ... Setting up logsave (1.45.6-1ubuntu1) ... Setting up libfdisk1:s390x (2.35.2-9ubuntu1) ... Setting up libubsan1:s390x (10.1.0-6ubuntu1) ... Setting up libcrypt-dev:s390x (1:4.4.16-1ubuntu1) ... Setting up gpgconf (2.2.20-1ubuntu1) ... Setting up libperl5.30:s390x (5.30.3-4) ... Setting up libbinutils:s390x (2.34.90.20200716-1ubuntu1) ... 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Setting up procps (2:3.3.16-5ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Removing obsolete conffile /etc/sysctl.d/10-link-restrictions.conf ... Setting up cpp-9 (9.3.0-16ubuntu1) ... Setting up libc6-dev:s390x (2.31-0ubuntu10) ... Setting up dpkg-dev (1.19.7ubuntu4) ... Setting up libgcc-9-dev:s390x (9.3.0-16ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Setting up gcc-9 (9.3.0-16ubuntu1) ... Setting up libstdc++-9-dev:s390x (9.3.0-16ubuntu1) ... Setting up g++-9 (9.3.0-16ubuntu1) ... Processing triggers for systemd (245.6-3ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19626925 s390x groovy-proposed -c chroot:build-PACKAGEBUILD-19626925 --arch=s390x --dist=groovy-proposed --nolog phyml_3.3.20200621-1.dsc Initiating build PACKAGEBUILD-19626925 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:15:38 UTC 2020 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-016.buildd +==============================================================================+ | phyml 3:3.3.20200621-1 (s390x) 23 Jul 2020 05:12 | +==============================================================================+ Package: phyml Version: 3:3.3.20200621-1 Source Version: 3:3.3.20200621-1 Distribution: groovy-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/phyml-rIHfDE/phyml-3.3.20200621' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-rIHfDE' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19626925/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phyml_3.3.20200621-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-qK9pOa/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-qK9pOa/apt_archive ./ InRelease Get:2 copy:/<>/resolver-qK9pOa/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-qK9pOa/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-qK9pOa/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-qK9pOa/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (272 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-qK9pOa/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12619 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath Filtered Build-Depends: debhelper-compat (= 13), pkg-config, libopenmpi-dev, chrpath dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<>/resolver-DgTweZ/apt_archive/sbuild-build-depends-phyml-dummy.deb'. Ign:1 copy:/<>/resolver-DgTweZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DgTweZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-DgTweZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DgTweZ/apt_archive ./ Sources [236 B] Get:5 copy:/<>/resolver-DgTweZ/apt_archive ./ Packages [555 B] Fetched 2910 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install phyml build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed5 libnettle7 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils 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 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-9-multilib 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 bsdextrautils 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-phyml-dummy zlib1g-dev 0 upgraded, 83 newly installed, 0 to remove and 0 not upgraded. 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Get:32 http://ftpmaster.internal/ubuntu groovy/main s390x libsigsegv2 s390x 2.12-2build1 [13.7 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main s390x m4 s390x 1.4.18-4 [196 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main s390x autoconf all 2.69-11.1 [321 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main s390x automake all 1:1.16.2-3ubuntu1 [548 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main s390x autopoint all 0.19.8.1-10build1 [412 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/universe s390x chrpath s390x 0.16-2 [13.2 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main s390x libtool all 2.4.6-14 [161 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main s390x dh-autoreconf all 19 [16.1 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main s390x libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:44 http://ftpmaster.internal/ubuntu groovy/main s390x libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main s390x dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:46 http://ftpmaster.internal/ubuntu groovy/main s390x dwz s390x 0.13-5 [146 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main s390x libcroco3 s390x 0.6.13-1 [73.7 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main s390x gettext s390x 0.19.8.1-10build1 [867 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main s390x po-debconf all 1.0.21 [233 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main s390x debhelper all 13.2ubuntu1 [878 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main s390x libgfortran5 s390x 10.1.0-6ubuntu1 [415 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x libgfortran-9-dev s390x 9.3.0-16ubuntu1 [413 kB] Get:54 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x gfortran-9 s390x 9.3.0-16ubuntu1 [6122 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-3-200 s390x 3.4.0-1 [50.3 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-route-3-200 s390x 3.4.0-1 [137 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main s390x libibverbs1 s390x 29.0-1build1 [51.1 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main s390x ibverbs-providers s390x 29.0-1build1 [222 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-2.1-7 s390x 2.1.12-stable-1 [126 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-core-2.1-7 s390x 2.1.12-stable-1 [82.6 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-extra-2.1-7 s390x 2.1.12-stable-1 [54.4 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-pthreads-2.1-7 s390x 2.1.12-stable-1 [7196 B] Get:63 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-openssl-2.1-7 s390x 2.1.12-stable-1 [13.5 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main s390x libevent-dev s390x 2.1.12-stable-1 [251 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc15 s390x 2.2.0+dfsg-3 [117 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main s390x libltdl7 s390x 2.4.6-14 [38.2 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main s390x libltdl-dev s390x 2.4.6-14 [162 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-3-dev s390x 3.4.0-1 [89.9 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main s390x libnl-route-3-dev s390x 3.4.0-1 [155 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main s390x libpciaccess0 s390x 0.16-0ubuntu1 [16.5 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main s390x libxnvctrl0 s390x 440.82-0ubuntu1 [10.9 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main s390x ocl-icd-libopencl1 s390x 2.2.12-4 [31.5 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc-plugins s390x 2.2.0+dfsg-3 [13.9 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/universe s390x libpmix2 s390x 3.1.5-1 [428 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/universe s390x libopenmpi3 s390x 4.0.3-6ubuntu2 [1822 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/universe s390x openmpi-common all 4.0.3-6ubuntu2 [151 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/universe s390x openmpi-bin s390x 4.0.3-6ubuntu2 [66.0 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main s390x pkg-config s390x 0.29.2-1ubuntu1 [45.0 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu1 [166 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main s390x libnuma-dev s390x 2.0.12-1build1 [32.4 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/universe s390x libhwloc-dev s390x 2.2.0+dfsg-3 [189 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main s390x libibverbs-dev s390x 29.0-1build1 [441 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/universe s390x libopenmpi-dev s390x 4.0.3-6ubuntu2 [812 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.6 MB in 2s (17.5 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 12619 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.35.2-9ubuntu1_s390x.deb ... Unpacking bsdextrautils (2.35.2-9ubuntu1) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../01-libuchardet0_0.0.7-1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_s390x.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../03-libpipeline1_1.5.2-2build1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_s390x.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.38-5_s390x.deb ... Unpacking libmagic-mgc (1:5.38-5) ... 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Unpacking libibverbs-dev:s390x (29.0-1build1) ... Selecting previously unselected package libopenmpi-dev:s390x. Preparing to unpack .../81-libopenmpi-dev_4.0.3-6ubuntu2_s390x.deb ... Unpacking libopenmpi-dev:s390x (4.0.3-6ubuntu2) ... Selecting previously unselected package sbuild-build-depends-phyml-dummy. Preparing to unpack .../82-sbuild-build-depends-phyml-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-phyml-dummy (0.invalid.0) ... Setting up libpipeline1:s390x (1.5.2-2build1) ... Setting up libpciaccess0:s390x (0.16-0ubuntu1) ... Setting up libxau6:s390x (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:s390x (1.6.1-2ubuntu1) ... Setting up bsdextrautils (2.35.2-9ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:s390x (2.64.4-1) ... No schema files found: doing nothing. Setting up libicu66:s390x (66.1-2ubuntu3) ... Setting up libdebhelper-perl (13.2ubuntu1) ... Setting up libmagic1:s390x (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libcbor0.6:s390x (0.6.0-0ubuntu2) ... Setting up libkrb5support0:s390x (1.17-10) ... Setting up autotools-dev (20180224.1) ... Setting up libx11-data (2:1.6.9-2ubuntu1) ... Setting up libsigsegv2:s390x (2.12-2build1) ... Setting up libhwloc15:s390x (2.2.0+dfsg-3) ... Setting up libevent-core-2.1-7:s390x (2.1.12-stable-1) ... Setting up libevent-2.1-7:s390x (2.1.12-stable-1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up libk5crypto3:s390x (1.17-10) ... Setting up libltdl7:s390x (2.4.6-14) ... Setting up libgfortran5:s390x (10.1.0-6ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-2ubuntu1) ... Setting up libnuma1:s390x (2.0.12-1build1) ... Setting up ocl-icd-libopencl1:s390x (2.2.12-4) ... Setting up libuchardet0:s390x (0.0.7-1) ... Setting up libnl-3-200:s390x (3.4.0-1) ... Setting up openmpi-common (4.0.3-6ubuntu2) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:s390x (1.17-10) ... Setting up libfido2-1:s390x (1.4.0-2) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libelf1:s390x (0.180-0ubuntu1) ... Setting up libxml2:s390x (2.9.10+dfsg-5) ... Setting up chrpath (0.16-2) ... Setting up libevent-pthreads-2.1-7:s390x (2.1.12-stable-1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu1) ... Setting up libevent-extra-2.1-7:s390x (2.1.12-stable-1) ... Setting up libxcb1:s390x (1.14-2) ... Setting up libtool (2.4.6-14) ... Setting up libedit2:s390x (3.1-20191231-1) ... Setting up libgfortran-9-dev:s390x (9.3.0-16ubuntu1) ... Setting up libevent-openssl-2.1-7:s390x (2.1.12-stable-1) ... Setting up m4 (1.4.18-4) ... Setting up libnuma-dev:s390x (2.0.12-1build1) ... Setting up libnl-route-3-200:s390x (3.4.0-1) ... Setting up libevent-dev (2.1.12-stable-1) ... Setting up libgssapi-krb5-2:s390x (1.17-10) ... Setting up libcroco3:s390x (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up libnl-3-dev:s390x (3.4.0-1) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:s390x (2:1.6.9-2ubuntu1) ... 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:s390x (29.0-1build1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up gfortran-9 (9.3.0-16ubuntu1) ... Setting up ibverbs-providers:s390x (29.0-1build1) ... Setting up openssh-client (1:8.3p1-1) ... Setting up libxext6:s390x (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxnvctrl0:s390x (440.82-0ubuntu1) ... Setting up libnl-route-3-dev:s390x (3.4.0-1) ... Setting up libltdl-dev:s390x (2.4.6-14) ... Setting up libhwloc-dev:s390x (2.2.0+dfsg-3) ... Setting up po-debconf (1.0.21) ... Setting up libibverbs-dev:s390x (29.0-1build1) ... Setting up libhwloc-plugins:s390x (2.2.0+dfsg-3) ... Setting up libpmix2:s390x (3.1.5-1) ... Setting up libopenmpi3:s390x (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:s390x (4.0.3-6ubuntu2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/openmpi/include to provide /usr/include/s390x-linux-gnu/mpi (mpi-s390x-linux-gnu) in auto mode Setting up dh-autoreconf (19) ... Setting up debhelper (13.2ubuntu1) ... Setting up sbuild-build-depends-phyml-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic s390x (s390x) Toolchain package versions: binutils_2.34.90.20200716-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-9_9.3.0-16ubuntu1 gcc-9_9.3.0-16ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-9-dev_9.3.0-16ubuntu1 libstdc++6_10.1.0-6ubuntu1 linux-libc-dev_5.4.0-42.46 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-s390x-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_9.3.0-16ubuntu1 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 fdisk_2.35.2-9ubuntu1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-16ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-6ubuntu1 gcc-9_9.3.0-16ubuntu1 gcc-9-base_9.3.0-16ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gfortran-9_9.3.0-16ubuntu1 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_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan5_9.3.0-16ubuntu1 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 libcap2_1:2.36-1 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 libcryptsetup12_2:2.3.3-1ubuntu3 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 libdevmapper1.02.1_2:1.02.167-1ubuntu3 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 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.35.2-9ubuntu1 libffi7_3.3-4 libfido2-1_1.4.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-16ubuntu1 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_9.3.0-16ubuntu1 libgfortran5_10.1.0-6ubuntu1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.1.0-6ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed5_3.5.1+really3.5.1-2 libhogweed6_3.6-2 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 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.1.0-6ubuntu1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-3_1.17-10 libkrb5support0_1.17-10 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 libncurses6_6.2-1 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 libprocps8_2:3.3.16-5ubuntu1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu4 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_9.3.0-16ubuntu1 libstdc++6_10.1.0-6ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-6ubuntu1 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_5.4.0-42.46 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 procps_2:3.3.16-5ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 systemd_245.6-3ubuntu3 systemd-sysv_245.6-3ubuntu3 systemd-timesyncd_245.6-3ubuntu3 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 ------------- gpgv: Signature made Wed Jul 22 19:49:47 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phyml_3.3.20200621-1.dsc dpkg-source: info: extracting phyml in phyml-3.3.20200621 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 disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 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-19626925 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19626925 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19626925 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- 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 s390x 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=s390x-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/s390x-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... s390x-ibm-linux-gnu checking host system type... s390x-ibm-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 s390x-ibm-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 -j4 "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 .: 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 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 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 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/s390x-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 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 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/s390x-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 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 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/s390x-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 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 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 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]: Nothing to be done for 'all-am'. 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=s390x-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/s390x-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... s390x-ibm-linux-gnu checking host system type... s390x-ibm-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 s390x-ibm-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 -j4 "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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 .: Building [phyml-mpi]. Version 3.3.3:3.3.20200621-1 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 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/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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 gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-linux-gnu/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'all-am'. 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 -j4 check VERBOSE=1 make[1]: Entering directory '/<>' Making check in src make[2]: Entering directory '/<>/src' gcc -pthread -I/usr/lib/s390x-linux-gnu/openmpi/include -I/usr/lib/s390x-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/s390x-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]: Nothing to be done for 'check-am'. 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 -j4 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: 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_s390x.deb'. pkgstripfiles: Truncating usr/share/doc/phyml/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package phyml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phyml' in '../phyml_3.3.20200621-1_s390x.deb'. Renaming phyml-dbgsym_3.3.20200621-1_s390x.deb to phyml-dbgsym_3.3.20200621-1_s390x.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../phyml_3.3.20200621-1_s390x.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 20200723-0513 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyml_3.3.20200621-1_s390x.changes: ----------------------------------- Format: 1.8 Date: Wed, 22 Jul 2020 16:25:36 +0000 Source: phyml Binary: phyml Architecture: s390x 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. Checksums-Sha1: 6dedabb45b8235ae7f738fbd5d5b39eb2141d489 34640 phyml-dbgsym_3.3.20200621-1_s390x.ddeb 58ba78af4568ceefce7e3824f787856320f4e28b 6901 phyml_3.3.20200621-1_s390x.buildinfo 53c5d30a08c7cd54a4186ceef095277e5f0de720 1799124 phyml_3.3.20200621-1_s390x.deb Checksums-Sha256: e70c8c465bb652fbd0414dd65915e4c7d6bf8cc2d606c4297100ac255144fb0a 34640 phyml-dbgsym_3.3.20200621-1_s390x.ddeb adbf28f9e93f5cd56929ee492ecbcd437ac1f87f81a9f9149543ca51d2122220 6901 phyml_3.3.20200621-1_s390x.buildinfo ab67a97728b09a3b016faf7be325ae1d46a513cea1da6eb958024a85f15b8843 1799124 phyml_3.3.20200621-1_s390x.deb Files: c3d7daaa4204062c0998059872f7b5e4 34640 debug optional phyml-dbgsym_3.3.20200621-1_s390x.ddeb e2ada0253d9f2fbccaec268ceaf9ebc9 6901 science optional phyml_3.3.20200621-1_s390x.buildinfo 787315262006e748a00dea36a9bc54da 1799124 science optional phyml_3.3.20200621-1_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyml_3.3.20200621-1_s390x.deb ------------------------------ new debian package, version 2.0. size 1799124 bytes: control archive=1936 bytes. 1757 bytes, 32 lines control 1773 bytes, 25 lines md5sums Package: phyml Version: 3:3.3.20200621-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7598 Depends: libc6 (>= 2.29), 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. . 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