Wed Apr 8 06:54:24 UTC 2020 I: starting to build phyml/buster/i386 on jenkins on '2020-04-08 06:54' Wed Apr 8 06:54:24 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/4792/console.log Wed Apr 8 06:54:24 UTC 2020 I: Downloading source for buster/phyml=3:3.3.20180621-2 --2020-04-08 06:54:25-- http://deb.debian.org/debian/pool/main/p/phyml/phyml_3.3.20180621-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2064 (2.0K) Saving to: ‘phyml_3.3.20180621-2.dsc’ 0K .. 100% 278M=0s 2020-04-08 06:54:25 (278 MB/s) - ‘phyml_3.3.20180621-2.dsc’ saved [2064/2064] Wed Apr 8 06:54:25 UTC 2020 I: phyml_3.3.20180621-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phyml Binary: phyml Architecture: any Version: 3:3.3.20180621-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Kevin Murray Homepage: http://www.atgc-montpellier.fr/phyml Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/phyml Vcs-Git: https://salsa.debian.org/med-team/phyml.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), pkg-config, libopenmpi-dev, chrpath Package-List: phyml deb science optional arch=any Checksums-Sha1: 2fb61293e900e62af0c9c55af72dae5905ddd8e0 2306290 phyml_3.3.20180621.orig.tar.gz dfa6766af7418f4daf74136b28a8da05889ceccf 16868 phyml_3.3.20180621-2.debian.tar.xz Checksums-Sha256: a66c1c5758408578c34a17733f92db11a67aa572a06a9b5e3046009ee8bed0d3 2306290 phyml_3.3.20180621.orig.tar.gz 1de90506bf598c98ad7ab95d586dab062d2a2f15e59e18e47fd6e7741e0287b0 16868 phyml_3.3.20180621-2.debian.tar.xz Files: 39f5df7eeb317466ab5724b38efb6915 2306290 phyml_3.3.20180621.orig.tar.gz dfeea593061288cef9af6bf00855177f 16868 phyml_3.3.20180621-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAlszu1wACgkQr8/sjmac 4cL7Rg/+KMR4P4dI15a6vNCnATbYCLt2KdlhAa0WgLrDS8fWfsICngJq/NsBhjy2 EAt08gIoFTNtO892P2p+23ZkFVJUcloiDr12E0tBjlVrpmt/DZCmUJtI9QvN97wF BBDboNbDXyzzCr+4y0aBElsUv0VDghB6qcwmf7KHvR/y5pnykaK45rsaCfNQT4dX 0JemGbGeLmcK565Zo5iCOJmJQ/1NmT3CGI8PNFau/sFF9YbbENo/P6KRy2kP1JJX 3PSCKqXbAqP9D9NRjk3ooY4IAYRSg4sHOFJ15vRWUSk2KBiIuygUQk1tF8tg5J/o P6Eys63InqmsOgLK5BTZ9JT6NdEpk7T5E5XwGsGzK5yKdUs479KCuJRv2AG/XDAM hahv70p690FOIvIW8sW1w7EdV0x/RYJzN9FYX/Fo8xdzSTivurAdYjA0grYGvgbY GsvBQCm07D55bdHyofPPaR0e/lHUHJ4/jLnxdTVSD3Q6cYV0FNGrBiunDB/WmwJo na1I0aJKUyj7JgQeUMnIxErscf8xSyy9fQKNOH+KptmJH3Pc1oTPbHjqzpe/heVb 7DPAz4XyhxQKkIVOskWBXc8nHGLwTiLc4wmGEyBED6KyqYcjGjD65bNrRLG3LS8R aDfEnD5Z4eOKvJSbhURj3m5K37wfPfdk/MyWwqkwwYvQtng4NHU= =+xdE -----END PGP SIGNATURE----- Wed Apr 8 06:54:25 UTC 2020 I: Checking whether the package is not for us Wed Apr 8 06:54:25 UTC 2020 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Wed Apr 8 06:54:25 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Wed Apr 8 06:59:14 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 7 18:54:29 -12 2020 I: pbuilder-time-stamp: 1586328869 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [phyml_3.3.20180621-2.dsc] I: copying [./phyml_3.3.20180621.orig.tar.gz] I: copying [./phyml_3.3.20180621-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jun 27 04:29:16 2018 -12 gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phyml_3.3.20180621-2.dsc dpkg-source: info: extracting phyml in phyml-3.3.20180621 dpkg-source: info: unpacking phyml_3.3.20180621.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20180621-2.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 I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), pkg-config, libopenmpi-dev, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} chrpath{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpsm-infinipath1{a} librdmacm1{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 30.5 MB of archives. After unpacking 111 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libedit2 i386 3.1-20181209-1 [98.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 14 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u2 [1538 kB] Get: 17 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 19 http://deb.debian.org/debian buster/main i386 openssh-client i386 1:7.9p1-10+deb10u2 [834 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 21 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 22 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 23 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 24 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 25 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 26 http://deb.debian.org/debian buster/main i386 chrpath i386 0.16-2+b1 [17.5 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 28 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 30 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 31 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 33 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 39 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 40 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 41 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 42 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libnl-3-200 i386 3.4.0-1 [65.8 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libnl-route-3-200 i386 3.4.0-1 [170 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libibverbs1 i386 22.1-1 [53.9 kB] Get: 46 http://deb.debian.org/debian buster/main i386 ibverbs-providers i386 22.1-1 [201 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libevent-2.1-6 i386 2.1.8-stable-4 [191 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libevent-core-2.1-6 i386 2.1.8-stable-4 [137 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libevent-pthreads-2.1-6 i386 2.1.8-stable-4 [48.1 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6 [178 kB] Get: 51 http://deb.debian.org/debian buster/main i386 librdmacm1 i386 22.1-1 [68.8 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libfabric1 i386 1.6.2-3 [364 kB] Get: 53 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libltdl7 i386 2.4.6-9 [392 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libnuma1 i386 2.0.12-1 [27.7 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libhwloc5 i386 1.11.12-3 [119 kB] Get: 57 http://deb.debian.org/debian buster/main i386 libnuma-dev i386 2.0.12-1 [40.9 kB] Get: 58 http://deb.debian.org/debian buster/main i386 libltdl-dev i386 2.4.6-9 [164 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libhwloc-dev i386 1.11.12-3 [185 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libpciaccess0 i386 0.14-1 [55.7 kB] Get: 61 http://deb.debian.org/debian buster/main i386 ocl-icd-libopencl1 i386 2.2.12-2 [37.2 kB] Get: 62 http://deb.debian.org/debian buster/main i386 libhwloc-plugins i386 1.11.12-3 [17.8 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libnl-3-dev i386 3.4.0-1 [107 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libnl-route-3-dev i386 3.4.0-1 [193 kB] Get: 65 http://deb.debian.org/debian buster/main i386 libibverbs-dev i386 22.1-1 [385 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libpmix2 i386 3.1.2-3 [541 kB] Get: 67 http://deb.debian.org/debian buster/main i386 libopenmpi3 i386 3.1.3-11 [2236 kB] Get: 68 http://deb.debian.org/debian buster/main i386 openmpi-common all 3.1.3-11 [165 kB] Get: 69 http://deb.debian.org/debian buster/main i386 openmpi-bin i386 3.1.3-11 [200 kB] Get: 70 http://deb.debian.org/debian buster/main i386 libopenmpi-dev i386 3.1.3-11 [963 kB] Get: 71 http://deb.debian.org/debian buster/main i386 pkg-config i386 0.29-6 [64.7 kB] Fetched 30.5 MB in 12s (2497 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../11-libedit2_3.1-20181209-1_i386.deb ... Unpacking libedit2:i386 (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../12-libkeyutils1_1.6-6_i386.deb ... Unpacking libkeyutils1:i386 (1.6-6) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../13-libkrb5support0_1.17-3_i386.deb ... Unpacking libkrb5support0:i386 (1.17-3) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../14-libk5crypto3_1.17-3_i386.deb ... Unpacking libk5crypto3:i386 (1.17-3) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../15-libssl1.1_1.1.1d-0+deb10u2_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u2) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../16-libkrb5-3_1.17-3_i386.deb ... Unpacking libkrb5-3:i386 (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../17-libgssapi-krb5-2_1.17-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.17-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../18-openssh-client_1%3a7.9p1-10+deb10u2_i386.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../19-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../20-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... 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Setting up openmpi-bin (3.1.3-11) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:i386 (3.1.3-11) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/phyml-3.3.20180621/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20180621-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Graham Inggs dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/phyml-3.3.20180621' # 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 make[1]: Leaving directory '/build/phyml-3.3.20180621' dh_clean debian/rules build dh build dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/phyml-3.3.20180621' dh_autoreconf --as-needed make[1]: Leaving directory '/build/phyml-3.3.20180621' debian/rules override_dh_auto_build make[1]: Entering directory '/build/phyml-3.3.20180621' # 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=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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... i686-pc-linux-gnu checking host system type... i686-pc-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 i686-pc-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 configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j10 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20180621' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20180621' Making all in src make[4]: Entering directory '/build/phyml-3.3.20180621/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o main.o main.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o utilities.o utilities.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o optimiz.o optimiz.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o lk.o lk.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o bionj.o bionj.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o models.o models.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o free.o free.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o help.o help.c .: Building [phyml]. Version 3.3.3:3.3.20180621-2 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o simu.o simu.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o eigen.o eigen.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o pars.o pars.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o alrt.o alrt.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o interface.o interface.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o cl.o cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o spr.o spr.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o draw.o draw.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o stats.o stats.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o rates.o rates.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mcmc.o mcmc.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o times.o times.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tiporder.o tiporder.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o m4.o m4.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o io.o io.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o make.o make.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o nexus.o nexus.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o init.o init.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o xml.o xml.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o date.o date.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o sse.o sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o avx.o avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tbe.o tbe.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mixt.o mixt.c gcc -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -Wl,-z,relro -Wl,-z,now -o phyml main.o utilities.o optimiz.o lk.o bionj.o models.o free.o help.o simu.o eigen.o pars.o alrt.o interface.o cl.o spr.o draw.o stats.o rates.o mcmc.o times.o tiporder.o m4.o io.o make.o nexus.o init.o xml.o date.o sse.o avx.o tbe.o mixt.o -lm -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20180621/src' make[4]: Entering directory '/build/phyml-3.3.20180621' make[4]: Leaving directory '/build/phyml-3.3.20180621' make[3]: Leaving directory '/build/phyml-3.3.20180621' make[2]: Leaving directory '/build/phyml-3.3.20180621' # move phyml binary to temporary dir inside debian/ mkdir -p /build/phyml-3.3.20180621/debian/bin mv src/phyml /build/phyml-3.3.20180621/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/build/phyml-3.3.20180621' Making distclean in src make[3]: Entering directory '/build/phyml-3.3.20180621/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/avx.Po rm -f ./.deps/beagle_utils.Po rm -f ./.deps/bionj.Po rm -f ./.deps/checkpoint.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/geo.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/invitee.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/m4.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-date.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-m4.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mcmc.Po rm -f ./.deps/phyml_mpi-mg.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-rates.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-times.Po rm -f ./.deps/phyml_mpi-tiporder.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/simu.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/tiporder.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/build/phyml-3.3.20180621/src' make[3]: Entering directory '/build/phyml-3.3.20180621' 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 '/build/phyml-3.3.20180621' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/build/phyml-3.3.20180621' dh_auto_configure -- --enable-mpi ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-mpi configure: WARNING: unrecognized options: --disable-maintainer-mode 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... i686-pc-linux-gnu checking host system type... i686-pc-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 i686-pc-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 configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j10 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/phyml-3.3.20180621' make all-recursive make[3]: Entering directory '/build/phyml-3.3.20180621' Making all in src make[4]: Entering directory '/build/phyml-3.3.20180621/src' gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c .: Building [phyml-mpi]. Version 3.3.3:3.3.20180621-2 :. gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-m4.o `test -f 'm4.c' || echo './'`m4.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -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/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c gcc -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -Wl,-z,relro -Wl,-z,now -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/i386-linux-gnu/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/build/phyml-3.3.20180621/src' make[4]: Entering directory '/build/phyml-3.3.20180621' make[4]: Leaving directory '/build/phyml-3.3.20180621' make[3]: Leaving directory '/build/phyml-3.3.20180621' make[2]: Leaving directory '/build/phyml-3.3.20180621' # move phyml binary to temporary dir inside debian/ # mkdir -p /build/phyml-3.3.20180621/debian/bin mv src/phyml-mpi /build/phyml-3.3.20180621/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/build/phyml-3.3.20180621' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/phyml-3.3.20180621' Making check in src make[2]: Entering directory '/build/phyml-3.3.20180621/src' gcc -pthread -I/usr/lib/i386-linux-gnu/openmpi/include -I/usr/lib/i386-linux-gnu/openmpi/include/openmpi -std=c99 -O2 -fomit-frame-pointer -funroll-loops -Wall -Winline -o phyml-mpi phyml_mpi-main.o phyml_mpi-utilities.o phyml_mpi-optimiz.o phyml_mpi-lk.o phyml_mpi-bionj.o phyml_mpi-models.o phyml_mpi-free.o phyml_mpi-help.o phyml_mpi-simu.o phyml_mpi-eigen.o phyml_mpi-pars.o phyml_mpi-alrt.o phyml_mpi-interface.o phyml_mpi-cl.o phyml_mpi-spr.o phyml_mpi-draw.o phyml_mpi-stats.o phyml_mpi-rates.o phyml_mpi-mcmc.o phyml_mpi-times.o phyml_mpi-tiporder.o phyml_mpi-mg.o phyml_mpi-m4.o phyml_mpi-io.o phyml_mpi-make.o phyml_mpi-nexus.o phyml_mpi-init.o phyml_mpi-xml.o phyml_mpi-mixt.o phyml_mpi-tbe.o phyml_mpi-date.o phyml_mpi-sse.o phyml_mpi-avx.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/i386-linux-gnu/openmpi/lib -lmpi -lm .: Building [phyml-mpi]. Version 3.3.3:3.3.20180621-2 :. Done. make[2]: Leaving directory '/build/phyml-3.3.20180621/src' make[2]: Entering directory '/build/phyml-3.3.20180621' make[2]: Leaving directory '/build/phyml-3.3.20180621' make[1]: Leaving directory '/build/phyml-3.3.20180621' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/phyml-3.3.20180621' dh_auto_install make -j10 install DESTDIR=/build/phyml-3.3.20180621/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/phyml-3.3.20180621' Making install in src make[3]: Entering directory '/build/phyml-3.3.20180621/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20180621-2 :. Done. make[4]: Entering directory '/build/phyml-3.3.20180621/src' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/phyml-3.3.20180621/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/build/phyml-3.3.20180621/debian/phyml/usr/bin' make[4]: Leaving directory '/build/phyml-3.3.20180621/src' make[3]: Leaving directory '/build/phyml-3.3.20180621/src' make[3]: Entering directory '/build/phyml-3.3.20180621' make[4]: Entering directory '/build/phyml-3.3.20180621' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/phyml-3.3.20180621' make[3]: Leaving directory '/build/phyml-3.3.20180621' make[2]: Leaving directory '/build/phyml-3.3.20180621' # install phyml binary we have kept safe above mkdir -p /build/phyml-3.3.20180621/debian/phyml/usr/lib/phyml/bin mv /build/phyml-3.3.20180621/debian/bin/* /build/phyml-3.3.20180621/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/build/phyml-3.3.20180621' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/phyml-3.3.20180621' dh_installdocs mv /build/phyml-3.3.20180621/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /build/phyml-3.3.20180621/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/build/phyml-3.3.20180621' dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/phyml-3.3.20180621' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/phyml-3.3.20180621' debian/rules override_dh_fixperms make[1]: Entering directory '/build/phyml-3.3.20180621' 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 '/build/phyml-3.3.20180621' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'phyml' in '../phyml_3.3.20180621-2_i386.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20180621-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phyml_3.3.20180621-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/10350 and its subdirectories I: Current time: Tue Apr 7 18:59:13 -12 2020 I: pbuilder-time-stamp: 1586329153 Wed Apr 8 06:59:14 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build6-i386.debian.net. Wed Apr 8 06:59:14 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build6-i386.debian.net. Wed Apr 8 06:59:57 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. Wed Apr 8 06:59:57 UTC 2020 I: phyml_3.3.20180621-2_i386.changes: Format: 1.8 Date: Wed, 27 Jun 2018 16:24:13 +0000 Source: phyml Binary: phyml phyml-dbgsym Architecture: i386 Version: 3:3.3.20180621-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Graham Inggs Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (3:3.3.20180621-2) unstable; urgency=medium . * Team upload . [ Andreas Tille ] * Install test script to user documentation . [ Graham Inggs ] * Allow MPI oversubscription in autopkgtests Checksums-Sha1: 8c33b74d9960f5773f71fa783e34c8201f41906c 35340 phyml-dbgsym_3.3.20180621-2_i386.deb 38bf92364781653670e68361e449c916fb754ce9 5868 phyml_3.3.20180621-2_i386.buildinfo 6ccbc85b8473c15546e4732dd32107a3b52ffa5d 1601048 phyml_3.3.20180621-2_i386.deb Checksums-Sha256: f948c3933712fd18994c5da9e9d07746c3aea36a9ecafd01d35ffcfece80bbcf 35340 phyml-dbgsym_3.3.20180621-2_i386.deb 2f527b4b64f8e4c9d9fe1bdab7a94ec00a1c3e0d4db826c5b909abaa10ab8798 5868 phyml_3.3.20180621-2_i386.buildinfo 5d05099b51399725a8ebe1c0faffdd7f293cab8186b75ba2593b89f3e48ff021 1601048 phyml_3.3.20180621-2_i386.deb Files: c9ffd4f9b02b45f89ac4b3b6465a6f6f 35340 debug optional phyml-dbgsym_3.3.20180621-2_i386.deb 1b4ce85fa59867255fbb9297bc3f1efa 5868 science optional phyml_3.3.20180621-2_i386.buildinfo 7e90c90690a320f028ef8fb1e57c50dc 1601048 science optional phyml_3.3.20180621-2_i386.deb Wed Apr 8 07:00:00 UTC 2020 I: diffoscope 137 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.51nJEAYwfp/phyml_3.3.20180621-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.51nJEAYwfp/phyml_3.3.20180621-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.51nJEAYwfp/phyml_3.3.20180621-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.51nJEAYwfp/b1/phyml_3.3.20180621-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.51nJEAYwfp/b2/phyml_3.3.20180621-2_i386.changes ## command (total time: 0.006s) 0.006s 1 call cmp (internal) ## has_same_content_as (total time: 0.006s) 0.006s 1 call abc.DotChangesFile ## main (total time: 0.521s) 0.521s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.077s) 0.077s 10 calls diffoscope.comparators.binary.FilesystemFile Wed Apr 8 07:00:05 UTC 2020 I: diffoscope 137 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 8 07:00:05 UTC 2020 I: phyml from buster built successfully and reproducibly on i386. Wed Apr 8 07:00:07 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Apr 8 07:00:07 UTC 2020 I: Submitting 8.0K b1/phyml_3.3.20180621-2_i386.buildinfo.asc Wed Apr 8 07:00:08 UTC 2020 I: Submitting 8.0K b2/phyml_3.3.20180621-2_i386.buildinfo.asc Wed Apr 8 07:00:09 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 8 07:00:09 UTC 2020 I: Done submitting .buildinfo files. Wed Apr 8 07:00:09 UTC 2020 I: Removing signed phyml_3.3.20180621-2_i386.buildinfo.asc files: removed './b1/phyml_3.3.20180621-2_i386.buildinfo.asc' removed './b2/phyml_3.3.20180621-2_i386.buildinfo.asc'