sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | phyml 3:3.3.20190321-1 (armhf) Sun, 04 Aug 2019 21:51:30 +0000 | +==============================================================================+ Package: phyml Version: 3:3.3.20190321-1 Source Version: 3:3.3.20190321-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-cc362f26-0f9e-4b1b-bb27-fc683a7ab898' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [149 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-04-0831.20.pdiff [9188 B] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-04-1436.39.pdiff [41.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-04-2015.14.pdiff [18.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-04-0831.20.pdiff [25.2 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-04-2015.14.pdiff [18.1 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-04-1436.39.pdiff [21.5 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-04-2015.14.pdiff [22.1 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-04-2015.14.pdiff [22.1 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8140 kB] Fetched 8483 kB in 4s (2008 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'phyml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phyml.git Please use: git clone https://salsa.debian.org/med-team/phyml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2242 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190321-1 (dsc) [2094 B] Get:2 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190321-1 (tar) [2223 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main phyml 3:3.3.20190321-1 (diff) [16.9 kB] Fetched 2242 kB in 0s (40.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phyml-54x0ZW/phyml-3.3.20190321' with '<>' I: NOTICE: Log filtering will replace 'build/phyml-54x0ZW' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-DBVSMI/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-DBVSMI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DBVSMI/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-DBVSMI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DBVSMI/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-DBVSMI/apt_archive ./ Packages [452 B] Fetched 1772 B in 0s (79.3 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 additional packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-9-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-armhf-cross libgcc1-dbg-armhf-cross libgomp1-dbg-armhf-cross libitm1-dbg-armhf-cross libatomic1-dbg-armhf-cross libasan5-dbg-armhf-cross liblsan0-dbg-armhf-cross libtsan0-dbg-armhf-cross libubsan1-dbg-armhf-cross libmpx2-dbg-armhf-cross libquadmath0-dbg-armhf-cross manpages-dev autoconf automake libtool flex bison gdb-arm-linux-gnueabihf gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-arm-linux-gnueabihf cpp-8-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf dpkg-cross file g++-8-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf gcc-8-arm-linux-gnueabihf-base gcc-8-cross-base gcc-9-cross-base gcc-arm-linux-gnueabihf libasan5-armhf-cross libatomic1-armhf-cross libc6-armhf-cross libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-armhf-cross libgcc1-armhf-cross libgomp1-armhf-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libstdc++-8-dev-armhf-cross libstdc++6-armhf-cross libubsan1-armhf-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armhf-cross sbuild-build-depends-core-dummy:armhf sensible-utils ucf 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 42.3 MB of archives. After this operation, 154 MB of additional disk space will be used. Get:1 copy:/<>/resolver-DBVSMI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.32.51.20190727-1 [2914 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf-base amd64 8.3.0-19cross1 [192 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [6549 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-19cross1 [187 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.1.0-8cross1 [185 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.28-10cross3 [1172 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-armhf-cross all 1:9.1.0-8cross1 [37.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 9.1.0-8cross1 [73.2 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 9.1.0-8cross1 [6692 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armhf-cross all 9.1.0-8cross1 [363 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 9.1.0-8cross1 [392 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 9.1.0-8cross1 [112 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-armhf-cross all 8.3.0-19cross1 [614 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [6979 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:8.3.0-1 [1456 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 4.19.37-5cross3 [1255 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.28-10cross3 [2150 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-armhf-cross all 8.3.0-19cross1 [1561 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-arm-linux-gnueabihf amd64 8.3.0-19cross1 [7130 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:8.3.0-1 [1180 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.3 MB in 1s (55.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11963 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.37-5_amd64.deb ... Unpacking libmagic-mgc (1:5.37-5) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.37-5_amd64.deb ... Unpacking libmagic1:amd64 (1:5.37-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.37-5_amd64.deb ... Unpacking file (1:5.37-5) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... 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Selecting previously unselected package dpkg-cross. Preparing to unpack .../42-dpkg-cross_2.6.15-3_all.deb ... Unpacking dpkg-cross (2.6.15-3) ... Selecting previously unselected package crossbuild-essential-armhf. Preparing to unpack .../43-crossbuild-essential-armhf_12.6_all.deb ... Unpacking crossbuild-essential-armhf (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:armhf. Preparing to unpack .../44-sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libc6-armhf-cross (2.28-10cross3) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up gcc-8-cross-base (8.3.0-19cross1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-3) ... Setting up gcc-8-arm-linux-gnueabihf-base:amd64 (8.3.0-19cross1) ... Setting up linux-libc-dev-armhf-cross (4.19.37-5cross3) ... Setting up gcc-9-cross-base (9.1.0-8cross1) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up binutils-arm-linux-gnueabihf (2.32.51.20190727-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up cpp-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up libgomp1-armhf-cross (9.1.0-8cross1) ... Setting up libc6-dev-armhf-cross (2.28-10cross3) ... Setting up libatomic1-armhf-cross (9.1.0-8cross1) ... Setting up libgcc1-armhf-cross (1:9.1.0-8cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up cpp-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libasan5-armhf-cross (9.1.0-8cross1) ... Setting up libstdc++6-armhf-cross (9.1.0-8cross1) ... Setting up libubsan1-armhf-cross (9.1.0-8cross1) ... Setting up libgcc-8-dev-armhf-cross (8.3.0-19cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-8-dev-armhf-cross (8.3.0-19cross1) ... Setting up gcc-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up gcc-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up g++-8-arm-linux-gnueabihf (8.3.0-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-arm-linux-gnueabihf (4:8.3.0-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armhf (12.6) ... Setting up sbuild-build-depends-core-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-DBVSMI/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-DBVSMI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DBVSMI/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-DBVSMI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DBVSMI/apt_archive ./ Sources [485 B] Get:5 copy:/<>/resolver-DBVSMI/apt_archive ./ Packages [571 B] Fetched 2019 B in 0s (106 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:armhf 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-DBVSMI/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:armhf. (Reading database ... 15015 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:armhf (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper-compat (= 12), pkg-config, libopenmpi-dev, chrpath dpkg-deb: building package 'sbuild-build-depends-phyml-dummy' in '/<>/resolver-DBVSMI/apt_archive/sbuild-build-depends-phyml-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-phyml-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-DBVSMI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DBVSMI/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-DBVSMI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DBVSMI/apt_archive ./ Sources [657 B] Get:5 copy:/<>/resolver-DBVSMI/apt_archive ./ Packages [737 B] Fetched 2357 B in 0s (127 kB/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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gcc-9-base:armhf gettext gettext-base groff-base ibverbs-providers:armhf intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libedit2 libelf1 libevent-2.1-6:armhf libevent-core-2.1-6:armhf libevent-pthreads-2.1-6:armhf libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgfortran5:armhf libglib2.0-0 libgomp1:armhf libgssapi-krb5-2 libhwloc-dev:armhf libhwloc-plugins:armhf libhwloc5:armhf libibverbs-dev:armhf libibverbs1:armhf libicu63:armhf libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev:armhf libltdl7:armhf liblzma5:armhf libncurses6 libnl-3-200:armhf libnl-3-dev:armhf libnl-route-3-200:armhf libnl-route-3-dev:armhf libopenmpi-dev:armhf libopenmpi3:armhf libpciaccess0:armhf libpipeline1 libpmix2:armhf libsigsegv2 libssl1.1 libstdc++-8-dev:armhf libstdc++6:armhf libsub-override-perl libtool libubsan1:armhf libuchardet0 libxml2:armhf linux-libc-dev:armhf m4 man-db ocl-icd-libopencl1:armhf openmpi-bin:armhf openmpi-common openssh-client pkg-config po-debconf zlib1g:armhf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf manpages-dev:armhf krb5-doc krb5-user libhwloc-contrib-plugins:armhf libtool-doc:armhf openmpi-doc:armhf pciutils:armhf libstdc++-8-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser opencl-icd:armhf gfortran:armhf | fortran-compiler:armhf keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armhf libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev:armhf libltdl-dev xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils chrpath debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:armhf gcc-9-base:armhf gettext gettext-base groff-base ibverbs-providers:armhf intltool-debian libarchive-zip-perl libasan5:armhf libatomic1:armhf libbsd0 libc6:armhf libc6-dev:armhf libcroco3 libedit2 libelf1 libevent-2.1-6:armhf libevent-core-2.1-6:armhf libevent-pthreads-2.1-6:armhf libfile-stripnondeterminism-perl libgcc-8-dev:armhf libgcc1:armhf libgfortran5:armhf libglib2.0-0 libgomp1:armhf libgssapi-krb5-2 libhwloc-dev:armhf libhwloc-plugins:armhf libhwloc5:armhf libibverbs-dev:armhf libibverbs1:armhf libicu63:armhf libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev:armhf libltdl7:armhf liblzma5:armhf libncurses6 libnl-3-200:armhf libnl-3-dev:armhf libnl-route-3-200:armhf libnl-route-3-dev:armhf libopenmpi-dev:armhf libopenmpi3:armhf libpciaccess0:armhf libpipeline1 libpmix2:armhf libsigsegv2 libssl1.1 libstdc++-8-dev:armhf libstdc++6:armhf libsub-override-perl libtool libubsan1:armhf libuchardet0 libxml2:armhf linux-libc-dev:armhf m4 man-db ocl-icd-libopencl1:armhf openmpi-bin:armhf openmpi-common openssh-client pkg-config po-debconf sbuild-build-depends-phyml-dummy:armhf zlib1g:armhf 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 36.8 MB of archives. After this operation, 141 MB of additional disk space will be used. Get:1 copy:/<>/resolver-DBVSMI/apt_archive ./ sbuild-build-depends-phyml-dummy 0.invalid.0 [900 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.6-1 [1294 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.1.0-10 [190 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libedit2 amd64 3.1-20190324-1 [94.3 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 openssh-client amd64 1:8.0p1-4 [807 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.4.0-1 [21.9 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.4.0-1 [14.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12.20190723-1 [80.6 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.60.6-1 [1294 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190713-2 [102 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.2.3 [1026 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main armhf gcc-8-base armhf 8.3.0-19 [192 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main armhf libgcc1 armhf 1:9.1.0-10 [37.3 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.28-10 [2390 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main armhf libnl-3-200 armhf 3.4.0-1 [55.6 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main armhf libnl-route-3-200 armhf 3.4.0-1 [136 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main armhf libibverbs1 armhf 24.0-2 [44.6 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main armhf ibverbs-providers armhf 24.0-2 [20.5 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.1.0-10 [370 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 9.1.0-10 [6880 B] Get:49 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 4.19.37-6 [1168 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.28-10 [2149 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [159 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [118 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 9.1.0-10 [75.1 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 9.1.0-10 [431 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 9.1.0-10 [113 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-8-dev armhf 8.3.0-19 [612 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main armhf libgfortran5 armhf 9.1.0-10 [238 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main armhf libltdl7 armhf 2.4.6-10 [387 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main armhf libhwloc5 armhf 1.11.13-1 [88.5 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main armhf libltdl-dev armhf 2.4.6-10 [160 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main armhf libhwloc-dev armhf 1.11.13-1 [154 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main armhf zlib1g armhf 1:1.2.11.dfsg-1 [87.9 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main armhf libicu63 armhf 63.2-2 [8005 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main armhf liblzma5 armhf 5.2.4-1 [145 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main armhf libhwloc-plugins armhf 1.11.13-1 [15.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main armhf libnl-3-dev armhf 3.4.0-1 [96.9 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main armhf libnl-route-3-dev armhf 3.4.0-1 [162 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main armhf libibverbs-dev armhf 24.0-2 [157 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main armhf libpmix2 armhf 3.1.4~rc2-1 [458 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main armhf libopenmpi3 armhf 3.1.3-11 [1890 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main armhf openmpi-bin armhf 3.1.3-11 [198 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main armhf libopenmpi-dev armhf 3.1.3-11 [964 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-8-dev armhf 8.3.0-19 [1561 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 pkg-config amd64 0.29-6 [63.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.8 MB in 1s (58.1 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15015 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.6-1_amd64.deb ... Unpacking man-db (2.8.6-1) ... Selecting previously unselected package gcc-9-base:armhf. Preparing to unpack .../06-gcc-9-base_9.1.0-10_armhf.deb ... Unpacking gcc-9-base:armhf (9.1.0-10) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../08-libedit2_3.1-20190324-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20190324-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../09-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../10-libkrb5support0_1.17-6_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-6) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../11-libk5crypto3_1.17-6_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-6) ... Selecting previously unselected package libssl1.1:amd64. 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Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up openmpi-common (3.1.3-11) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libbsd0:amd64 (0.9.1-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up chrpath (0.16-2+b1) ... Setting up gcc-9-base:armhf (9.1.0-10) ... Setting up libfile-stripnondeterminism-perl (1.4.0-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libtool (2.4.6-10) ... Setting up libedit2:amd64 (3.1-20190324-1) ... Setting up m4 (1.4.18-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12.20190723-1) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up openssh-client (1:8.0p1-4) ... Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.6-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:armhf (2.28-10) ... Setting up ocl-icd-libopencl1:armhf (2.2.12-2) ... Setting up libnl-3-200:armhf (3.4.0-1) ... Setting up libc6-dev:armhf (2.28-10) ... Setting up liblzma5:armhf (5.2.4-1) ... Setting up libgcc1:armhf (1:9.1.0-10) ... Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ... Setting up libgomp1:armhf (9.1.0-10) ... Setting up libnl-route-3-200:armhf (3.4.0-1) ... Setting up dh-autoreconf (19) ... Setting up libasan5:armhf (9.1.0-10) ... Setting up libatomic1:armhf (9.1.0-10) ... Setting up libltdl7:armhf (2.4.6-10) ... Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ... Setting up libgfortran5:armhf (9.1.0-10) ... Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ... Setting up libnl-3-dev:armhf (3.4.0-1) ... Setting up libstdc++6:armhf (9.1.0-10) ... Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ... Setting up libpciaccess0:armhf (0.14-1) ... Setting up libibverbs1:armhf (24.0-2) ... Setting up ibverbs-providers:armhf (24.0-2) ... Setting up libhwloc5:armhf (1.11.13-1) ... Setting up debhelper (12.2.3) ... Setting up libicu63:armhf (63.2-2) ... Setting up libnl-route-3-dev:armhf (3.4.0-1) ... Setting up libltdl-dev:armhf (2.4.6-10) ... Setting up libubsan1:armhf (9.1.0-10) ... Setting up dh-strip-nondeterminism (1.4.0-1) ... Setting up libhwloc-dev:armhf (1.11.13-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libibverbs-dev:armhf (24.0-2) ... Setting up libhwloc-plugins:armhf (1.11.13-1) ... Setting up libgcc-8-dev:armhf (8.3.0-19) ... Setting up libstdc++-8-dev:armhf (8.3.0-19) ... Setting up libpmix2:armhf (3.1.4~rc2-1) ... Setting up libopenmpi3:armhf (3.1.3-11) ... Setting up openmpi-bin:armhf (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:armhf (3.1.3-11) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode Setting up sbuild-build-depends-phyml-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190727-1 dpkg-dev_1.19.7 g++-8_8.3.0-19 gcc-8_8.3.0-19 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-armhf-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-armhf-cross_9.1.0-8cross1 linux-libc-dev_4.19.37-6 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190727-1 binutils-arm-linux-gnueabihf_2.32.51.20190727-1 binutils-common_2.32.51.20190727-1 binutils-x86-64-linux-gnu_2.32.51.20190727-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.6 bzip2_1.0.6-9.2 chrpath_0.16-2+b1 coreutils_8.30-3 cpp_4:8.3.0-1 cpp-8_8.3.0-19 cpp-8-arm-linux-gnueabihf_8.3.0-19cross1 cpp-arm-linux-gnueabihf_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-armhf_12.6 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.2.3 debian-archive-keyring_2019.1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.4.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12.20190723-1 e2fsprogs_1.45.3-3 fakeroot_1.23-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.6.0+git+20190510-2 g++_4:8.3.0-1 g++-8_8.3.0-19 g++-8-arm-linux-gnueabihf_8.3.0-19cross1 g++-arm-linux-gnueabihf_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-19 gcc-8-arm-linux-gnueabihf_8.3.0-19cross1 gcc-8-arm-linux-gnueabihf-base_8.3.0-19cross1 gcc-8-base_8.3.0-19 gcc-8-cross-base_8.3.0-19cross1 gcc-9-base_9.1.0-10 gcc-9-cross-base_9.1.0-8cross1 gcc-arm-linux-gnueabihf_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 ibverbs-providers_24.0-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_9.1.0-10 libasan5-armhf-cross_9.1.0-8cross1 libatomic1_9.1.0-10 libatomic1-armhf-cross_9.1.0-8cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190727-1 libblkid1_2.34-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.2 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-armhf-cross_2.28-10cross3 libc6-dev_2.28-10 libc6-dev-armhf-cross_2.28-10cross3 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-10 libcom-err2_1.45.3-3 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libedit2_3.1-20190324-1 libelf1_0.176-1.1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libext2fs2_1.45.3-3 libfakeroot_1.23-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.4.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-19 libgcc-8-dev-armhf-cross_8.3.0-19cross1 libgcc1_1:9.1.0-10 libgcc1-armhf-cross_1:9.1.0-8cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4+b1 libgdbm6_1.18.1-4+b1 libgfortran5_9.1.0-10 libglib2.0-0_2.60.6-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-3 libgomp1_9.1.0-10 libgomp1-armhf-cross_9.1.0-8cross1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libhogweed4_3.4.1-1 libhwloc-dev_1.11.13-1 libhwloc-plugins_1.11.13-1 libhwloc5_1.11.13-1 libibverbs-dev_24.0-2 libibverbs1_24.0-2 libicu63_63.2-2 libidn2-0_2.2.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_9.1.0-10 libk5crypto3_1.17-6 libkeyutils1_1.6-6 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblocale-gettext-perl_1.07-3+b4 liblsan0_9.1.0-10 libltdl-dev_2.4.6-10 libltdl7_2.4.6-10 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-19 libncurses6_6.1+20190713-2 libncursesw6_6.1+20190713-2 libnettle6_3.4.1-1 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 libopenmpi-dev_3.1.3-11 libopenmpi3_3.1.3-11 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpmix2_3.1.4~rc2-1 libquadmath0_9.1.0-10 libseccomp2_2.4.1-2 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.3-3 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-armhf-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-armhf-cross_9.1.0-8cross1 libsub-override-perl_0.09-2 libsystemd0_241-7 libtasn1-6_4.14-2 libtinfo6_6.1+20190713-2 libtool_2.4.6-10 libtsan0_9.1.0-10 libubsan1_9.1.0-10 libubsan1-armhf-cross_9.1.0-8cross1 libuchardet0_0.0.6-3 libudev1_241-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_4.19.37-6 linux-libc-dev-armhf-cross_4.19.37-5cross3 login_1:4.7-2 logsave_1.45.3-3 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190713-2 ncurses-bin_6.1+20190713-2 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-11 openmpi-common_3.1.3-11 openssh-client_1:8.0p1-4 passwd_1:4.7-2 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pkg-config_0.29-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-phyml-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.95-4 tar_1.30+dfsg-6 tzdata_2019b-1 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Aug 1 20:20:09 2019 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_3.3.20190321-1.dsc dpkg-source: info: extracting phyml in /<> dpkg-source: info: unpacking phyml_3.3.20190321.orig.tar.gz dpkg-source: info: unpacking phyml_3.3.20190321-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sse_only_if_supported.patch dpkg-source: info: applying no-stdc++.patch dpkg-source: info: applying no-configure-ac-date.patch dpkg-source: info: applying fix_declaration_of_temp.patch dpkg-source: info: applying fix_wrong_initialisation_of_array.patch dpkg-source: info: applying no-march-native.patch dpkg-source: info: applying cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-cc362f26-0f9e-4b1b-bb27-fc683a7ab898 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package phyml dpkg-buildpackage: info: source version 3:3.3.20190321-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' # save pdf from cleaning mv doc/phyml-manual.pdf . dh_auto_clean mv phyml-manual.pdf doc # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' dh_autoreconf --as-needed configure.ac:16: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' src/Makefile.am: installing './depcomp' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable # The hack includes saving the documentation from beeing cleaned up mv doc/phyml-manual.pdf . dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabihf configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armhf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabihf-strip... arm-linux-gnueabihf-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabihf checking for arm-linux-gnueabihf-gcc... arm-linux-gnueabihf-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabihf-gcc accepts -g... yes checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabihf-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabihf-gcc... none checking dependency style of arm-linux-gnueabihf-gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf" checking for log in -lm... yes checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... (cached) yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for arm-linux-gnueabihf-pkg-config... /usr/bin/arm-linux-gnueabihf-pkg-config checking pkg-config is at least version 0.9.0... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j1 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' .: Building [phyml]. Version 3.3.3:3.3.20190321-1 :. arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o main.o main.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o utilities.o utilities.c utilities.c: In function 'Assign_State_With_Ambiguity': utilities.c:3033:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:3033:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utilities.c: In function 'Are_Compatible': utilities.c:4863:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:4863:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o optimiz.o optimiz.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o lk.o lk.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o bionj.o bionj.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o models.o models.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o free.o free.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o help.o help.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o simu.o simu.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o eigen.o eigen.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o pars.o pars.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o alrt.o alrt.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o interface.o interface.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o cl.o cl.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o spr.o spr.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o draw.o draw.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o stats.o stats.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o rates.o rates.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mcmc.o mcmc.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o times.o times.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tiporder.o tiporder.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o m4.o m4.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o io.o io.c io.c: In function 'Print_Fp_Out': io.c:2744:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~ io.c:2744:43: note: directive argument in the range [1, 2147483647] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from io.h:18, from io.c:13: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o make.o make.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o nexus.o nexus.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o init.o init.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o xml.o xml.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o date.o date.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o sse.o sse.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o avx.o avx.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o tbe.o tbe.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o ancestral.o ancestral.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o mixt.o mixt.c arm-linux-gnueabihf-gcc -std=c99 -O3 -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 ancestral.o mixt.o -lm -lm Done. make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # move phyml binary to temporary dir inside debian/ mkdir -p /<>/debian/bin mv src/phyml /<>/debian/bin/phyml /usr/bin/make distclean make[2]: Entering directory '/<>' Making distclean in src make[3]: Entering directory '/<>/src' test -z "phyml" || rm -f phyml rm -f *.o rm -f *.tab.c test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f ./.deps/alrt.Po rm -f ./.deps/ancestral.Po rm -f ./.deps/avx.Po rm -f ./.deps/beagle_utils.Po rm -f ./.deps/bionj.Po rm -f ./.deps/checkpoint.Po rm -f ./.deps/cl.Po rm -f ./.deps/date.Po rm -f ./.deps/draw.Po rm -f ./.deps/eigen.Po rm -f ./.deps/free.Po rm -f ./.deps/geo.Po rm -f ./.deps/help.Po rm -f ./.deps/init.Po rm -f ./.deps/interface.Po rm -f ./.deps/invitee.Po rm -f ./.deps/io.Po rm -f ./.deps/lk.Po rm -f ./.deps/m4.Po rm -f ./.deps/main.Po rm -f ./.deps/make.Po rm -f ./.deps/mcmc.Po rm -f ./.deps/mg.Po rm -f ./.deps/mixt.Po rm -f ./.deps/models.Po rm -f ./.deps/nexus.Po rm -f ./.deps/optimiz.Po rm -f ./.deps/pars.Po rm -f ./.deps/phyml_mpi-alrt.Po rm -f ./.deps/phyml_mpi-ancestral.Po rm -f ./.deps/phyml_mpi-avx.Po rm -f ./.deps/phyml_mpi-bionj.Po rm -f ./.deps/phyml_mpi-cl.Po rm -f ./.deps/phyml_mpi-date.Po rm -f ./.deps/phyml_mpi-draw.Po rm -f ./.deps/phyml_mpi-eigen.Po rm -f ./.deps/phyml_mpi-free.Po rm -f ./.deps/phyml_mpi-help.Po rm -f ./.deps/phyml_mpi-init.Po rm -f ./.deps/phyml_mpi-interface.Po rm -f ./.deps/phyml_mpi-io.Po rm -f ./.deps/phyml_mpi-lk.Po rm -f ./.deps/phyml_mpi-m4.Po rm -f ./.deps/phyml_mpi-main.Po rm -f ./.deps/phyml_mpi-make.Po rm -f ./.deps/phyml_mpi-mcmc.Po rm -f ./.deps/phyml_mpi-mg.Po rm -f ./.deps/phyml_mpi-mixt.Po rm -f ./.deps/phyml_mpi-models.Po rm -f ./.deps/phyml_mpi-mpi_boot.Po rm -f ./.deps/phyml_mpi-nexus.Po rm -f ./.deps/phyml_mpi-optimiz.Po rm -f ./.deps/phyml_mpi-pars.Po rm -f ./.deps/phyml_mpi-rates.Po rm -f ./.deps/phyml_mpi-simu.Po rm -f ./.deps/phyml_mpi-spr.Po rm -f ./.deps/phyml_mpi-sse.Po rm -f ./.deps/phyml_mpi-stats.Po rm -f ./.deps/phyml_mpi-tbe.Po rm -f ./.deps/phyml_mpi-times.Po rm -f ./.deps/phyml_mpi-tiporder.Po rm -f ./.deps/phyml_mpi-utilities.Po rm -f ./.deps/phyml_mpi-xml.Po rm -f ./.deps/phyrex.Po rm -f ./.deps/rates.Po rm -f ./.deps/simu.Po rm -f ./.deps/spr.Po rm -f ./.deps/sse.Po rm -f ./.deps/stats.Po rm -f ./.deps/tbe.Po rm -f ./.deps/times.Po rm -f ./.deps/tiporder.Po rm -f ./.deps/utilities.Po rm -f ./.deps/xml.Po rm -f Makefile make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>' test -z "" || rm -f test . = "." || test -z "" || rm -f rm -f config.h stamp-h1 rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags rm -f cscope.out cscope.in.out cscope.po.out cscope.files make[3]: Leaving directory '/<>' rm -f config.status config.cache config.log configure.lineno config.status.lineno rm -f Makefile make[2]: Leaving directory '/<>' dh_auto_configure -- --enable-mpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabihf --enable-mpi configure: WARNING: unrecognized options: --disable-maintainer-mode configure: loading site script /etc/dpkg-cross/cross-config.armhf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabihf-strip... arm-linux-gnueabihf-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking host system type... arm-unknown-linux-gnueabihf checking for arm-linux-gnueabihf-gcc... arm-linux-gnueabihf-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabihf-gcc accepts -g... yes checking for arm-linux-gnueabihf-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabihf-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabihf-gcc... none checking dependency style of arm-linux-gnueabihf-gcc... (cached) none configure: "Do not use MSSE = because not available on arch arm-unknown-linux-gnueabihf" checking for log in -lm... yes checking how to run the C preprocessor... arm-linux-gnueabihf-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for pdflatex... no checking for latex... no configure: WARNING: Documentation will not be built! checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... (cached) yes checking for vprintf... yes checking for _doprnt... no checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strstr... yes checking for arm-linux-gnueabihf-pkg-config... /usr/bin/arm-linux-gnueabihf-pkg-config checking pkg-config is at least version 0.9.0... yes checking for MPI_C... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -- LDFLAGS="-Wl,-z,relro -Wl,-z,now" make -j1 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in src make[4]: Entering directory '/<>/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20190321-1 :. arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-main.o `test -f 'main.c' || echo './'`main.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-utilities.o `test -f 'utilities.c' || echo './'`utilities.c utilities.c: In function 'Assign_State_With_Ambiguity': utilities.c:3033:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:3033:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utilities.c: In function 'Are_Compatible': utilities.c:4863:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(format,"%%%dd",stepsize); ^~ utilities.c:4863:26: note: directive argument in the range [0, 2147483647] sprintf(format,"%%%dd",stepsize); ^~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from utilities.c:12: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-optimiz.o `test -f 'optimiz.c' || echo './'`optimiz.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-lk.o `test -f 'lk.c' || echo './'`lk.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-bionj.o `test -f 'bionj.c' || echo './'`bionj.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-models.o `test -f 'models.c' || echo './'`models.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-free.o `test -f 'free.c' || echo './'`free.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-help.o `test -f 'help.c' || echo './'`help.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-simu.o `test -f 'simu.c' || echo './'`simu.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-eigen.o `test -f 'eigen.c' || echo './'`eigen.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-pars.o `test -f 'pars.c' || echo './'`pars.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-alrt.o `test -f 'alrt.c' || echo './'`alrt.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-interface.o `test -f 'interface.c' || echo './'`interface.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-cl.o `test -f 'cl.c' || echo './'`cl.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-spr.o `test -f 'spr.c' || echo './'`spr.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-draw.o `test -f 'draw.c' || echo './'`draw.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-stats.o `test -f 'stats.c' || echo './'`stats.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-rates.o `test -f 'rates.c' || echo './'`rates.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-times.o `test -f 'times.c' || echo './'`times.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-tiporder.o `test -f 'tiporder.c' || echo './'`tiporder.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mg.o `test -f 'mg.c' || echo './'`mg.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-m4.o `test -f 'm4.c' || echo './'`m4.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-io.o `test -f 'io.c' || echo './'`io.c io.c: In function 'Print_Fp_Out': io.c:2744:47: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 6 [-Wformat-truncation=] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~ io.c:2744:43: note: directive argument in the range [1, 2147483647] if (precision > 0) snprintf (format, 8, "%%.%df", precision); ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/stdio.h:873, from utilities.h:19, from io.h:18, from io.c:13: /usr/arm-linux-gnueabihf/include/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 5 and 14 bytes into a destination of size 8 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-make.o `test -f 'make.c' || echo './'`make.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-nexus.o `test -f 'nexus.c' || echo './'`nexus.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-init.o `test -f 'init.c' || echo './'`init.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-xml.o `test -f 'xml.c' || echo './'`xml.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mixt.o `test -f 'mixt.c' || echo './'`mixt.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-tbe.o `test -f 'tbe.c' || echo './'`tbe.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-date.o `test -f 'date.c' || echo './'`date.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-sse.o `test -f 'sse.c' || echo './'`sse.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-avx.o `test -f 'avx.c' || echo './'`avx.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-ancestral.o `test -f 'ancestral.c' || echo './'`ancestral.c arm-linux-gnueabihf-gcc -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -c -o phyml_mpi-mpi_boot.o `test -f 'mpi_boot.c' || echo './'`mpi_boot.c arm-linux-gnueabihf-gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -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-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm Done. make[4]: Leaving directory '/<>/src' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # move phyml binary to temporary dir inside debian/ # mkdir -p /<>/debian/bin mv src/phyml-mpi /<>/debian/bin/phyml-mpi mv phyml-manual.pdf doc make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install make -j1 install DESTDIR=/<>/debian/phyml AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in src make[3]: Entering directory '/<>/src' .: Building [phyml-mpi]. Version 3.3.3:3.3.20190321-1 :. arm-linux-gnueabihf-gcc -pthread -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -std=c99 -O3 -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-ancestral.o phyml_mpi-mpi_boot.o -lm -L/usr/lib/arm-linux-gnueabihf/openmpi/lib -lmpi -lm Done. make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/phyml/usr/bin' /usr/bin/install -c phyml-mpi '/<>/debian/phyml/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # install phyml binary we have kept safe above mkdir -p /<>/debian/phyml/usr/lib/phyml/bin mv /<>/debian/bin/* /<>/debian/phyml/usr/lib/phyml/bin chrpath --delete debian/phyml/usr/lib/phyml/bin/phyml* make[1]: Leaving directory '/<>' dh_install -a debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs mv /<>/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf /<>/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf make[1]: Leaving directory '/<>' dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/*/usr/share/doc -name "*.nxs" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.xml" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.mat" -exec chmod -x \{\} \; find debian/*/usr/share/doc -name "*.txt" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a debian/rules override_dh_dwz make[1]: Entering directory '/<>' echo "Do not run dh_dwz" Do not run dh_dwz make[1]: Leaving directory '/<>' dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phyml' in '../phyml_3.3.20190321-1_armhf.deb'. dpkg-deb: building package 'phyml-dbgsym' in '../phyml-dbgsym_3.3.20190321-1_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phyml_3.3.20190321-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2019-08-04T21:54:24Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-DBVSMI/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-phyml-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-DBVSMI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-DBVSMI/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-DBVSMI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-DBVSMI/apt_archive ./ Sources [777 B] Get:5 copy:/<>/resolver-DBVSMI/apt_archive ./ Packages [854 B] Fetched 2594 B in 0s (127 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparams-classify-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libhtml-template-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libclass-xsaccessor-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libparams-classify-perl libparse-debianchangelog-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armhf t1utils 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 6899 kB of archives. After this operation, 18.5 MB of additional disk space will be used. Get:1 copy:/<>/resolver-DBVSMI/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-2 [72.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-2 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1 [33.4 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.29.0-1 [645 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-1 [320 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.41-1 [79.0 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006003-1 [19.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libparse-debianchangelog-perl all 1.2.0-13 [59.5 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.79+repack-2 [34.0 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.16.0 [1189 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6899 kB in 0s (28.7 MB/s) Selecting previously unselected package readline-common. (Reading database ... 19544 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-2_all.deb ... Unpacking readline-common (8.0-2) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-2_amd64.deb ... Unpacking libreadline8:amd64 (8.0-2) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1_amd64.deb ... Unpacking diffstat (1.62-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. 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Setting up libnet-dns-perl (1.20-1) ... Setting up libdevel-callchecker-perl (0.008-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up gpgconf (2.2.17-3) ... Setting up libio-socket-ssl-perl (2.066-1) ... Setting up gpg (2.2.17-3) ... Setting up libparams-classify-perl (0.015-1+b1) ... Setting up libcgi-pm-perl (4.44-1) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libparse-debianchangelog-perl (1.2.0-13) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.003004-2) ... Setting up lintian (2.16.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.8.6-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.28-10) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phyml_3.3.20190321-1_armhf.changes: ----------------------------------- Format: 1.8 Date: Thu, 01 Aug 2019 22:05:12 +0200 Source: phyml Binary: phyml phyml-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 3:3.3.20190321-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phyml - Phylogenetic estimation using Maximum Likelihood Changes: phyml (3:3.3.20190321-1) unstable; urgency=medium . * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 * Do not run dh_dwz Checksums-Sha1: 0f00aa6f28cf1641330762b4015364af45a7ae9c 43000 phyml-dbgsym_3.3.20190321-1_armhf.deb d19de8a3a77336d367c20f853b60e0864eb07690 5690 phyml_3.3.20190321-1_armhf.buildinfo dbd151ec893f44d04ffc3719ed1b9e5a7a3e52e3 1561204 phyml_3.3.20190321-1_armhf.deb Checksums-Sha256: 87ac4c2e59983d8a7132c04521b71bf7be033b6f47a1520da6db49ed8e5a5b4a 43000 phyml-dbgsym_3.3.20190321-1_armhf.deb 8c31c0774f150ef25c3d541284b2c8da8f86e658de014fad44950f65485fe2aa 5690 phyml_3.3.20190321-1_armhf.buildinfo ac39ec4eec4db5e3e5499c2df06c2b3f927f4b51a1a03c30ef2e3cac593ea05c 1561204 phyml_3.3.20190321-1_armhf.deb Files: 96b35d93dfcd45b6d911405ac03570bb 43000 debug optional phyml-dbgsym_3.3.20190321-1_armhf.deb 5042a14289571d254bb8e27ffe440d46 5690 science optional phyml_3.3.20190321-1_armhf.buildinfo f15c451f86046a883bf26b3c281b317b 1561204 science optional phyml_3.3.20190321-1_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phyml Binary: phyml Architecture: armhf Version: 3:3.3.20190321-1 Checksums-Md5: 96b35d93dfcd45b6d911405ac03570bb 43000 phyml-dbgsym_3.3.20190321-1_armhf.deb f15c451f86046a883bf26b3c281b317b 1561204 phyml_3.3.20190321-1_armhf.deb Checksums-Sha1: 0f00aa6f28cf1641330762b4015364af45a7ae9c 43000 phyml-dbgsym_3.3.20190321-1_armhf.deb dbd151ec893f44d04ffc3719ed1b9e5a7a3e52e3 1561204 phyml_3.3.20190321-1_armhf.deb Checksums-Sha256: 87ac4c2e59983d8a7132c04521b71bf7be033b6f47a1520da6db49ed8e5a5b4a 43000 phyml-dbgsym_3.3.20190321-1_armhf.deb ac39ec4eec4db5e3e5499c2df06c2b3f927f4b51a1a03c30ef2e3cac593ea05c 1561204 phyml_3.3.20190321-1_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 04 Aug 2019 21:54:24 +0000 Build-Path: /<> Installed-Build-Depends: adduser (= 3.118), autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.32.51.20190727-1), binutils-common (= 2.32.51.20190727-1), binutils-x86-64-linux-gnu (= 2.32.51.20190727-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9.2), chrpath (= 0.16-2+b1), coreutils (= 8.30-3), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-19), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.2.3), debianutils (= 4.8.6.3), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.4.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.12.20190723-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.6.0+git+20190510-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-19), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-19), gcc-8-base (= 8.3.0-19), gcc-9-base (= 9.1.0-10), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), hostname (= 3.21), ibverbs-providers (= 24.0-2), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.64-1), libasan5 (= 9.1.0-10), libatomic1 (= 9.1.0-10), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.32.51.20190727-1), libblkid1 (= 2.34-0.1), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9.2), libc-bin (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 9.1.0-10), libcom-err2 (= 1.45.3-3), libcroco3 (= 0.6.12-3), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdpkg-perl (= 1.19.7), libedit2 (= 3.1-20190324-1), libelf1 (= 0.176-1.1), libevent-2.1-6 (= 2.1.8-stable-4), libevent-core-2.1-6 (= 2.1.8-stable-4), libevent-pthreads-2.1-6 (= 2.1.8-stable-4), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.4.0-1), libgcc-8-dev (= 8.3.0-19), libgcc1 (= 1:9.1.0-10), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4+b1), libgdbm6 (= 1.18.1-4+b1), libgfortran5 (= 9.1.0-10), libglib2.0-0 (= 2.60.6-1), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.1.0-10), libgpg-error0 (= 1.36-7), libgssapi-krb5-2 (= 1.17-6), libhwloc-dev (= 1.11.13-1), libhwloc-plugins (= 1.11.13-1), libhwloc5 (= 1.11.13-1), libibverbs-dev (= 24.0-2), libibverbs1 (= 24.0-2), libicu63 (= 63.2-2), libisl19 (= 0.20-2), libitm1 (= 9.1.0-10), libk5crypto3 (= 1.17-6), libkeyutils1 (= 1.6-6), libkrb5-3 (= 1.17-6), libkrb5support0 (= 1.17-6), liblsan0 (= 9.1.0-10), libltdl-dev (= 2.4.6-10), libltdl7 (= 2.4.6-10), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-19), libncurses6 (= 6.1+20190713-2), libncursesw6 (= 6.1+20190713-2), 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), libopenmpi-dev (= 3.1.3-11), libopenmpi3 (= 3.1.3-11), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpciaccess0 (= 0.14-1), libpcre2-8-0 (= 10.32-5), libpcre3 (= 2:8.39-12), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libpmix2 (= 3.1.4~rc2-1), libquadmath0 (= 9.1.0-10), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2), libsemanage-common (= 2.9-3), libsemanage1 (= 2.9-3), libsepol1 (= 2.9-2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libssl1.1 (= 1.1.1c-1), libstdc++-8-dev (= 8.3.0-19), libstdc++6 (= 9.1.0-10), libsub-override-perl (= 0.09-2), libsystemd0 (= 241-7), libtinfo6 (= 6.1+20190713-2), libtool (= 2.4.6-10), libtsan0 (= 9.1.0-10), libubsan1 (= 9.1.0-10), libuchardet0 (= 0.0.6-3), libudev1 (= 241-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 4.19.37-6), login (= 1:4.7-2), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.6-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190713-2), ncurses-bin (= 6.1+20190713-2), ocl-icd-libopencl1 (= 2.2.12-2), openmpi-bin (= 3.1.3-11), openmpi-common (= 3.1.3-11), openssh-client (= 1:8.0p1-4), passwd (= 1:4.7-2), patch (= 2.7.6-6), perl (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), pkg-config (= 0.29-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.95-4), tar (= 1.30+dfsg-6), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1564689912" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phyml-dbgsym_3.3.20190321-1_armhf.deb ------------------------------------- new Debian package, version 2.0. size 43000 bytes: control archive=656 bytes. 462 bytes, 12 lines control 318 bytes, 3 lines md5sums Package: phyml-dbgsym Source: phyml Version: 3:3.3.20190321-1 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 305 Depends: phyml (= 3:3.3.20190321-1) Section: debug Priority: optional Description: debug symbols for phyml Build-Ids: ce2403b35227f1f8a37b6d38def7b70b280c092f d398b8ad2dd1b25a1a0b08c145853450e60113b1 d69b936531bda4c662eba51df5abcc019f4d2984 drwxr-xr-x root/root 0 2019-08-01 20:05 ./ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/debug/.build-id/ce/ -rw-r--r-- root/root 99408 2019-08-01 20:05 ./usr/lib/debug/.build-id/ce/2403b35227f1f8a37b6d38def7b70b280c092f.debug drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/debug/.build-id/d3/ -rw-r--r-- root/root 98508 2019-08-01 20:05 ./usr/lib/debug/.build-id/d3/98b8ad2dd1b25a1a0b08c145853450e60113b1.debug drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/debug/.build-id/d6/ -rw-r--r-- root/root 99408 2019-08-01 20:05 ./usr/lib/debug/.build-id/d6/9b936531bda4c662eba51df5abcc019f4d2984.debug drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-08-01 20:05 ./usr/share/doc/phyml-dbgsym -> phyml phyml_3.3.20190321-1_armhf.deb ------------------------------ new Debian package, version 2.0. size 1561204 bytes: control archive=1884 bytes. 1666 bytes, 31 lines control 1695 bytes, 24 lines md5sums Package: phyml Version: 3:3.3.20190321-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 4322 Depends: libc6 (>= 2.7), libopenmpi3, openmpi-bin Section: science Priority: optional Homepage: http://www.atgc-montpellier.fr/phyml Description: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. . This package also includes PhyTime. drwxr-xr-x root/root 0 2019-08-01 20:05 ./ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/bin/ -rwxr-xr-x root/root 579 2019-08-01 20:05 ./usr/bin/phyml -rwxr-xr-x root/root 1043872 2019-08-01 20:05 ./usr/bin/phyml-mpi drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/phyml/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/lib/phyml/bin/ -rwxr-xr-x root/root 1039320 2019-08-01 20:05 ./usr/lib/phyml/bin/phyml -rwxr-xr-x root/root 1043416 2019-08-01 20:05 ./usr/lib/phyml/bin/phyml-mpi drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/doc-base/ -rw-r--r-- root/root 202 2019-08-01 20:05 ./usr/share/doc-base/phyml drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/doc/phyml/ -rw-r--r-- root/root 2446 2019-08-01 20:05 ./usr/share/doc/phyml/README.Debian -rw-r--r-- root/root 2979 2019-08-01 20:05 ./usr/share/doc/phyml/changelog.Debian.gz -rw-r--r-- root/root 1489 2019-08-01 20:05 ./usr/share/doc/phyml/copyright drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/doc/phyml/examples/ -rw-r--r-- root/root 20905 2019-08-01 20:05 ./usr/share/doc/phyml/examples/example.nex drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/ -rw-r--r-- root/root 1900 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X1.mat -rw-r--r-- root/root 1899 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X2.mat -rw-r--r-- root/root 1893 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X3.mat -rw-r--r-- root/root 1895 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/X4.mat -rw-r--r-- root/root 1994 2019-04-04 07:13 ./usr/share/doc/phyml/examples/lg4x/lg4x.xml -rw-r--r-- root/root 2175 2019-04-04 07:13 ./usr/share/doc/phyml/examples/nexus_example.nxs -rwxr-xr-x root/root 60771 2019-04-04 07:13 ./usr/share/doc/phyml/examples/nucleic drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/ -rw-r--r-- root/root 70310 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/h1n1.nxs -rw-r--r-- root/root 1784 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phyrex/usa_coord.txt drwxr-xr-x root/root 0 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/ -rw-r--r-- root/root 2189 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/dating_example.xml -rw-r--r-- root/root 100171 2019-04-04 07:13 ./usr/share/doc/phyml/examples/phytime/seq.txt -rwxr-xr-x root/root 25990 2019-04-04 07:13 ./usr/share/doc/phyml/examples/proteic -rw-r--r-- root/root 965863 2019-04-04 07:13 ./usr/share/doc/phyml/phyml_manual.pdf -rw-r--r-- root/root 1046 2019-08-01 20:05 ./usr/share/doc/phyml/run-unit-test drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/man/ drwxr-xr-x root/root 0 2019-08-01 20:05 ./usr/share/man/man1/ -rw-r--r-- root/root 2899 2019-08-01 20:05 ./usr/share/man/man1/phyml.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 16556 Build-Time: 132 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 29 Job: phyml_3:3.3.20190321-1 Lintian: pass Machine Architecture: amd64 Package: phyml Package-Time: 174 Source-Version: 3:3.3.20190321-1 Space: 16556 Status: successful Version: 3:3.3.20190321-1 -------------------------------------------------------------------------------- Finished at 2019-08-04T21:54:24Z Build needed 00:02:54, 16556k disk space