https://launchpad.net/ubuntu/+source/paml/4.9j+dfsg-3/+build/19375088 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-016 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 29 May 17:50:40 ntpdate[1878]: adjust time server 10.211.37.1 offset 0.003594 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19375088 --image-type chroot /home/buildd/filecache-default/a77e1afdcf3761e08e999e63510e3d2f5c5a8a8d Creating target for build PACKAGEBUILD-19375088 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19375088 Starting target for build PACKAGEBUILD-19375088 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19375088 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19375088 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19375088 Updating target for build PACKAGEBUILD-19375088 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [935 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8420 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5175 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf Packages [38.7 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [26.3 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf Packages [201 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [119 kB] Fetched 16.0 MB in 7s (2382 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 cpp-9 dash debconf debianutils e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libbz2-1.0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libkmod2 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libuuid1 linux-libc-dev logsave make mount ncurses-base ncurses-bin perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 78 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 46.4 MB of archives. After this operation, 434 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main armhf libcrypt-dev armhf 1:4.4.15-1ubuntu1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libcrypt1 armhf 1:4.4.15-1ubuntu1 [93.4 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu7 [59.7 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bsdutils armhf 1:2.35.1-5ubuntu2 [78.9 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf debianutils armhf 4.11 [84.3 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libperl5.30 armhf 5.30.2-1 [3296 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf perl armhf 5.30.2-1 [224 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf perl-base armhf 5.30.2-1 [1409 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bzip2 armhf 1.0.8-3 [31.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libbz2-1.0 armhf 1.0.8-3 [31.0 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf debconf all 1.5.74 [121 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf dash armhf 0.5.10.2-7 [79.2 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gzip armhf 1.10-2ubuntu1 [90.8 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-bin armhf 6.2-1 [164 kB] Get:16 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libblkid1 armhf 2.35.1-5ubuntu2 [120 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libuuid1 armhf 2.35.1-5ubuntu2 [21.5 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libfdisk1 armhf 2.35.1-5ubuntu2 [159 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libmount1 armhf 2.35.1-5ubuntu2 [132 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf libncurses6 armhf 6.2-1 [79.7 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf libncursesw6 armhf 6.2-1 [106 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libtinfo6 armhf 6.2-1 [73.6 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsmartcols1 armhf 2.35.1-5ubuntu2 [84.3 kB] Get:24 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf fdisk armhf 2.35.1-5ubuntu2 [113 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf util-linux armhf 2.35.1-5ubuntu2 [985 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-base all 6.2-1 [18.7 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf sysvinit-utils armhf 2.96-3ubuntu1 [19.1 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf libatomic1 armhf 10.1.0-3ubuntu1 [7184 B] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf libubsan1 armhf 10.1.0-3ubuntu1 [121 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libgomp1 armhf 10.1.0-3ubuntu1 [86.9 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-10-base armhf 10.1.0-3ubuntu1 [20.0 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf libgcc-s1 armhf 10.1.0-3ubuntu1 [36.2 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf libcc1-0 armhf 10.1.0-3ubuntu1 [34.6 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf libstdc++6 armhf 10.1.0-3ubuntu1 [440 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf systemd-sysv armhf 245.5-3ubuntu1 [10.3 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main armhf systemd-timesyncd armhf 245.5-3ubuntu1 [27.9 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main armhf libacl1 armhf 2.2.53-8 [16.0 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main armhf libapparmor1 armhf 2.13.3-7ubuntu6 [29.2 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main armhf libcap2 armhf 1:2.34-2 [15.6 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main armhf libudev1 armhf 245.5-3ubuntu1 [67.1 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu2 [119 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main armhf libcryptsetup12 armhf 2:2.3.1-1ubuntu1 [172 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main armhf libidn2-0 armhf 2.3.0-1 [49.9 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libkmod2 armhf 27+20200310-2ubuntu1 [38.2 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libseccomp2 armhf 2.4.3-1ubuntu2 [32.4 kB] Get:46 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf mount armhf 2.35.1-5ubuntu2 [112 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf systemd armhf 245.5-3ubuntu1 [3644 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main armhf libsystemd0 armhf 245.5-3ubuntu1 [245 kB] Get:49 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libapt-pkg6.0 armhf 2.1.5 [757 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf gpgv armhf 2.2.20-1ubuntu1 [170 kB] Get:51 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf apt armhf 2.1.5 [1244 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main armhf logsave armhf 1.45.6-1ubuntu1 [9676 B] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf libext2fs2 armhf 1.45.6-1ubuntu1 [170 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf e2fsprogs armhf 1.45.6-1ubuntu1 [510 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf libcom-err2 armhf 1.45.6-1ubuntu1 [8708 B] Get:56 http://ftpmaster.internal/ubuntu groovy/main armhf libprocps8 armhf 2:3.3.16-4ubuntu1 [29.9 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main armhf libss2 armhf 1.45.6-1ubuntu1 [9384 B] Get:58 http://ftpmaster.internal/ubuntu groovy/main armhf procps armhf 2:3.3.16-4ubuntu1 [222 kB] Get:59 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsqlite3-0 armhf 3.32.1-1 [469 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main armhf tzdata all 2020a-0ubuntu1 [293 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main armhf libctf0 armhf 2.34-7ubuntu1 [37.1 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-arm-linux-gnueabihf armhf 2.34-7ubuntu1 [2093 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main armhf libbinutils armhf 2.34-7ubuntu1 [317 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main armhf binutils armhf 2.34-7ubuntu1 [3364 B] Get:65 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-common armhf 2.34-7ubuntu1 [207 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main armhf libctf-nobfd0 armhf 2.34-7ubuntu1 [38.0 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main armhf libasan5 armhf 9.3.0-13ubuntu1 [387 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main armhf g++-9 armhf 9.3.0-13ubuntu1 [6688 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-9 armhf 9.3.0-13ubuntu1 [6554 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main armhf libstdc++-9-dev armhf 9.3.0-13ubuntu1 [1782 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main armhf libgcc-9-dev armhf 9.3.0-13ubuntu1 [687 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main armhf cpp-9 armhf 9.3.0-13ubuntu1 [5882 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-9-base armhf 9.3.0-13ubuntu1 [19.6 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main armhf gpg armhf 2.2.20-1ubuntu1 [427 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main armhf gpgconf armhf 2.2.20-1ubuntu1 [107 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main armhf gpg-agent armhf 2.2.20-1ubuntu1 [195 kB] Get:77 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf linux-libc-dev armhf 5.4.0-33.37 [1078 kB] Get:78 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf make armhf 4.3-1 [156 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.4 MB in 3s (17.2 MB/s) (Reading database ... 12562 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19375088 armhf groovy-proposed -c chroot:build-PACKAGEBUILD-19375088 --arch=armhf --dist=groovy-proposed --nolog paml_4.9j+dfsg-3.dsc Initiating build PACKAGEBUILD-19375088 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-016.buildd +==============================================================================+ | paml 4.9j+dfsg-3 (armhf) 29 May 2020 17:52 | +==============================================================================+ Package: paml Version: 4.9j+dfsg-3 Source Version: 4.9j+dfsg-3 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/paml-thBQcU/paml-4.9j+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/paml-thBQcU' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19375088/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- paml_4.9j+dfsg-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-mrqvDs/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-mrqvDs/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mrqvDs/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mrqvDs/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mrqvDs/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-mrqvDs/apt_archive ./ Packages [529 B] Fetched 2862 B in 0s (32.0 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 NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-mrqvDs/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (20.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12570 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12) Filtered Build-Depends: debhelper-compat (= 12) dpkg-deb: building package 'sbuild-build-depends-paml-dummy' in '/<>/resolver-JuUHgZ/apt_archive/sbuild-build-depends-paml-dummy.deb'. Ign:1 copy:/<>/resolver-JuUHgZ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-JuUHgZ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-JuUHgZ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-JuUHgZ/apt_archive ./ Sources [210 B] Get:5 copy:/<>/resolver-JuUHgZ/apt_archive ./ Packages [528 B] Fetched 2857 B in 0s (25.8 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install paml 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 debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-paml-dummy 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.5 MB of archives. After this operation, 61.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-JuUHgZ/apt_archive ./ sbuild-build-depends-paml-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf bsdmainutils armhf 11.1.2ubuntu3 [176 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf libuchardet0 armhf 0.0.6-3build1 [62.4 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf man-db armhf 2.9.1-1 [1077 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic-mgc armhf 1:5.38-5 [218 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic1 armhf 1:5.38-5 [68.4 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf file armhf 1:5.38-5 [22.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf libelf1 armhf 0.176-1.1build1 [41.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf libglib2.0-0 armhf 2.64.2-1 [1123 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf libicu66 armhf 66.1-2ubuntu2 [8222 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf libxml2 armhf 2.9.10+dfsg-5 [546 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf gettext-base armhf 0.19.8.1-10build1 [46.0 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main armhf m4 armhf 1.4.18-4 [187 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main armhf autoconf all 2.69-11.1 [321 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf automake all 1:1.16.2-1ubuntu1 [521 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf autopoint all 0.19.8.1-10build1 [412 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libtool all 2.4.6-14 [161 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main armhf dh-autoreconf all 19 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf libdebhelper-perl all 13ubuntu1 [62.5 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [17.1 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf dh-strip-nondeterminism all 1.8.1-1 [5232 B] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf dwz armhf 0.13-5 [153 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf po-debconf all 1.0.21 [233 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf debhelper all 13ubuntu1 [877 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.5 MB in 1s (15.5 MB/s) Selecting previously unselected package libbsd0:armhf. (Reading database ... 12570 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ... Unpacking libbsd0:armhf (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3build1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-5_armhf.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.1-1_armhf.deb ... Unpacking man-db (2.9.1-1) ... 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Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13ubuntu1_all.deb ... Unpacking debhelper (13ubuntu1) ... Selecting previously unselected package sbuild-build-depends-paml-dummy. Preparing to unpack .../33-sbuild-build-depends-paml-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-paml-dummy (0.invalid.0) ... Setting up libpipeline1:armhf (1.5.2-2build1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.64.2-1) ... No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu2) ... Setting up libdebhelper-perl (13ubuntu1) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libuchardet0:armhf (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1build1) ... Setting up libxml2:armhf (2.9.10+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up bsdmainutils (11.1.2ubuntu3) ... 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 libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up automake (1:1.16.2-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10build1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13ubuntu1) ... Setting up sbuild-build-depends-paml-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-3ubuntu1 linux-libc-dev_5.4.0-33.37 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-7ubuntu1 binutils-arm-linux-gnueabihf_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-3ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.5 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-13ubuntu1 libassuan0_2.5.3-7ubuntu2 libatomic1_10.1.0-3ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblkid1_2.35.1-5ubuntu2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.31-0ubuntu9 libc-dev-bin_2.31-0ubuntu9 libc6_2.31-0ubuntu9 libc6-dev_2.31-0ubuntu9 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.34-2 libcc1-0_10.1.0-3ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1ubuntu1 libcrypt1_1:4.4.15-1ubuntu1 libcryptsetup12_2:2.3.1-1ubuntu1 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_13ubuntu1 libdevmapper1.02.1_2:1.02.167-1ubuntu2 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libfdisk1_2.35.1-5ubuntu2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-13ubuntu1 libgcc-s1_10.1.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10.1.0-3ubuntu1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu66_66.1-2ubuntu2 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-7 libkmod2_27+20200310-2ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.2-1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-4ubuntu1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5ubuntu2 libsqlite3-0_3.32.1-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-3ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.5-3ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-3ubuntu1 libuchardet0_0.0.6-3build1 libudev1_245.5-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.35.1-5ubuntu2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-33.37 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu5 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-1 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-5ubuntu2 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu5 patch_2.7.6-6 perl_5.30.2-1 perl-base_5.30.2-1 perl-modules-5.30_5.30.2-1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-4ubuntu1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-paml-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 util-linux_2.35.1-5ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri May 29 09:44:32 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./paml_4.9j+dfsg-3.dsc dpkg-source: info: extracting paml in paml-4.9j+dfsg dpkg-source: info: unpacking paml_4.9j+dfsg.orig.tar.xz dpkg-source: info: unpacking paml_4.9j+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying add_clean_target.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19375088 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19375088 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19375088 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package paml dpkg-buildpackage: info: source version 4.9j+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/paml-4.9j+dfsg' dh_auto_clean cd src && make -j4 clean make[2]: Entering directory '/<>/paml-4.9j+dfsg/src' rm -f baseml codeml basemlg mcmctree pamp evolver yn00 chi2 infinitesites make[2]: Leaving directory '/<>/paml-4.9j+dfsg/src' rm -f src/baseml src/basemlg src/chi2 src/codeml src/evolver src/infinitesites src/mcmctree src/pamp src/yn00 make[1]: Leaving directory '/<>/paml-4.9j+dfsg' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary-arch dh binary-arch --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src dh_auto_build -a -O--sourcedirectory=src cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/paml-4.9j+dfsg/src' cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o baseml baseml.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o codeml codeml.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o basemlg basemlg.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o mcmctree mcmctree.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from baseml.c:131: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from baseml.c:11: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘ReadSeq’: treesub.c:858:31: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 858 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c:866:28: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 866 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 0, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘printPatterns’: treesub.c:1093:25: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 1093 | printsma(fout, com.spname, com.z, com.ns, com.npatt, com.npatt, gap, com.seqtype, 1, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘AllPatterns’: treesub.c:1361:25: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types] 1361 | printsma(fout, com.spname, com.z, com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL); | ~~~^~~~~~~ | | | unsigned char ** In file included from basemlg.c:11: paml.h:153:31: note: expected ‘char **’ but argument is of type ‘unsigned char **’ 153 | int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype, | ~~~~~^~~~~~~~ In file included from mcmctree.c:192: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from mcmctree.c:22: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from basemlg.c:80: treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘readx’: treesub.c:3956:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from codeml.c:238: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from codeml.c:17: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from baseml.c:131: treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘readx’: treesub.c:3956:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘Perturbation’: treesub.c:4565:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘StarDecomposition’: treesub.c:4867:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘rell’: treesub.c:5728:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5752:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5752 | fscanf(flnf, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from mcmctree.c:192: treesub.c: In function ‘ReadMorphology’: treesub.c:447:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 447 | fscanf(fin, "%s", com.spname[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:450:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5758:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5763:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeSeqs’: treesub.c:8742:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘AdHocRateSmoothing’: treesub.c:9574:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 9574 | fscanf(finStep1, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9672:36: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9765:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 9765 | scanf("%lf", &Rj[j]); | ^~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘DatingHeteroData’: treesub.c:9884:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeSeqs’: treesub.c:8742:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘ReadBlengthGH’: mcmctree.c:840:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 840 | fscanf(fBGH, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:861:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:868:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:870:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 870 | fscanf(fBGH, "%s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘GenerateBlengthGH’: mcmctree.c:1028:7: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1028 | system(line); | ^~~~~~~~~~~~ mcmctree.c: In function ‘Infinitesites’: mcmctree.c:1385:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 1385 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ mcmctree.c:1396:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 1396 | fscanf(fin, "%lf", &FixedDs[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘DescriptiveStatisticsSimpleMCMCTREE’: mcmctree.c:3824:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3824 | fscanf(fin, "%lf", &dat[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from codeml.c:238: treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘readx’: treesub.c:3956:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘Perturbation’: treesub.c:4565:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘StarDecomposition’: treesub.c:4867:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘rell’: treesub.c:5728:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5752:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5752 | fscanf(flnf, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~~ treesub.c:5758:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5758 | fscanf(flnf, "%d%d%lf", &j, &k, &y); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:5763:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeSeqs’: treesub.c:8742:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘AdHocRateSmoothing’: treesub.c:9574:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 9574 | fscanf(finStep1, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9672:36: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 9672 | for (i = 0; i < com.np; i++) fscanf(finStep2, "%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:9765:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 9765 | scanf("%lf", &Rj[j]); | ^~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘DatingHeteroData’: treesub.c:9884:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 9884 | scanf("%lf%d? ", &nu_AHRS, &nbrate); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function ‘GetDaa’: codeml.c:3911:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3911 | fscanf(fdaa, "%lf", &daa[i*naa + j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function ‘GetOmegaAA’: codeml.c:4036:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4036 | if (fin) fscanf(fin, "%d", &com.nOmegaType); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codeml.c:4052:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4052 | fscanf(fin, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~ codeml.c:4056:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4056 | fgets(line, nline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function ‘PairwiseCodon’: codeml.c:4318:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 4318 | scanf("%d%d", &is, &js); | ^~~~~~~~~~~~~~~~~~~~~~~ codeml.c: In function ‘lfunNSsites_rate’: codeml.c:5238:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5238 | scanf("%d", &continuous); | ^~~~~~~~~~~~~~~~~~~~~~~~ codeml.c:5251:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5251 | fscanf(fsites, "%d%s", &it, sitelabel); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:3861:54: warning: ‘%.6g’ directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=] 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~ mcmctree.c:3861:36: note: assuming directive output of 12 bytes 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from paml.h:7, from mcmctree.c:22: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 17 and 41 bytes into a destination of size 32 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o pamp pamp.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from pamp.c:66: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from pamp.c:8: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from pamp.c:66: treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pamp.c: In function ‘main’: pamp.c:115:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 115 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from mcmctree.c:192: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from mcmctree.c:22: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from mcmctree.c:192: treesub.c: In function ‘ReadMorphology’: treesub.c:447:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 447 | fscanf(fin, "%s", com.spname[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:450:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 450 | fscanf(fin, "%lf", &data.zmorph[locus][i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeSeqs’: treesub.c:8742:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 8742 | fscanf(ftree, "%d%d", &stree.nspecies, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘ReadBlengthGH’: mcmctree.c:840:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 840 | fscanf(fBGH, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:861:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 861 | fscanf(fBGH, "%lf", &data.blMLE[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:868:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 868 | fscanf(fBGH, "%lf", &data.Gradient[locus][i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:870:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 870 | fscanf(fBGH, "%s", line); | ^~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘GenerateBlengthGH’: mcmctree.c:1028:7: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result] 1028 | system(line); | ^~~~~~~~~~~~ mcmctree.c: In function ‘Infinitesites’: mcmctree.c:1385:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 1385 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ mcmctree.c:1396:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 1396 | fscanf(fin, "%lf", &FixedDs[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: In function ‘DescriptiveStatisticsSimpleMCMCTREE’: mcmctree.c:3824:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3824 | fscanf(fin, "%lf", &dat[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o evolver evolver.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from evolver.c:66: treesub.c: In function ‘ReadTreeB’: treesub.c:2812:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 2812 | fscanf(ftree, "%d", &tree.nbranch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:2827:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 2827 | if (popline) fgets(line, 254, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeN’: treesub.c:3091:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 3091 | fscanf(ftree, "%lf", &nodes[inode].branch); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘GetNSfromTreeFile’: treesub.c:4159:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4159 | fscanf(ftree, "%lf", &y); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘CladeSupport’: treesub.c:4369:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4369 | fscanf(fM, "%d%d", &i, &ntreeM); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:4397:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 4397 | fgets(line, lline, ft); | ^~~~~~~~~~~~~~~~~~~~~~ treesub.c:4419:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 4419 | fscanf(fM, "%d%d", &s, &ntreeM); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘main’: evolver.c:155:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 155 | scanf("%d", &option); | ^~~~~~~~~~~~~~~~~~~~ evolver.c:161:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 161 | scanf("%d", &com.ns); | ^~~~~~~~~~~~~~~~~~~~ evolver.c:168:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 168 | scanf("%d%d", &ntree, &i); | ^~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:171:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 171 | scanf("%d", &BD); | ^~~~~~~~~~~~~~~~ evolver.c:191:16: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 191 | scanf("%lf%lf%lf%lf", &birth, &death, &sample, &mut); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:213:13: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 213 | scanf("%s%s", treefile, mastertreefile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘between_f_and_x’: evolver.c:243:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 243 | scanf("%d", &fromf); | ^~~~~~~~~~~~~~~~~~~ evolver.c:245:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 245 | scanf("%d", &n); if (n > 100) error2("too many classes"); | ^~~~~~~~~~~~~~~ evolver.c:247:21: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 247 | FOR(i, n - 1) scanf("%lf", &x[i]); | ^~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘LabelClades’: evolver.c:269:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 269 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:271:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 271 | scanf("%d", &unrooted); | ^~~~~~~~~~~~~~~~~~~~~~ evolver.c:274:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 274 | fscanf(ftree, "%d%d", &com.ns, &j); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:291:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 291 | scanf("%s", key); | ^~~~~~~~~~~~~~~~ evolver.c: In function ‘TreeDistanceDistribution’: evolver.c:390:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 390 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:393:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 393 | fscanf(ftree, "%d%d", &com.ns, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘TreeDistances’: evolver.c:446:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 446 | scanf("%s", treef); | ^~~~~~~~~~~~~~~~~~ evolver.c:449:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 449 | fscanf(ftree, "%d%d", &com.ns, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:458:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 458 | scanf("%d", &k); | ^~~~~~~~~~~~~~~ evolver.c: In function ‘GetDaa’: evolver.c:638:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 638 | fscanf(fdaa, "%lf", &daa[i*n + j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘Simulate’: evolver.c:809:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 809 | fscanf(fin, "%d", &format); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:810:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 810 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:814:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 814 | fscanf(fin, "%d", &i); | ^~~~~~~~~~~~~~~~~~~~~ evolver.c:815:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 815 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:817:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 817 | fscanf(fin, "%d%d%d", &com.ns, &com.ls, &nr); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:818:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 818 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:830:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 830 | fscanf(fin, "%lf", &tlength); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:830:39: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 830 | fscanf(fin, "%lf", &tlength); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:854:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 854 | fscanf(fin, "%lf%lf%lf%lf", &birth, &death, &sample, &mut); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:855:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 855 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:860:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 860 | fscanf(fin, "%d", &com.model); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:861:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 861 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:868:21: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 868 | FOR(i, nrate) fscanf(fin, "%lf", &Qrates[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:869:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 869 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:882:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 882 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:882:43: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 882 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:884:28: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 884 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:884:64: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 884 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:885:28: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 885 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.rK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:885:64: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 885 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.rK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:891:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 891 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:891:43: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 891 | fscanf(fin, "%d", &com.ncatG); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:893:28: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 893 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:893:64: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 893 | FOR(i, com.ncatG) fscanf(fin, "%lf", &com.freqK[i]); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:924:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 924 | fscanf(fin, "%lf", &com.omega); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:925:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 925 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:931:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 931 | fscanf(fin, "%lf", &com.kappa); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:931:41: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 931 | fscanf(fin, "%lf", &com.kappa); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:936:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 936 | fscanf(fin, "%lf%d", &com.alpha, &com.ncatG); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:937:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 937 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:953:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 953 | fscanf(fin, "%d", &com.model); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:955:29: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 955 | if (com.model >= 2) { fscanf(fin, "%s", com.daafile); GetDaa(NULL, com.daa); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:956:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 956 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c:963:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 963 | for (k = 0; k < com.ncode; k++) fscanf(fin, "%lf", &com.pi[k]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:970:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 970 | fscanf(fin, "%d", &com.icode); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ evolver.c:970:40: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 970 | fscanf(fin, "%d", &com.icode); fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ evolver.c: In function ‘CladeMrBayesProbabilities’: evolver.c:1268:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 1268 | fscanf(ftree, "%d%d", &i, &k); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o yn00 yn00.c tools.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from yn00.c:70: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from yn00.c:13: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from yn00.c:70: treesub.c: In function ‘ReadSeq’: treesub.c:627:13: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c:3861:54: warning: ‘%.6g’ directive writing between 1 and 13 bytes into a region of size between 7 and 19 [-Wformat-overflow=] 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~ mcmctree.c:3861:36: note: assuming directive output of 12 bytes 3861 | sprintf(nodes[j].annotation, "[&95%%HPD={%.6g, %.6g}]", xHPD025[jj], xHPD975[jj]); | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from paml.h:7, from mcmctree.c:22: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 17 and 41 bytes into a destination of size 32 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘gfopen’: tools.c:1148:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 1148 | scanf("%s", filename); | ^~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘scanfile’: tools.c:5356:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 5356 | fgets(line, lline, fin); | ^~~~~~~~~~~~~~~~~~~~~~~ tools.c: In function ‘DescriptiveStatistics’: tools.c:5678:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 5678 | fscanf(fin, "%lf", &data[j*n + i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tools.c:5689:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 5689 | scanf("%d%d", &ivar_f2d[i][0], &ivar_f2d[i][1]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/paml-4.9j+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -o chi2 chi2.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now chi2.c: In function ‘main’: chi2.c:54:10: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 54 | scanf ("%d%lf", &df, &chi2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/paml-4.9j+dfsg/src' dh_auto_test -a -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_auto_install -a -O--sourcedirectory=src debian/rules override_dh_install-arch make[1]: Entering directory '/<>/paml-4.9j+dfsg' dh_install -a for datfile in debian/paml//usr/lib/paml/data/*.ctl ; do \ for item in seqfile treefile ; do \ sed -i -e "s?\(${item} =\).*[^a-z^A-Z^0-9^.^ ]\+\([a-zA-Z0-9]\+\.[a-z]\+\)?\1 /usr/lib/paml/data/\2?" \ -e "s?\(${item} =\) \([a-zA-Z0-9]\+\.[a-z]\+\)?\1 /usr/lib/paml/data/\2?" \ ${datfile} ; \ done ; \ done sed -i 's?\(aaRatefile = \)\(dat/jones.dat\)?\1/usr/lib/paml/data/\2?' debian/paml//usr/lib/paml/data/codeml.ctl make[1]: Leaving directory '/<>/paml-4.9j+dfsg' dh_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/<>/paml-4.9j+dfsg' dh_installexamples for d in `find debian -name examples -a -type d`; do \ find $d \! -type d | xargs -r chmod -x ; \ done make[1]: Leaving directory '/<>/paml-4.9j+dfsg' dh_installinit -a -O--sourcedirectory=src dh_installsystemduser -a -O--sourcedirectory=src dh_perl -a -O--sourcedirectory=src debian/rules override_dh_link-arch make[1]: Entering directory '/<>/paml-4.9j+dfsg' dh_link -a mkdir -p debian/paml/etc/paml/ for datfile in debian/paml//usr/lib/paml/data/*.ctl ; do \ ln -s /usr/lib/paml/data/`basename ${datfile}` debian/paml/etc/paml ; \ done make[1]: Leaving directory '/<>/paml-4.9j+dfsg' dh_strip_nondeterminism -a -O--sourcedirectory=src dh_compress -a -O--sourcedirectory=src debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>/paml-4.9j+dfsg' dh_fixperms -a find debian/*/usr/lib/paml/data -type f -exec chmod -x \{\} \; make[1]: Leaving directory '/<>/paml-4.9j+dfsg' dh_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing paml-dbgsym (in debian/.debhelper/paml/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing paml (in debian/paml); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/paml/dbgsym-root/DEBIAN/control, package paml-dbgsym, directory debian/.debhelper/paml/dbgsym-root dpkg-deb: building package 'paml-dbgsym' in 'debian/.debhelper/scratch-space/build-paml/paml-dbgsym_4.9j+dfsg-3_armhf.deb'. pkgstripfiles: processing control file: debian/paml/DEBIAN/control, package paml, directory debian/paml pkgstripfiles: Truncating usr/share/doc/paml/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package paml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-3_armhf.deb'. Renaming paml-dbgsym_4.9j+dfsg-3_armhf.deb to paml-dbgsym_4.9j+dfsg-3_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../paml_4.9j+dfsg-3_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 20200529-1755 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ paml_4.9j+dfsg-3_armhf.changes: ------------------------------- Format: 1.8 Date: Fri, 29 May 2020 09:20:27 +0530 Source: paml Binary: paml Architecture: armhf Version: 4.9j+dfsg-3 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Pranav Ballaney Description: paml - Phylogenetic Analysis by Maximum Likelihood (PAML) Changes: paml (4.9j+dfsg-3) unstable; urgency=medium . * Team upload. . [ Etienne Mollier ] * upstream informed of the patch . [ Pranav Ballaney ] * Add autopkgtests Checksums-Sha1: 0f89f3991f176b377c757bbf970d2bd4a9122e40 2099724 paml-dbgsym_4.9j+dfsg-3_armhf.ddeb e42c649b80bb6f478ec2c69ff5ca963fa5f424b9 4948 paml_4.9j+dfsg-3_armhf.buildinfo 101b0e1659614d406bf18951b92ec40f223444d4 555508 paml_4.9j+dfsg-3_armhf.deb Checksums-Sha256: 54d415649ac717d783c008d35b8c05a1b4b94c4ce7a119a23c1220f0b4a5086c 2099724 paml-dbgsym_4.9j+dfsg-3_armhf.ddeb 7d2497ab863f8ed71455908aea0ced37f9211624c865425091d806ae7c6dbeb9 4948 paml_4.9j+dfsg-3_armhf.buildinfo 6a874b8a7bc57236ab2541613e397538b596b30456c4c691ddec66359b2bd5b7 555508 paml_4.9j+dfsg-3_armhf.deb Files: efd66b1364797bc1b8713170c5de22a2 2099724 debug optional paml-dbgsym_4.9j+dfsg-3_armhf.ddeb b62e2f30fd3546c8451c3b00a380b376 4948 science optional paml_4.9j+dfsg-3_armhf.buildinfo 69671d8ffd651f2d474bd4af6a57f600 555508 science optional paml_4.9j+dfsg-3_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ paml_4.9j+dfsg-3_armhf.deb -------------------------- new debian package, version 2.0. size 555508 bytes: control archive=2392 bytes. 770 bytes, 16 lines control 4016 bytes, 62 lines md5sums Package: paml Version: 4.9j+dfsg-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1873 Depends: libc6 (>= 2.29) Section: science Priority: optional Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Description: Phylogenetic Analysis by Maximum Likelihood (PAML) PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. drwxr-xr-x root/root 0 2020-05-29 03:50 ./ drwxr-xr-x root/root 0 2020-05-29 03:50 ./etc/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./etc/paml/ lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/aaml.ctl -> /usr/lib/paml/data/aaml.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/baseml.ctl -> /usr/lib/paml/data/baseml.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/codeml.ctl -> /usr/lib/paml/data/codeml.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/codonml.ctl -> /usr/lib/paml/data/codonml.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/mcmctree.ctl -> /usr/lib/paml/data/mcmctree.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/pamp.ctl -> /usr/lib/paml/data/pamp.ctl lrwxrwxrwx root/root 0 2020-05-29 03:50 ./etc/paml/yn00.ctl -> /usr/lib/paml/data/yn00.ctl drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/bin/ lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/baseml -> ../lib/debian-med/bin/baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/basemlg -> ../lib/debian-med/bin/basemlg lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/chi2 -> ../lib/debian-med/bin/chi2 lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/codeml -> ../lib/debian-med/bin/codeml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/mcmctree -> ../lib/debian-med/bin/mcmctree lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/paml-evolver -> ../lib/debian-med/bin/evolver lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/pamp -> ../lib/debian-med/bin/pamp lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/bin/yn00 -> ../lib/debian-med/bin/yn00 drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 190 2020-05-29 03:50 ./usr/lib/debian-med/bin/baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/basemlg -> baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/chi2 -> ../../paml/bin/chi2 lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/codeml -> baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/evolver -> ../../paml/bin/evolver lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/mcmctree -> baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/pamp -> baseml lrwxrwxrwx root/root 0 2020-05-29 03:50 ./usr/lib/debian-med/bin/yn00 -> baseml drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/paml/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/paml/bin/ -rwxr-xr-x root/root 300360 2020-05-29 03:50 ./usr/lib/paml/bin/baseml -rwxr-xr-x root/root 185288 2020-05-29 03:50 ./usr/lib/paml/bin/basemlg -rwxr-xr-x root/root 9768 2020-05-29 03:50 ./usr/lib/paml/bin/chi2 -rwxr-xr-x root/root 403704 2020-05-29 03:50 ./usr/lib/paml/bin/codeml -rwxr-xr-x root/root 172920 2020-05-29 03:50 ./usr/lib/paml/bin/evolver -rwxr-xr-x root/root 238640 2020-05-29 03:50 ./usr/lib/paml/bin/mcmctree -rwxr-xr-x root/root 181056 2020-05-29 03:50 ./usr/lib/paml/bin/pamp -rwxr-xr-x root/root 164688 2020-05-29 03:50 ./usr/lib/paml/bin/yn00 drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/lib/paml/data/ -rw-r--r-- root/root 56 2019-10-18 14:02 ./usr/lib/paml/data/3s.trees -rw-r--r-- root/root 97 2019-10-18 14:02 ./usr/lib/paml/data/4s.trees -rw-r--r-- root/root 299 2019-10-18 14:02 ./usr/lib/paml/data/5s.trees -rw-r--r-- root/root 124 2019-10-18 14:02 ./usr/lib/paml/data/6s.trees -rw-r--r-- root/root 161 2019-10-18 14:02 ./usr/lib/paml/data/9s.trees -rw-r--r-- root/root 1403 2019-10-18 14:02 ./usr/lib/paml/data/MCaa.dat -rw-r--r-- root/root 1781 2019-10-18 14:02 ./usr/lib/paml/data/MCbase.dat -rw-r--r-- root/root 2033 2019-10-18 14:02 ./usr/lib/paml/data/MCbaseRandomTree.dat -rw-r--r-- root/root 4276 2019-10-18 14:02 ./usr/lib/paml/data/MCcodon.dat -rw-r--r-- root/root 493 2020-05-29 03:50 ./usr/lib/paml/data/aaml.ctl -rw-r--r-- root/root 6186 2019-10-18 14:02 ./usr/lib/paml/data/abglobin.nuc -rw-r--r-- root/root 1794 2020-05-29 03:50 ./usr/lib/paml/data/baseml.ctl -rw-r--r-- root/root 5830 2019-10-18 14:02 ./usr/lib/paml/data/brown.nuc -rw-r--r-- root/root 278 2019-10-18 14:02 ./usr/lib/paml/data/brown.rooted.trees -rw-r--r-- root/root 100 2019-10-18 14:02 ./usr/lib/paml/data/brown.trees -rw-r--r-- root/root 2999 2020-05-29 03:50 ./usr/lib/paml/data/codeml.ctl -rw-r--r-- root/root 660 2020-05-29 03:50 ./usr/lib/paml/data/codonml.ctl drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/lib/paml/data/dat/ -rw-r--r-- root/root 1850 2019-10-18 14:02 ./usr/lib/paml/data/dat/MtZoa.dat -rw-r--r-- root/root 10073 2019-10-18 14:02 ./usr/lib/paml/data/dat/cpREV10.dat -rw-r--r-- root/root 1874 2019-10-18 14:02 ./usr/lib/paml/data/dat/cpREV64.dat -rw-r--r-- root/root 2972 2019-10-18 14:02 ./usr/lib/paml/data/dat/dayhoff-dcmut.dat -rw-r--r-- root/root 5284 2019-10-18 14:02 ./usr/lib/paml/data/dat/dayhoff.dat -rw-r--r-- root/root 1536 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974a.dat -rw-r--r-- root/root 1372 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974c.dat -rw-r--r-- root/root 1130 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974p.dat -rw-r--r-- root/root 1359 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974v.dat -rw-r--r-- root/root 1681 2019-10-18 14:02 ./usr/lib/paml/data/dat/grantham.dat -rw-r--r-- root/root 2960 2019-10-18 14:02 ./usr/lib/paml/data/dat/jones-dcmut.dat -rw-r--r-- root/root 12131 2019-10-18 14:02 ./usr/lib/paml/data/dat/jones.dat -rw-r--r-- root/root 2713 2019-10-18 14:02 ./usr/lib/paml/data/dat/lg.dat -rw-r--r-- root/root 1258 2019-10-18 14:02 ./usr/lib/paml/data/dat/miyata.dat -rw-r--r-- root/root 4886 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtArt.dat -rw-r--r-- root/root 2370 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtREV24.dat -rw-r--r-- root/root 3844 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtmam.dat -rw-r--r-- root/root 3337 2019-10-18 14:02 ./usr/lib/paml/data/dat/wag.dat -rw-r--r-- root/root 4124 2019-10-18 14:02 ./usr/lib/paml/data/lysozymeSmall.nuc -rw-r--r-- root/root 769 2019-10-18 14:02 ./usr/lib/paml/data/lysozymeSmall.trees -rw-r--r-- root/root 1299 2020-05-29 03:50 ./usr/lib/paml/data/mcmctree.ctl -rw-r--r-- root/root 338 2019-10-18 14:02 ./usr/lib/paml/data/mtCDNApri.trees -rw-r--r-- root/root 70466 2019-10-18 14:02 ./usr/lib/paml/data/mtCDNApri123.txt -rw-r--r-- root/root 11708 2019-10-18 14:02 ./usr/lib/paml/data/mtprim9.nuc -rw-r--r-- root/root 374 2020-05-29 03:50 ./usr/lib/paml/data/pamp.ctl -rw-r--r-- root/root 1008 2019-10-18 14:02 ./usr/lib/paml/data/stewart.aa -rw-r--r-- root/root 143 2019-10-18 14:02 ./usr/lib/paml/data/stewart.trees -rw-r--r-- root/root 719 2020-05-29 03:50 ./usr/lib/paml/data/yn00.ctl drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/share/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/share/doc/paml/ -rw-r--r-- root/root 675 2019-10-18 14:02 ./usr/share/doc/paml/GeneticCode.txt.gz -rw-r--r-- root/root 898 2020-05-29 03:50 ./usr/share/doc/paml/README.Debian -rw-r--r-- root/root 278 2020-05-29 03:50 ./usr/share/doc/paml/README.test -rw-r--r-- root/root 1419 2019-10-18 14:02 ./usr/share/doc/paml/README.txt -rw-r--r-- root/root 1026 2020-05-29 03:50 ./usr/share/doc/paml/changelog.Debian.gz -rw-r--r-- root/root 827 2020-05-29 03:50 ./usr/share/doc/paml/copyright drwxr-xr-x root/root 0 2020-05-29 03:50 ./usr/share/doc/paml/profile.d/ -rw-r--r-- root/root 147 2020-05-29 03:50 ./usr/share/doc/paml/profile.d/paml -rw-r--r-- root/root 1427 2020-05-29 03:50 ./usr/share/doc/paml/run-unit-test +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 23968 Build-Time: 168 Distribution: groovy-proposed Host Architecture: armhf Install-Time: 29 Job: paml_4.9j+dfsg-3.dsc Machine Architecture: arm64 Package: paml Package-Time: 201 Source-Version: 4.9j+dfsg-3 Space: 23968 Status: successful Version: 4.9j+dfsg-3 -------------------------------------------------------------------------------- Finished at 20200529-1755 Build needed 00:03:21, 23968k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19375088 Scanning for processes to kill in build PACKAGEBUILD-19375088