https://launchpad.net/ubuntu/+source/paml/4.9j+dfsg-4/+build/25421396 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-062 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:22 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_225~602~ubuntu20.04.1 python3-lpbuildd_225~602~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 24 Dec 23:16:23 ntpdate[1898]: adjust time server 10.131.248.1 offset 0.002930 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25421396 --image-type chroot /home/buildd/filecache-default/bc95a5beca317e426bf1850638bb0efa95f27a71 Creating target for build PACKAGEBUILD-25421396 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25421396 Starting target for build PACKAGEBUILD-25421396 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25421396 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25421396 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25421396 Updating target for build PACKAGEBUILD-25421396 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 Packages [1393 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe amd64 Packages [14.8 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5867 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 Packages [203 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [85.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe amd64 Packages [1777 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [629 kB] Fetched 25.9 MB in 2s (11.4 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: lsb-base* The following NEW packages will be installed: libjansson4 libperl5.36 perl-modules-5.36 The following packages will be upgraded: adduser binutils binutils-common binutils-x86-64-linux-gnu ca-certificates coreutils cpp-12 dash debconf diffutils dpkg dpkg-dev g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv libapparmor1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libcap2 libcc1-0 libctf-nobfd0 libctf0 libdpkg-perl libgcc-12-dev libgcc-s1 libgomp1 libgprofng0 libgssapi-krb5-2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 liblzma5 libpcre3 libquadmath0 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtsan2 libubsan1 libudev1 linux-libc-dev openssl perl perl-base systemd systemd-sysv sysvinit-utils xz-utils zlib1g 64 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 88.4 MB of archives. After this operation, 48.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 coreutils amd64 9.1-1ubuntu1 [1408 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblzma5 amd64 5.4.0-0.1 [124 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 dpkg amd64 1.21.13ubuntu1 [1345 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-9ubuntu1 [88.5 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 diffutils amd64 1:3.8-3 [176 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-modules-5.36 all 5.36.0-6 [2985 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libperl5.36 amd64 5.36.0-6 [4805 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl amd64 5.36.0-6 [235 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 perl-base amd64 5.36.0-6 [1780 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu3 [61.6 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 sysvinit-utils amd64 3.05-7ubuntu1 [26.2 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 systemd-sysv amd64 252.1-1ubuntu1 [11.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit-common all 1:3.0.7-1ubuntu3 [4864 B] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libaudit1 amd64 1:3.0.7-1ubuntu3 [45.1 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 debconf all 1.5.80 [125 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 libssl3 amd64 3.0.5-2ubuntu2 [1893 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkmod2 amd64 30+20220905-1ubuntu1 [49.6 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 libapparmor1 amd64 3.0.8-1ubuntu1 [36.9 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcap2 amd64 1:2.66-3 [27.8 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 liblz4-1 amd64 1.9.4-1 [63.1 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 systemd amd64 252.1-1ubuntu1 [2994 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsystemd-shared amd64 252.1-1ubuntu1 [1756 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsystemd0 amd64 252.1-1ubuntu1 [330 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libubsan1 amd64 12.2.0-10ubuntu1 [969 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgomp1 amd64 12.2.0-10ubuntu1 [125 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libitm1 amd64 12.2.0-10ubuntu1 [29.5 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libatomic1 amd64 12.2.0-10ubuntu1 [10.4 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libasan8 amd64 12.2.0-10ubuntu1 [2429 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 liblsan0 amd64 12.2.0-10ubuntu1 [1060 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libquadmath0 amd64 12.2.0-10ubuntu1 [152 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 cpp-12 amd64 12.2.0-10ubuntu1 [10.6 MB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libcc1-0 amd64 12.2.0-10ubuntu1 [46.5 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf-nobfd0 amd64 2.39.50.20221224-1ubuntu1 [99.7 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgprofng0 amd64 2.39.50.20221224-1ubuntu1 [897 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libctf0 amd64 2.39.50.20221224-1ubuntu1 [97.4 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main amd64 libjansson4 amd64 2.14-2 [33.0 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.39.50.20221224-1ubuntu1 [2456 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libbinutils amd64 2.39.50.20221224-1ubuntu1 [631 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils-common amd64 2.39.50.20221224-1ubuntu1 [235 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 binutils amd64 2.39.50.20221224-1ubuntu1 [3258 B] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gcc-12-base amd64 12.2.0-10ubuntu1 [19.6 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libstdc++6 amd64 12.2.0-10ubuntu1 [678 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libstdc++-12-dev amd64 12.2.0-10ubuntu1 [2158 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 g++-12 amd64 12.2.0-10ubuntu1 [12.0 MB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gcc-12 amd64 12.2.0-10ubuntu1 [21.4 MB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgcc-12-dev amd64 12.2.0-10ubuntu1 [2577 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libtsan2 amd64 12.2.0-10ubuntu1 [2456 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgcc-s1 amd64 12.2.0-10ubuntu1 [53.9 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libudev1 amd64 252.1-1ubuntu1 [88.7 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgv amd64 2.2.40-1ubuntu2 [137 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libpcre3 amd64 2:8.39-15 [250 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main amd64 openssl amd64 3.0.5-2ubuntu2 [1178 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main amd64 ca-certificates all 20211016ubuntu1 [141 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkeyutils1 amd64 1.6.3-2 [9356 B] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5support0 amd64 1.20.1-1build1 [31.4 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libk5crypto3 amd64 1.20.1-1build1 [81.1 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-1build1 [142 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libkrb5-3 amd64 1.20.1-1build1 [346 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libsqlite3-0 amd64 3.40.0-2 [655 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 xz-utils amd64 5.4.0-0.1 [176 kB] Get:62 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 dpkg-dev all 1.21.13ubuntu1 [1070 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdpkg-perl all 1.21.13ubuntu1 [242 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg amd64 2.2.40-1ubuntu2 [523 kB] Get:65 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpgconf amd64 2.2.40-1ubuntu2 [93.7 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 gpg-agent amd64 2.2.40-1ubuntu2 [217 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 linux-libc-dev amd64 5.19.0-23.24 [1345 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.4 MB in 1s (118 MB/s) (Reading database ... 13639 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu1_amd64.deb ... Unpacking coreutils (9.1-1ubuntu1) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu1) ... (Reading database ... 13639 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.0-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.4.0-0.1) over (5.2.9-0.0) ... Setting up liblzma5:amd64 (5.4.0-0.1) ... (Reading database ... 13639 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.13ubuntu1_amd64.deb ... Unpacking dpkg (1.21.13ubuntu1) over (1.21.11ubuntu2) ... Setting up dpkg (1.21.13ubuntu1) ... (Reading database ... 13639 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1_amd64.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) over (0.5.11+git20210903+057cd650a4ed-8ubuntu1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... 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Setting up libkrb5support0:amd64 (1.20.1-1build1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up perl-modules-5.36 (5.36.0-6) ... Setting up xz-utils (5.4.0-0.1) ... Setting up libquadmath0:amd64 (12.2.0-10ubuntu1) ... Setting up libatomic1:amd64 (12.2.0-10ubuntu1) ... Setting up libk5crypto3:amd64 (1.20.1-1build1) ... Setting up libubsan1:amd64 (12.2.0-10ubuntu1) ... Setting up libasan8:amd64 (12.2.0-10ubuntu1) ... Setting up gpgconf (2.2.40-1ubuntu2) ... Setting up libkrb5-3:amd64 (1.20.1-1build1) ... Setting up libtsan2:amd64 (12.2.0-10ubuntu1) ... Setting up libbinutils:amd64 (2.39.50.20221224-1ubuntu1) ... Setting up openssl (3.0.5-2ubuntu2) ... Setting up libcc1-0:amd64 (12.2.0-10ubuntu1) ... Setting up libperl5.36:amd64 (5.36.0-6) ... Setting up gpg (2.2.40-1ubuntu2) ... Setting up liblsan0:amd64 (12.2.0-10ubuntu1) ... Setting up libitm1:amd64 (12.2.0-10ubuntu1) ... Setting up libkmod2:amd64 (30+20220905-1ubuntu1) ... Setting up libctf0:amd64 (2.39.50.20221224-1ubuntu1) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up ca-certificates (20211016ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 0 added, 3 removed; done. Setting up perl (5.36.0-6) ... Setting up libgprofng0:amd64 (2.39.50.20221224-1ubuntu1) ... Setting up libgcc-12-dev:amd64 (12.2.0-10ubuntu1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-1build1) ... Setting up libsystemd-shared:amd64 (252.1-1ubuntu1) ... Setting up libdpkg-perl (1.21.13ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.39.50.20221224-1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-10ubuntu1) ... Setting up systemd (252.1-1ubuntu1) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.39.50.20221224-1ubuntu1) ... Setting up dpkg-dev (1.21.13ubuntu1) ... Setting up gcc-12 (12.2.0-10ubuntu1) ... Setting up g++-12 (12.2.0-10ubuntu1) ... Setting up systemd-sysv (252.1-1ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... (Reading database ... 15586 files and directories currently installed.) Purging configuration files for lsb-base (11.2ubuntu1) ... Processing triggers for ca-certificates (20211016ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-25421396 amd64 lunar-proposed -c chroot:build-PACKAGEBUILD-25421396 --arch=amd64 --dist=lunar-proposed --nolog -A paml_4.9j+dfsg-4.dsc Initiating build PACKAGEBUILD-25421396 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:22 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-062.buildd +==============================================================================+ | paml 4.9j+dfsg-4 (amd64) Sat, 24 Dec 2022 23:16:43 +0000 | +==============================================================================+ Package: paml Version: 4.9j+dfsg-4 Source Version: 4.9j+dfsg-4 Distribution: lunar-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25421396/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/paml-3RdAxS/resolver-ITqGmQ' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- paml_4.9j+dfsg-4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/paml-3RdAxS/paml-4.9j+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/paml-3RdAxS' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [370 B] Get:5 copy:/<>/apt_archive ./ Packages [449 B] Fetched 1776 B in 0s (105 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 18.6 MB of archives. After this operation, 66.3 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [670 B] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libelf1 amd64 0.188-2 [52.9 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main amd64 libicu71 amd64 71.1-3ubuntu1 [10.6 MB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.1 [762 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main amd64 bsdextrautils amd64 2.38.1-4ubuntu1 [71.0 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic-mgc amd64 1:5.41-4 [257 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main amd64 libmagic1 amd64 1:5.41-4 [87.3 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main amd64 file amd64 1:5.41-4 [21.5 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext-base amd64 0.21-10 [37.6 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main amd64 groff-base amd64 1.22.4-9 [937 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main amd64 man-db amd64 2.11.1-1 [1218 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main amd64 m4 amd64 1.4.19-1 [244 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main amd64 autoconf all 2.71-2 [338 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main amd64 autopoint all 0.21-10 [421 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main amd64 libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main amd64 libtool all 2.4.7-5 [166 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-autoreconf all 20 [16.1 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:24 http://ftpmaster.internal/ubuntu lunar/main amd64 libfile-stripnondeterminism-perl all 1.13.0-2 [18.2 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main amd64 dh-strip-nondeterminism all 1.13.0-2 [5308 B] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main amd64 libdw1 amd64 0.188-2 [251 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main amd64 dwz amd64 0.14+20220924-2 [112 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main amd64 gettext amd64 0.21-10 [867 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main amd64 debhelper all 13.10.1ubuntu1 [924 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.6 MB in 1s (26.4 MB/s) Selecting previously unselected package libelf1:amd64. (Reading database ... 15586 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.188-2_amd64.deb ... Unpacking libelf1:amd64 (0.188-2) ... Selecting previously unselected package libicu71:amd64. Preparing to unpack .../01-libicu71_71.1-3ubuntu1_amd64.deb ... Unpacking libicu71:amd64 (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../03-bsdextrautils_2.38.1-4ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.38.1-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../31-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu71:amd64 (71.1-3ubuntu1) ... Setting up bsdextrautils (2.38.1-4ubuntu1) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.10.1ubuntu1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up gettext-base (0.21-10) ... Setting up m4 (1.4.19-1) ... Setting up file (1:5.41-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-10) ... Setting up autoconf (2.71-2) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.188-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-2) ... Setting up libdw1:amd64 (0.188-2) ... Setting up gettext (0.21-10) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.0-2) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up debugedit (1:5.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.1-1) ... 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 debhelper (13.10.1ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:22 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.39.50.20221224-1ubuntu1 dpkg-dev_1.21.13ubuntu1 g++-12_12.2.0-10ubuntu1 gcc-12_12.2.0-10ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-10ubuntu1 libstdc++6_12.2.0-10ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 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gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-2 libapparmor1_3.0.8-1ubuntu1 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-10ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-10ubuntu1 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1ubuntu3 libaudit1_1:3.0.7-1ubuntu3 libbinutils_2.39.50.20221224-1ubuntu1 libblkid1_2.38.1-4ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcap-ng0_0.8.3-1build1 libcap2_1:2.66-3 libcc1-0_12.2.0-10ubuntu1 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcryptsetup12_2:2.5.0-6ubuntu3 libctf-nobfd0_2.39.50.20221224-1ubuntu1 libctf0_2.39.50.20221224-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.13ubuntu1 libdw1_0.188-2 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systemd_252.1-1ubuntu1 systemd-sysv_252.1-1ubuntu1 sysvinit-utils_3.05-7ubuntu1 tar_1.34+dfsg-1.1 tzdata_2022g-0ubuntu2 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paml Binary: paml, paml-doc Architecture: any all Version: 4.9j+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Pjotr Prins , Steffen Moeller , Andreas Tille Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/paml Vcs-Git: https://salsa.debian.org/med-team/paml.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: paml deb science optional arch=any paml-doc deb doc optional arch=all Checksums-Sha1: d40ca19fbd5a49c232a1bd1b863f0d5d69e21bc3 1375380 paml_4.9j+dfsg.orig.tar.xz 6df72417f214dbdbc854288f858daf2dc4f4b4d6 7128 paml_4.9j+dfsg-4.debian.tar.xz Checksums-Sha256: af7ccf450cb26b6b235559f3e6e70241ac59ed87caacf57bd91d6cdfaf81b9b8 1375380 paml_4.9j+dfsg.orig.tar.xz 4b5e900cf702a91e62edaba0d2da4bc780dcd1f6fede76b37b8477ab4980ae57 7128 paml_4.9j+dfsg-4.debian.tar.xz Files: 1300f92065c7d3249a649caf2dad9417 1375380 paml_4.9j+dfsg.orig.tar.xz 4b23b0a163d9adf4f1f3547a12f82adb 7128 paml_4.9j+dfsg-4.debian.tar.xz Dgit: bafdf0890b7a0f08f1b07d2d1fc4d1bfc60aebb3 debian archive/debian/4.9j+dfsg-4 https://git.dgit.debian.org/paml -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOnFIgUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrx0RAAovVjfUQxla9ZeV6ShMvIjfui7XyS YjpYPoof0F8ldB9co6NSadVeoonLMdYx0g2Q2XumcNxcpiWFsgqBR8WRcJ5OvW0N VuqhF3dcKM38aXM0TAxSAVEGD0/F26IXJFfeWLN4EEE9GFvE3z5rePYpKfAaaTED iUTt9buwcV6mfb/tDawAEyqWqeHHQM0xOlCzflW24/rQkEITuuMKphYhh2bbzEHK WYMo7sgL1zYMWsVvp5XofPu806gef+uyf0iph7BlPIFtsTvZC5yT1IzEXWtN/K7L 0cnCUvPJaxeqANN8xwh5FqEAX1jhg10W9c49r/7GXaMg49q2bunPnmAF30trG735 WdZhUTIuDo39Un9hV5+buCN1DdR5QTU/W7T/odpPfdvVNzt0ewHprHUtoWEF71R6 B7X15nR2jT1x73LKmELaLBJJxKLo/vD4OSuL7+2VKVxoHh5Br7uaX/pjAWYyzxQK j++6K7QKU+pH3r9u2A/Kfgwy4YW4/X58OBj3lJNLT1qlKR/yxmTYGgU11J3KrJ/P v6qtTBB7HhZ0yJnNsC19EER3P3n+aWLnYDd1dq47NaaHWUtHXTEbtrvjmzgtKOdk jBlqIjgOtB+9MCAR5T1CKpRbIxLJxuEuqqFqrft7IiF1NImCfJ0rchKJueLhKe8j GaAyJ6oK4bSajyQ= =9Rt6 -----END PGP SIGNATURE----- gpgv: Signature made Sat Dec 24 15:02:32 2022 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./paml_4.9j+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting paml in /<> dpkg-source: info: unpacking paml_4.9j+dfsg.orig.tar.xz dpkg-source: info: unpacking paml_4.9j+dfsg-4.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 disk 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-25421396 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25421396 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25421396 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package paml dpkg-buildpackage: info: source version 4.9j+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean cd src && make -j4 clean make[2]: Entering directory '/<>/src' rm -f baseml codeml basemlg mcmctree pamp evolver yn00 chi2 infinitesites make[2]: Leaving directory '/<>/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 '/<>' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/src' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o baseml baseml.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o codeml codeml.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o basemlg basemlg.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o mcmctree mcmctree.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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, | ~~~~~^~~~~~~~ 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 ** 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, | ~~~~~^~~~~~~~ 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 ** 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 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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 ** 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 codeml.c:238: treesub.c: In function ‘IdenticalSeqs’: 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 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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 ‘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 ‘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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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’: mcmctree.c: In function ‘DescriptiveStatisticsSimpleMCMCTREE’: 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ‘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: In function ‘ReadTreeB’: 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: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 ‘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: 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: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: 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: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: In function ‘StarDecomposition’: 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: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:906, from paml.h:7: In function ‘sprintf’, inlined from ‘DescriptiveStatisticsSimpleMCMCTREE’ at mcmctree.c:3861:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 41 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o pamp pamp.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o infinitesites -D INFINITESITES mcmctree.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o evolver evolver.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:906, from paml.h:7: In function ‘sprintf’, inlined from ‘DescriptiveStatisticsSimpleMCMCTREE’ at mcmctree.c:3861:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__sprintf_chk’ output between 17 and 41 bytes into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o yn00 yn00.c tools.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -O3 -o chi2 chi2.c -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lm 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src debian/rules override_dh_install-arch make[1]: Entering directory '/<>' 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 '/<>' dh_install -O--sourcedirectory=src -Npaml dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installexamples make[1]: Entering directory '/<>' 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 '/<>' dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src debian/rules override_dh_link-arch make[1]: Entering directory '/<>' 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 '/<>' dh_link -O--sourcedirectory=src -Npaml dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>' dh_fixperms -a find debian/*/usr/lib/paml/data -type f -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_fixperms -O--sourcedirectory=src -Npaml dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src debugedit: debian/paml/usr/lib/paml/bin/yn00: Unknown DWARF DW_FORM_0x1f21 b9a29560a7cefb8bb770eddfae2e9e6fedd14534 debugedit: debian/paml/usr/lib/paml/bin/basemlg: Unknown DWARF DW_FORM_0x1f21 7c7290259af09cdf1d0f707bab4d545e49d1e7ae debugedit: debian/paml/usr/lib/paml/bin/mcmctree: Unknown DWARF DW_FORM_0x1f20 fe93bc15d7b8c39c749a9e4ef640407cbe525762 debugedit: debian/paml/usr/lib/paml/bin/baseml: Unknown DWARF DW_FORM_0x1f20 bb9287db46633837d0be9547d6fb2291cd9fac2d debugedit: debian/paml/usr/lib/paml/bin/pamp: Unknown DWARF DW_FORM_0x1f21 f5ff96e693c0ffb047826b8f8157790f4bc4e36a debugedit: debian/paml/usr/lib/paml/bin/codeml: Unknown DWARF DW_FORM_0x1f20 2d361a54bdc372f45f2df96f50200a87a4360e84 debugedit: debian/paml/usr/lib/paml/bin/chi2: Unknown DWARF DW_FORM_0x1f20 79868638de14a2dcd4753d2a15e5e5cfe87b316c debugedit: debian/paml/usr/lib/paml/bin/evolver: Unknown DWARF DW_FORM_0x1f20 39fa31a126f273becca5737ee69c17151dd6ccf6 dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing paml (in debian/paml); do_strip: , oemstrip: pkgstriptranslations: processing paml-doc (in debian/paml-doc); do_strip: , oemstrip: pkgstriptranslations: processing paml-dbgsym (in debian/.debhelper/paml/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/paml/DEBIAN/control, package paml, directory debian/paml pkgstripfiles: Running PNG optimization (using 4 cpus) for package paml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'paml' in '../paml_4.9j+dfsg-4_amd64.deb'. pkgstripfiles: processing control file: debian/paml-doc/DEBIAN/control, package paml-doc, directory debian/paml-doc pkgstripfiles: Disabled PNG optimization for -doc package paml-doc (to save build time) dpkg-deb: building package 'paml-doc' in '../paml-doc_4.9j+dfsg-4_all.deb'. 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-4_amd64.deb'. Renaming paml-dbgsym_4.9j+dfsg-4_amd64.deb to paml-dbgsym_4.9j+dfsg-4_amd64.ddeb dpkg-genbuildinfo --build=binary -O../paml_4.9j+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../paml_4.9j+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-24T23:17:34Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ paml_4.9j+dfsg-4_amd64.changes: ------------------------------- Format: 1.8 Date: Sat, 24 Dec 2022 13:14:11 +0100 Source: paml Binary: paml paml-doc Built-For-Profiles: noudeb Architecture: amd64 all Version: 4.9j+dfsg-4 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: paml - Phylogenetic Analysis by Maximum Likelihood (PAML) paml-doc - Documentation for PAML Closes: 1026913 Changes: paml (4.9j+dfsg-4) unstable; urgency=medium . * Team upload. * hardening.patch: fortify source and fix crossbuilds. * add_clean_target.patch: refresh. * d/t/run-unit-test: only run Test 4 on !amd64. 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50abfc56ff9f1033862559d1b7ebda7860859ec9 1309120 paml-dbgsym_4.9j+dfsg-4_amd64.ddeb 4b55c7fe49d7922e90585f2652a577199eb51ae7 1003288 paml-doc_4.9j+dfsg-4_all.deb 64bf687d251a7144488fa47c4d30360865c15c54 641056 paml_4.9j+dfsg-4_amd64.deb Checksums-Sha256: 37d0b8b6e6270eade9b148d55c6cb33d2c40196b3c4052535dc968c2b423bdbb 1309120 paml-dbgsym_4.9j+dfsg-4_amd64.ddeb 8f3af4879bfc1f5f3f844eeb2860c0eb314226deab5a52749eef50e5687409b8 1003288 paml-doc_4.9j+dfsg-4_all.deb d0d6cff8d7d12027028782448382d90cd0bad6b41837b19befcfacf7920f19cc 641056 paml_4.9j+dfsg-4_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Sat, 24 Dec 2022 23:17:33 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39.50.20221224-1ubuntu1), binutils-common (= 2.39.50.20221224-1ubuntu1), binutils-x86-64-linux-gnu (= 2.39.50.20221224-1ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-10ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.80), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-2), diffutils (= 1:3.8-3), dpkg (= 1.21.13ubuntu1), dpkg-dev (= 1.21.13ubuntu1), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-10ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-10ubuntu1), gcc-12-base (= 12.2.0-10ubuntu1), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-10ubuntu1), libatomic1 (= 12.2.0-10ubuntu1), libattr1 (= 1:2.5.1-3), libaudit-common (= 1:3.0.7-1ubuntu3), libaudit1 (= 1:3.0.7-1ubuntu3), libbinutils (= 2.39.50.20221224-1ubuntu1), libblkid1 (= 2.38.1-4ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.66-3), libcc1-0 (= 12.2.0-10ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39.50.20221224-1ubuntu1), libctf0 (= 2.39.50.20221224-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdpkg-perl (= 1.21.13ubuntu1), libdw1 (= 0.188-2), libelf1 (= 0.188-2), libfile-stripnondeterminism-perl (= 1.13.0-2), libgcc-12-dev (= 12.2.0-10ubuntu1), libgcc-s1 (= 12.2.0-10ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgomp1 (= 12.2.0-10ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39.50.20221224-1ubuntu1), libgssapi-krb5-2 (= 1.20.1-1build1), libicu71 (= 71.1-3ubuntu1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-10ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), liblsan0 (= 12.2.0-10ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.0-0.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.40-1ubuntu1), libperl5.36 (= 5.36.0-6), libpipeline1 (= 1.5.7-1), libquadmath0 (= 12.2.0-10ubuntu1), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build1), libsmartcols1 (= 2.38.1-4ubuntu1), libssl3 (= 3.0.5-2ubuntu2), libstdc++-12-dev (= 12.2.0-10ubuntu1), libstdc++6 (= 12.2.0-10ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.1-1ubuntu1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-10ubuntu1), libubsan1 (= 12.2.0-10ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.1-1ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 36), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.36.0-6), perl-base (= 5.36.0-6), perl-modules-5.36 (= 5.36.0-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.05-7ubuntu1), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), xz-utils (= 5.4.0-0.1), zlib1g (= 1:1.2.13.dfsg-1ubuntu3) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1671884051" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ paml-doc_4.9j+dfsg-4_all.deb ---------------------------- new Debian package, version 2.0. size 1003288 bytes: control archive=3631 bytes. 868 bytes, 20 lines control 9227 bytes, 107 lines md5sums Package: paml-doc Source: paml Version: 4.9j+dfsg-4 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6466 Section: doc Priority: optional Multi-Arch: foreign Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html Description: Documentation for 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. . The source code comes with a series of PDF files to help with further insights for the working of, and with, PAML. drwxr-xr-x root/root 0 2022-12-24 12:14 ./ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/doc/paml-doc/ -rw-r--r-- root/root 543 2022-12-24 12:14 ./usr/share/doc/paml-doc/README.Debian -rw-r--r-- root/root 747 2022-12-24 12:14 ./usr/share/doc/paml-doc/changelog.Debian.gz -rw-r--r-- root/root 827 2022-12-24 12:14 ./usr/share/doc/paml-doc/copyright drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/doc/paml/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/doc/paml/examples/ -rw-r--r-- root/root 161 2019-10-18 14:02 ./usr/share/doc/paml/examples/9s.trees drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/CladeModelCD/ -rw-r--r-- root/root 7789 2019-10-18 14:02 ./usr/share/doc/paml/examples/CladeModelCD/ECP_EDN_15.nuc -rw-r--r-- root/root 1486 2019-10-18 14:02 ./usr/share/doc/paml/examples/CladeModelCD/codeml.CladeC.ctl -rw-r--r-- root/root 1485 2019-10-18 14:02 ./usr/share/doc/paml/examples/CladeModelCD/codeml.CladeD.ctl -rw-r--r-- root/root 256 2019-10-18 14:02 ./usr/share/doc/paml/examples/CladeModelCD/tree.txt drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/DatingSoftBound/ -rw-r--r-- root/root 20563 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/BF.Clock23.xlsx -rw-r--r-- root/root 796 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/FixedDsClock23.txt -rw-r--r-- root/root 863 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/README.BayesFactor.txt -rw-r--r-- root/root 1917 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/README.txt drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/DatingSoftBound/bf1/ -rw-r--r-- root/root 1313 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/bf1/mcmctree.ctl drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/DatingSoftBound/bf2/ -rw-r--r-- root/root 1310 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/bf2/mcmctree.ctl -rw-r--r-- root/root 1280 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/mcmctree.Infinitesites.ctl -rw-r--r-- root/root 1380 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/mcmctree.ctl -rw-r--r-- root/root 338 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/mtCDNApri.trees -rw-r--r-- root/root 70466 2019-10-18 14:02 ./usr/share/doc/paml/examples/DatingSoftBound/mtCDNApri123.txt drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/HIVNSsites/ -rw-r--r-- root/root 546 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden.trees -rw-r--r-- root/root 3881 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden.txt -rw-r--r-- root/root 46 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden4s.trees -rw-r--r-- root/root 1149 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/HIVenvSweden4s.txt -rw-r--r-- root/root 1006 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/README.txt -rw-r--r-- root/root 1751 2019-10-18 14:02 ./usr/share/doc/paml/examples/HIVNSsites/codeml.ctl drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/MHC.Swanson2002MBE/ -rw-r--r-- root/root 1935 2019-10-18 14:02 ./usr/share/doc/paml/examples/MHC.Swanson2002MBE/README.txt -rw-r--r-- root/root 165390 2019-10-18 14:02 ./usr/share/doc/paml/examples/MHC.Swanson2002MBE/bigmhc.phy -rw-r--r-- root/root 6249 2019-10-18 14:02 ./usr/share/doc/paml/examples/MHC.Swanson2002MBE/bigmhc.trees -rw-r--r-- root/root 713 2019-10-18 14:02 ./usr/share/doc/paml/examples/MHC.Swanson2002MBE/codeml.ctl drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/MouseLemurs/ -rw-r--r-- root/root 23884 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.aa -rw-r--r-- root/root 85468 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.nuc -rw-r--r-- root/root 2006 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/MouseLemurs.trees -rw-r--r-- root/root 65998 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/MouseLemurs123.nuc -rw-r--r-- root/root 4344 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/README.txt -rw-r--r-- root/root 12301 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/README2.txt -rw-r--r-- root/root 1611 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/aaml.ctl -rw-r--r-- root/root 1260 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/aaml2.ctl -rw-r--r-- root/root 1243 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/baseml.ctl -rw-r--r-- root/root 1340 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/baseml2.ctl -rw-r--r-- root/root 1569 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/codeml.ctl -rw-r--r-- root/root 1542 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/codonml.ctl -rw-r--r-- root/root 1214 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/codonml2.ctl -rw-r--r-- root/root 3827 2019-10-18 14:02 ./usr/share/doc/paml/examples/MouseLemurs/mtmam.dat -rw-r--r-- root/root 1829 2019-10-18 14:02 ./usr/share/doc/paml/examples/README.txt drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/TipDate.FluH1/ -rw-r--r-- root/root 67522 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.Beast.Nulldata.xml -rw-r--r-- root/root 561423 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.Beast.xml -rw-r--r-- root/root 31742 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.NodeNumbers.tre -rw-r--r-- root/root 503817 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.nexus -rw-r--r-- root/root 8660 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.tre -rw-r--r-- root/root 502851 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/H1.txt -rw-r--r-- root/root 1922 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/baseml.ctl -rw-r--r-- root/root 555 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/commands.txt -rw-r--r-- root/root 3664025 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/in.BV.HKYG5 -rw-r--r-- root/root 2023 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock1.ctl -rw-r--r-- root/root 1921 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock2.ctl -rw-r--r-- root/root 1921 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.FluH1/mcmctreeClock3.ctl drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/TipDate.HIV2/ -rw-r--r-- root/root 2167 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/FigTree.tre -rw-r--r-- root/root 2329 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/HIV2ge.tre -rw-r--r-- root/root 37103 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/HIV2ge.txt -rw-r--r-- root/root 4026 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/README.txt -rw-r--r-- root/root 2071 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/baseml.ctl -rw-r--r-- root/root 42152 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/in.BV.HKYG5 -rw-r--r-- root/root 1602 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/mcmctree.ExactlnL.ctl -rw-r--r-- root/root 1542 2019-10-18 14:02 ./usr/share/doc/paml/examples/TipDate.HIV2/mcmctree.ctl -rw-r--r-- root/root 3249 2019-10-18 14:02 ./usr/share/doc/paml/examples/YN00abglobin.result -rw-r--r-- root/root 1711 2019-10-18 14:02 ./usr/share/doc/paml/examples/abglobin.aa -rw-r--r-- root/root 6186 2019-10-18 14:02 ./usr/share/doc/paml/examples/abglobin.nuc -rw-r--r-- root/root 339 2019-10-18 14:02 ./usr/share/doc/paml/examples/abglobin.trees -rw-r--r-- root/root 5706 2019-10-18 14:02 ./usr/share/doc/paml/examples/dNdSGene1.nuc -rw-r--r-- root/root 40688 2019-10-18 14:02 ./usr/share/doc/paml/examples/horai.nuc -rw-r--r-- root/root 65 2019-10-18 14:02 ./usr/share/doc/paml/examples/horai.trees drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/lysin/ -rw-r--r-- root/root 6186 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/README.txt -rw-r--r-- root/root 4274 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/RasMol.txt -rw-r--r-- root/root 1527 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/SiteNumbering.txt -rw-r--r-- root/root 1740 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/codeml.ctl -rw-r--r-- root/root 1553 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/codemlYangSwanson2002.ctl -rw-r--r-- root/root 14880 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/lysin.nuc -rw-r--r-- root/root 527 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/lysin.trees -rw-r--r-- root/root 14530 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysin/lysinYangSwanson2002.nuc drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/lysozyme/ -rw-r--r-- root/root 4727 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/README.txt -rw-r--r-- root/root 1854 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/codeml.ctl -rw-r--r-- root/root 1768 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeLarge.ctl -rw-r--r-- root/root 11716 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeLarge.nuc -rw-r--r-- root/root 662 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeLarge.trees -rw-r--r-- root/root 1871 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeSmall.ctl -rw-r--r-- root/root 4124 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeSmall.nuc -rw-r--r-- root/root 769 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeSmall.trees -rw-r--r-- root/root 3060 2019-10-18 14:02 ./usr/share/doc/paml/examples/lysozyme/lysozymeSmall.txt drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/mtCDNA/ -rw-r--r-- root/root 5489 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/AAcodon.result.txt -rw-r--r-- root/root 3596 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/README.txt -rw-r--r-- root/root 3443 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/codeml.AAcodon.ctl -rw-r--r-- root/root 1446 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/codeml.ctl -rw-r--r-- root/root 1258 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/miyata.dat -rw-r--r-- root/root 208154 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/mtCDNAmam.nuc -rw-r--r-- root/root 96 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/mtCDNAmam.trees -rw-r--r-- root/root 23466 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/mtCDNApri.aa -rw-r--r-- root/root 73244 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/mtCDNApri.nuc -rw-r--r-- root/root 331 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNA/mtCDNApri.trees drwxr-xr-x root/root 0 2019-10-18 13:55 ./usr/share/doc/paml/examples/mtCDNAape/ -rw-r--r-- root/root 36 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/2s.trees -rw-r--r-- root/root 1742 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/OmegaAA.dat -rw-r--r-- root/root 2245 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/README.txt -rw-r--r-- root/root 1842 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/codeml.HC.ctl -rw-r--r-- root/root 2123 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/codeml.ctl -rw-r--r-- root/root 22901 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/mtCDNA.HC.txt -rw-r--r-- root/root 248 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/mtCDNAape.trees -rw-r--r-- root/root 67235 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtCDNAape/mtCDNAape.txt -rw-r--r-- root/root 11708 2019-10-18 14:02 ./usr/share/doc/paml/examples/mtprim9.nuc -rw-r--r-- root/root 29697 2019-10-18 14:02 ./usr/share/doc/paml/pamlHistory.txt.gz paml_4.9j+dfsg-4_amd64.deb -------------------------- new Debian package, version 2.0. size 641056 bytes: control archive=2325 bytes. 770 bytes, 16 lines control 4016 bytes, 62 lines md5sums Package: paml Version: 4.9j+dfsg-4 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1626 Depends: libc6 (>= 2.34) 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 2022-12-24 12:14 ./ drwxr-xr-x root/root 0 2022-12-24 12:14 ./etc/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./etc/paml/ lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/aaml.ctl -> /usr/lib/paml/data/aaml.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/baseml.ctl -> /usr/lib/paml/data/baseml.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/codeml.ctl -> /usr/lib/paml/data/codeml.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/codonml.ctl -> /usr/lib/paml/data/codonml.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/mcmctree.ctl -> /usr/lib/paml/data/mcmctree.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/pamp.ctl -> /usr/lib/paml/data/pamp.ctl lrwxrwxrwx root/root 0 2022-12-24 12:14 ./etc/paml/yn00.ctl -> /usr/lib/paml/data/yn00.ctl drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/bin/ lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/baseml -> ../lib/debian-med/bin/baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/basemlg -> ../lib/debian-med/bin/basemlg lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/chi2 -> ../lib/debian-med/bin/chi2 lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/codeml -> ../lib/debian-med/bin/codeml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/mcmctree -> ../lib/debian-med/bin/mcmctree lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/paml-evolver -> ../lib/debian-med/bin/evolver lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/pamp -> ../lib/debian-med/bin/pamp lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/bin/yn00 -> ../lib/debian-med/bin/yn00 drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 190 2022-12-24 12:14 ./usr/lib/debian-med/bin/baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/basemlg -> baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/chi2 -> ../../paml/bin/chi2 lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/codeml -> baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/evolver -> ../../paml/bin/evolver lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/mcmctree -> baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/pamp -> baseml lrwxrwxrwx root/root 0 2022-12-24 12:14 ./usr/lib/debian-med/bin/yn00 -> baseml drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/lib/paml/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/lib/paml/bin/ -rwxr-xr-x root/root 318152 2022-12-24 12:14 ./usr/lib/paml/bin/baseml -rwxr-xr-x root/root 108984 2022-12-24 12:14 ./usr/lib/paml/bin/basemlg -rwxr-xr-x root/root 18736 2022-12-24 12:14 ./usr/lib/paml/bin/chi2 -rwxr-xr-x root/root 510640 2022-12-24 12:14 ./usr/lib/paml/bin/codeml -rwxr-xr-x root/root 100808 2022-12-24 12:14 ./usr/lib/paml/bin/evolver -rwxr-xr-x root/root 162432 2022-12-24 12:14 ./usr/lib/paml/bin/mcmctree -rwxr-xr-x root/root 96848 2022-12-24 12:14 ./usr/lib/paml/bin/pamp -rwxr-xr-x root/root 87736 2022-12-24 12:14 ./usr/lib/paml/bin/yn00 drwxr-xr-x root/root 0 2022-12-24 12:14 ./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 2022-12-24 12:14 ./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 2022-12-24 12:14 ./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 2022-12-24 12:14 ./usr/lib/paml/data/codeml.ctl -rw-r--r-- root/root 660 2022-12-24 12:14 ./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 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2022-12-24 12:14 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-24 12:14 ./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 2022-12-24 12:14 ./usr/share/doc/paml/README.Debian -rw-r--r-- root/root 278 2022-12-24 12:14 ./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 746 2022-12-24 12:14 ./usr/share/doc/paml/changelog.Debian.gz -rw-r--r-- root/root 827 2022-12-24 12:14 ./usr/share/doc/paml/copyright drwxr-xr-x root/root 0 2022-12-24 12:14 ./usr/share/doc/paml/profile.d/ -rw-r--r-- root/root 147 2022-12-24 12:14 ./usr/share/doc/paml/profile.d/paml -rw-r--r-- root/root 1665 2022-12-24 12:14 ./usr/share/doc/paml/run-unit-test +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 26804 Build-Time: 46 Distribution: lunar-proposed Host Architecture: amd64 Install-Time: 5 Job: paml_4.9j+dfsg-4.dsc Machine Architecture: amd64 Package: paml Package-Time: 51 Source-Version: 4.9j+dfsg-4 Space: 26804 Status: successful Version: 4.9j+dfsg-4 -------------------------------------------------------------------------------- Finished at 2022-12-24T23:17:34Z Build needed 00:00:51, 26804k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=amd64 PACKAGEBUILD-25421396 Scanning for processes to kill in build PACKAGEBUILD-25421396