https://launchpad.net/ubuntu/+source/paml/4.9j+dfsg-4/+build/25421397 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-080 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 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 23:17:06 ntpdate[1829]: adjust time server 10.211.37.1 offset 0.012130 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25421397 --image-type chroot /home/buildd/filecache-default/0ff053c85babb2453d3b9b9b50ec5a50c26e70b3 Creating target for build PACKAGEBUILD-25421397 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25421397 Starting target for build PACKAGEBUILD-25421397 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25421397 '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-25421397 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25421397 Updating target for build PACKAGEBUILD-25421397 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 arm64 Packages [1372 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe arm64 Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5867 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 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 arm64 Packages [1771 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [629 kB] Fetched 25.6 MB in 14s (1873 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: 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-aarch64-linux-gnu binutils-common 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 libhwasan0 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 liblzma5 libpcre3 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 83.4 MB of archives. After this operation, 53.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 coreutils arm64 9.1-1ubuntu1 [1347 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblzma5 arm64 5.4.0-0.1 [121 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 dpkg arm64 1.21.13ubuntu1 [1343 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main arm64 dash arm64 0.5.11+git20210903+057cd650a4ed-9ubuntu1 [88.2 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 diffutils arm64 1:3.8-3 [172 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl-modules-5.36 all 5.36.0-6 [2985 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libperl5.36 arm64 5.36.0-6 [4677 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl arm64 5.36.0-6 [235 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 perl-base arm64 5.36.0-6 [1726 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 zlib1g arm64 1:1.2.13.dfsg-1ubuntu3 [59.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 sysvinit-utils arm64 3.05-7ubuntu1 [25.8 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 systemd-sysv arm64 252.1-1ubuntu1 [11.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libaudit-common all 1:3.0.7-1ubuntu3 [4864 B] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libaudit1 arm64 1:3.0.7-1ubuntu3 [45.2 kB] Get:15 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 debconf all 1.5.80 [125 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main arm64 libssl3 arm64 3.0.5-2ubuntu2 [1752 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libkmod2 arm64 30+20220905-1ubuntu1 [47.7 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main arm64 libapparmor1 arm64 3.0.8-1ubuntu1 [36.9 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libcap2 arm64 1:2.66-3 [27.7 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main arm64 liblz4-1 arm64 1.9.4-1 [63.4 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 systemd arm64 252.1-1ubuntu1 [2898 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsystemd-shared arm64 252.1-1ubuntu1 [1673 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsystemd0 arm64 252.1-1ubuntu1 [321 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libcc1-0 arm64 12.2.0-10ubuntu1 [44.1 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libctf-nobfd0 arm64 2.39.50.20221224-1ubuntu1 [96.6 kB] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgprofng0 arm64 2.39.50.20221224-1ubuntu1 [792 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libctf0 arm64 2.39.50.20221224-1ubuntu1 [93.0 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main arm64 libjansson4 arm64 2.14-2 [34.3 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils-aarch64-linux-gnu arm64 2.39.50.20221224-1ubuntu1 [3121 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libbinutils arm64 2.39.50.20221224-1ubuntu1 [764 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils-common arm64 2.39.50.20221224-1ubuntu1 [235 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 binutils arm64 2.39.50.20221224-1ubuntu1 [3214 B] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgomp1 arm64 12.2.0-10ubuntu1 [122 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libitm1 arm64 12.2.0-10ubuntu1 [27.9 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libatomic1 arm64 12.2.0-10ubuntu1 [10.7 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libasan8 arm64 12.2.0-10ubuntu1 [2384 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 liblsan0 arm64 12.2.0-10ubuntu1 [1028 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libtsan2 arm64 12.2.0-10ubuntu1 [2514 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libubsan1 arm64 12.2.0-10ubuntu1 [957 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libhwasan0 arm64 12.2.0-10ubuntu1 [1109 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gcc-12-base arm64 12.2.0-10ubuntu1 [19.6 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libstdc++6 arm64 12.2.0-10ubuntu1 [647 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 g++-12 arm64 12.2.0-10ubuntu1 [10.9 MB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libstdc++-12-dev arm64 12.2.0-10ubuntu1 [2155 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgcc-12-dev arm64 12.2.0-10ubuntu1 [1157 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gcc-12 arm64 12.2.0-10ubuntu1 [19.1 MB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 cpp-12 arm64 12.2.0-10ubuntu1 [9581 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgcc-s1 arm64 12.2.0-10ubuntu1 [39.5 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libudev1 arm64 252.1-1ubuntu1 [86.7 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 adduser all 3.129ubuntu1 [59.0 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gpgv arm64 2.2.40-1ubuntu2 [133 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libpcre3 arm64 2:8.39-15 [233 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main arm64 openssl arm64 3.0.5-2ubuntu2 [1158 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main arm64 ca-certificates all 20211016ubuntu1 [141 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libkeyutils1 arm64 1.6.3-2 [9296 B] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libkrb5support0 arm64 1.20.1-1build1 [31.4 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libk5crypto3 arm64 1.20.1-1build1 [85.0 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libgssapi-krb5-2 arm64 1.20.1-1build1 [139 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libkrb5-3 arm64 1.20.1-1build1 [345 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libsqlite3-0 arm64 3.40.0-2 [660 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 xz-utils arm64 5.4.0-0.1 [177 kB] Get:62 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 dpkg-dev all 1.21.13ubuntu1 [1070 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libdpkg-perl all 1.21.13ubuntu1 [242 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gpg arm64 2.2.40-1ubuntu2 [509 kB] Get:65 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gpgconf arm64 2.2.40-1ubuntu2 [92.5 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 gpg-agent arm64 2.2.40-1ubuntu2 [211 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 linux-libc-dev arm64 5.19.0-23.24 [1320 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.4 MB in 49s (1703 kB/s) (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu1_arm64.deb ... Unpacking coreutils (9.1-1ubuntu1) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu1) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.0-0.1_arm64.deb ... Unpacking liblzma5:arm64 (5.4.0-0.1) over (5.2.9-0.0) ... Setting up liblzma5:arm64 (5.4.0-0.1) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.13ubuntu1_arm64.deb ... Unpacking dpkg (1.21.13ubuntu1) over (1.21.11ubuntu2) ... Setting up dpkg (1.21.13ubuntu1) ... (Reading database ... 13661 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-9ubuntu1_arm64.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 libpcre3:arm64 (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 libatomic1:arm64 (12.2.0-10ubuntu1) ... Setting up libk5crypto3:arm64 (1.20.1-1build1) ... Setting up libubsan1:arm64 (12.2.0-10ubuntu1) ... Setting up libhwasan0:arm64 (12.2.0-10ubuntu1) ... Setting up libasan8:arm64 (12.2.0-10ubuntu1) ... Setting up gpgconf (2.2.40-1ubuntu2) ... Setting up libkrb5-3:arm64 (1.20.1-1build1) ... Setting up libtsan2:arm64 (12.2.0-10ubuntu1) ... Setting up libbinutils:arm64 (2.39.50.20221224-1ubuntu1) ... Setting up openssl (3.0.5-2ubuntu2) ... Setting up libcc1-0:arm64 (12.2.0-10ubuntu1) ... Setting up libperl5.36:arm64 (5.36.0-6) ... Setting up gpg (2.2.40-1ubuntu2) ... Setting up liblsan0:arm64 (12.2.0-10ubuntu1) ... Setting up libitm1:arm64 (12.2.0-10ubuntu1) ... Setting up libkmod2:arm64 (30+20220905-1ubuntu1) ... Setting up libctf0:arm64 (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:arm64 (2.39.50.20221224-1ubuntu1) ... Setting up libgcc-12-dev:arm64 (12.2.0-10ubuntu1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-1build1) ... Setting up libsystemd-shared:arm64 (252.1-1ubuntu1) ... Setting up libdpkg-perl (1.21.13ubuntu1) ... Setting up libstdc++-12-dev:arm64 (12.2.0-10ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.39.50.20221224-1ubuntu1) ... 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 ... 15615 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-25421397 arm64 lunar-proposed -c chroot:build-PACKAGEBUILD-25421397 --arch=arm64 --dist=lunar-proposed --nolog paml_4.9j+dfsg-4.dsc Initiating build PACKAGEBUILD-25421397 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-080.buildd +==============================================================================+ | paml 4.9j+dfsg-4 (arm64) Sat, 24 Dec 2022 23:18:29 +0000 | +==============================================================================+ Package: paml Version: 4.9j+dfsg-4 Source Version: 4.9j+dfsg-4 Distribution: lunar-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25421397/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/paml-LZ6Ej0/resolver-LYzWbe' 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-LZ6Ej0/paml-4.9j+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/paml-LZ6Ej0' 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 [452 B] Fetched 1779 B in 0s (103 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 18.4 MB of archives. After this operation, 68.2 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [666 B] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libelf1 arm64 0.188-2 [53.0 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main arm64 libicu71 arm64 71.1-3ubuntu1 [10.5 MB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libxml2 arm64 2.9.14+dfsg-1.1 [722 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main arm64 bsdextrautils arm64 2.38.1-4ubuntu1 [69.1 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic-mgc arm64 1:5.41-4 [257 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main arm64 libmagic1 arm64 1:5.41-4 [85.0 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main arm64 file arm64 1:5.41-4 [21.6 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext-base arm64 0.21-10 [36.5 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main arm64 libuchardet0 arm64 0.0.7-1build2 [77.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main arm64 groff-base arm64 1.22.4-9 [899 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main arm64 libpipeline1 arm64 1.5.7-1 [23.3 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main arm64 man-db arm64 2.11.1-1 [1213 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main arm64 m4 arm64 1.4.19-1 [240 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main arm64 autoconf all 2.71-2 [338 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main arm64 autopoint all 0.21-10 [421 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main arm64 libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main arm64 libtool all 2.4.7-5 [166 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-autoreconf all 20 [16.1 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main arm64 libsub-override-perl all 0.09-4 [8706 B] Get:24 http://ftpmaster.internal/ubuntu lunar/main arm64 libfile-stripnondeterminism-perl all 1.13.0-2 [18.2 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main arm64 dh-strip-nondeterminism all 1.13.0-2 [5308 B] Get:26 http://ftpmaster.internal/ubuntu lunar-proposed/main arm64 libdw1 arm64 0.188-2 [247 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main arm64 dwz arm64 0.14+20220924-2 [110 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main arm64 gettext arm64 0.21-10 [842 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main arm64 debhelper all 13.10.1ubuntu1 [924 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.4 MB in 6s (2975 kB/s) Selecting previously unselected package libelf1:arm64. (Reading database ... 15615 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.188-2_arm64.deb ... Unpacking libelf1:arm64 (0.188-2) ... Selecting previously unselected package libicu71:arm64. Preparing to unpack .../01-libicu71_71.1-3ubuntu1_arm64.deb ... Unpacking libicu71:arm64 (71.1-3ubuntu1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.1_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../03-bsdextrautils_2.38.1-4ubuntu1_arm64.deb ... Unpacking bsdextrautils (2.38.1-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.41-4_arm64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../05-libmagic1_1%3a5.41-4_arm64.deb ... Unpacking libmagic1:arm64 (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_arm64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu71:arm64 (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:arm64 (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:arm64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2) ... Setting up libxml2:arm64 (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:arm64 (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 (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 arm64 (aarch64) 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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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-25421397 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25421397 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25421397 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 arm64 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-arch dh binary-arch --sourcedirectory=src dh_update_autotools_config -a -O--sourcedirectory=src dh_autoreconf -a -O--sourcedirectory=src dh_auto_configure -a -O--sourcedirectory=src dh_auto_build -a -O--sourcedirectory=src cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/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 baseml.c:131: treesub.c: In function ‘IdenticalSeqs’: 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:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from baseml.c:11: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ In file included from codeml.c:238: treesub.c: In function ‘IdenticalSeqs’: treesub.c:1310:33: warning: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types] 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1); | ~~~^~~~~~~ | | | char ** In file included from codeml.c:17: paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format); | ~~~~~~~~~~~~~~~^~~~~~~~~ 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 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 ‘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, | ~~~~~^~~~~~~~ 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 ‘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 ‘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 ‘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); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadSeq’: 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:627:13: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 627 | fgets(line, lline, fseq); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:660:39: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 660 | if (com.ngene > 9) fscanf(fseq, "%d", &ch); | ^~~~~~~~~~~~~~~~~~~~~~~ treesub.c:949:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fscanf(fseq, "%lf", &com.fpatt[h]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmctree.c: 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 ‘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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ‘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 ‘StarDecomposition’: treesub.c:4867:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘rell’: treesub.c:5728:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5728 | fscanf(flnf, "%d%d%d", &ntree0, &ls0, &npatt0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: 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:5752:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5752 | fscanf(flnf, "%d", &j); | ^~~~~~~~~~~~~~~~~~~~~~ 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: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: 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:5763:10: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5763 | fgets(line, lline, flnf); | ^~~~~~~~~~~~~~~~~~~~~~~~ treesub.c:3151:7: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3151 | fgets(line, lline, ftree); | ^~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘readx’: treesub.c:3956:4: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3956 | fscanf(finitials, "%lf", &xin[i = 0]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘Perturbation’: treesub.c:4565:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4565 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘StarDecomposition’: treesub.c:4867:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4867 | fscanf(ftree, "%d%d", &i, &ntree); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ treesub.c: In function ‘ReadTreeSeqs’: treesub.c: In function ‘rell’: 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: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 ‘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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/aarch64-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/aarch64-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 -a -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=src dh_prep -a -O--sourcedirectory=src dh_auto_install -a -O--sourcedirectory=src debian/rules override_dh_install-arch make[1]: Entering directory '/<>' 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_installdocs -a -O--sourcedirectory=src dh_installchangelogs -a -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 -a -O--sourcedirectory=src dh_perl -a -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_strip_nondeterminism -a -O--sourcedirectory=src dh_compress -a -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_missing -a -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src debugedit: debian/paml/usr/lib/paml/bin/chi2: Unknown DWARF DW_FORM_0x1f20 008f821cabf57da916d14fce3c9457a29aafef8e debugedit: debian/paml/usr/lib/paml/bin/baseml: Unknown DWARF DW_FORM_0x1f20 33d5cd131abcbd75de325f39b0e51f63ddb05e8d debugedit: debian/paml/usr/lib/paml/bin/yn00: Unknown DWARF DW_FORM_0x1f20 5f8106dfdbc933c03695f7adc39fb8a3b8632a55 debugedit: debian/paml/usr/lib/paml/bin/mcmctree: Unknown DWARF DW_FORM_0x1f20 51ff4a4d0b089efaffa4fbe8b513105e985bb09f debugedit: debian/paml/usr/lib/paml/bin/codeml: Unknown DWARF DW_FORM_0x1f20 4eae913861912109ec7a46a54c65ef112c453482 debugedit: debian/paml/usr/lib/paml/bin/basemlg: Unknown DWARF DW_FORM_0x1f21 4ba2437b38237ddf8960d92173fa8572dc12b5a3 debugedit: debian/paml/usr/lib/paml/bin/evolver: Unknown DWARF DW_FORM_0x1f20 cce93a9d291c62f5b68d6a99edbc0cd7261e5210 debugedit: debian/paml/usr/lib/paml/bin/pamp: Unknown DWARF DW_FORM_0x1f21 91bd6b539a7d5c4f221df503f404ca2516456177 dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -a -O--sourcedirectory=src dh_gencontrol -a -O--sourcedirectory=src dh_md5sums -a -O--sourcedirectory=src dh_builddeb -a -O--sourcedirectory=src INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing paml (in debian/paml); 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 " 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_arm64.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_arm64.deb'. Renaming paml-dbgsym_4.9j+dfsg-4_arm64.deb to paml-dbgsym_4.9j+dfsg-4_arm64.ddeb dpkg-genbuildinfo --build=any -O../paml_4.9j+dfsg-4_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../paml_4.9j+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-24T23:19:41Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ paml_4.9j+dfsg-4_arm64.changes: ------------------------------- Format: 1.8 Date: Sat, 24 Dec 2022 13:14:11 +0100 Source: paml Binary: paml Built-For-Profiles: noudeb Architecture: arm64 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) 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. (Closes: #1026913) * Standards-Version: 4.6.2 (routine-update) * paml-doc: Add Multi-Arch: foreign. * debhelper-compat 13 (routine-update) * watch file standard 4 (routine-update) Checksums-Sha1: 82666e4d66df77629ab8bd882a3981f16ea76731 1241146 paml-dbgsym_4.9j+dfsg-4_arm64.ddeb 5c3a734044ac4d93530bfcfb7cce814e25027cc5 5743 paml_4.9j+dfsg-4_arm64.buildinfo 4f866b9c040f065cd7e8e2d0108ad5aaba9f17d0 615914 paml_4.9j+dfsg-4_arm64.deb Checksums-Sha256: 71242f12307d750ce54ac736449e7003f2d7365eb289671d3b1945e713942fd9 1241146 paml-dbgsym_4.9j+dfsg-4_arm64.ddeb 0e4148351d0a298cc03cc6e62c9070207b74e01d963443f334262673d15d2fae 5743 paml_4.9j+dfsg-4_arm64.buildinfo d70e9bfa231f85c6a7956fe35dca9690dc8803a6fd4ee1235167372005e34459 615914 paml_4.9j+dfsg-4_arm64.deb Files: fa876dec4d4d20c121fd36d4e01a352f 1241146 debug optional paml-dbgsym_4.9j+dfsg-4_arm64.ddeb aa13edea1581feef091479647410adb1 5743 science optional paml_4.9j+dfsg-4_arm64.buildinfo aad953fe3cbee3f94c62265449f955e0 615914 science optional paml_4.9j+dfsg-4_arm64.deb /<>/paml_4.9j+dfsg-4_arm64.changes.new could not be renamed to /<>/paml_4.9j+dfsg-4_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: paml Binary: paml paml-dbgsym Architecture: arm64 Version: 4.9j+dfsg-4 Checksums-Md5: fa876dec4d4d20c121fd36d4e01a352f 1241146 paml-dbgsym_4.9j+dfsg-4_arm64.ddeb aad953fe3cbee3f94c62265449f955e0 615914 paml_4.9j+dfsg-4_arm64.deb Checksums-Sha1: 82666e4d66df77629ab8bd882a3981f16ea76731 1241146 paml-dbgsym_4.9j+dfsg-4_arm64.ddeb 4f866b9c040f065cd7e8e2d0108ad5aaba9f17d0 615914 paml_4.9j+dfsg-4_arm64.deb Checksums-Sha256: 71242f12307d750ce54ac736449e7003f2d7365eb289671d3b1945e713942fd9 1241146 paml-dbgsym_4.9j+dfsg-4_arm64.ddeb d70e9bfa231f85c6a7956fe35dca9690dc8803a6fd4ee1235167372005e34459 615914 paml_4.9j+dfsg-4_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Sat, 24 Dec 2022 23:19:41 +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-aarch64-linux-gnu (= 2.39.50.20221224-1ubuntu1), binutils-common (= 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), libhwasan0 (= 12.2.0-10ubuntu1), 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), 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_4.9j+dfsg-4_arm64.deb -------------------------- new Debian package, version 2.0. size 615914 bytes: control archive=2318 bytes. 770 bytes, 16 lines control 4016 bytes, 62 lines md5sums Package: paml Version: 4.9j+dfsg-4 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1754 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 330504 2022-12-24 12:14 ./usr/lib/paml/bin/baseml -rwxr-xr-x root/root 133576 2022-12-24 12:14 ./usr/lib/paml/bin/basemlg -rwxr-xr-x root/root 67664 2022-12-24 12:14 ./usr/lib/paml/bin/chi2 -rwxr-xr-x root/root 465544 2022-12-24 12:14 ./usr/lib/paml/bin/codeml -rwxr-xr-x root/root 133376 2022-12-24 12:14 ./usr/lib/paml/bin/evolver -rwxr-xr-x root/root 199328 2022-12-24 12:14 ./usr/lib/paml/bin/mcmctree -rwxr-xr-x root/root 133520 2022-12-24 12:14 ./usr/lib/paml/bin/pamp -rwxr-xr-x root/root 71088 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 2019-10-18 14:02 ./usr/lib/paml/data/dat/dayhoff-dcmut.dat -rw-r--r-- root/root 5284 2019-10-18 14:02 ./usr/lib/paml/data/dat/dayhoff.dat -rw-r--r-- root/root 1536 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974a.dat -rw-r--r-- root/root 1372 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974c.dat -rw-r--r-- root/root 1130 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974p.dat -rw-r--r-- root/root 1359 2019-10-18 14:02 ./usr/lib/paml/data/dat/g1974v.dat -rw-r--r-- root/root 1681 2019-10-18 14:02 ./usr/lib/paml/data/dat/grantham.dat -rw-r--r-- root/root 2960 2019-10-18 14:02 ./usr/lib/paml/data/dat/jones-dcmut.dat -rw-r--r-- root/root 12131 2019-10-18 14:02 ./usr/lib/paml/data/dat/jones.dat -rw-r--r-- root/root 2713 2019-10-18 14:02 ./usr/lib/paml/data/dat/lg.dat -rw-r--r-- root/root 1258 2019-10-18 14:02 ./usr/lib/paml/data/dat/miyata.dat -rw-r--r-- root/root 4886 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtArt.dat -rw-r--r-- root/root 2370 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtREV24.dat -rw-r--r-- root/root 3844 2019-10-18 14:02 ./usr/lib/paml/data/dat/mtmam.dat -rw-r--r-- root/root 3337 2019-10-18 14:02 ./usr/lib/paml/data/dat/wag.dat -rw-r--r-- root/root 4124 2019-10-18 14:02 ./usr/lib/paml/data/lysozymeSmall.nuc -rw-r--r-- root/root 769 2019-10-18 14:02 ./usr/lib/paml/data/lysozymeSmall.trees -rw-r--r-- root/root 1299 2022-12-24 12:14 ./usr/lib/paml/data/mcmctree.ctl -rw-r--r-- root/root 338 2019-10-18 14:02 ./usr/lib/paml/data/mtCDNApri.trees -rw-r--r-- root/root 70466 2019-10-18 14:02 ./usr/lib/paml/data/mtCDNApri123.txt -rw-r--r-- root/root 11708 2019-10-18 14:02 ./usr/lib/paml/data/mtprim9.nuc -rw-r--r-- root/root 374 2022-12-24 12:14 ./usr/lib/paml/data/pamp.ctl -rw-r--r-- root/root 1008 2019-10-18 14:02 ./usr/lib/paml/data/stewart.aa -rw-r--r-- root/root 143 2019-10-18 14:02 ./usr/lib/paml/data/stewart.trees -rw-r--r-- root/root 719 2022-12-24 12:14 ./usr/lib/paml/data/yn00.ctl 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/ -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: arm64 Build Type: any Build-Space: 18580 Build-Time: 60 Distribution: lunar-proposed Host Architecture: arm64 Install-Time: 11 Job: paml_4.9j+dfsg-4.dsc Machine Architecture: arm64 Package: paml Package-Time: 72 Source-Version: 4.9j+dfsg-4 Space: 18580 Status: successful Version: 4.9j+dfsg-4 -------------------------------------------------------------------------------- Finished at 2022-12-24T23:19:41Z Build needed 00:01:12, 18580k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=arm64 PACKAGEBUILD-25421397 Scanning for processes to kill in build PACKAGEBUILD-25421397