https://launchpad.net/ubuntu/+source/phast/1.6+dfsg-5/+build/28286490 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-ppc64el-012 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:55:42 UTC 2024 ppc64le Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 May 05:26:06 ntpdate[1931]: adjust time server 10.211.37.1 offset -0.001223 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=ppc64el PACKAGEBUILD-28286490 --image-type chroot /home/buildd/filecache-default/d42c54d6e204d222772cc047f01d282d9c30a0e5 Creating target for build PACKAGEBUILD-28286490 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=ppc64el PACKAGEBUILD-28286490 Starting target for build PACKAGEBUILD-28286490 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=ppc64el PACKAGEBUILD-28286490 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28286490 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=ppc64el PACKAGEBUILD-28286490 Updating target for build PACKAGEBUILD-28286490 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [64.6 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [64.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [64.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el Packages [1335 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el Packages [14.7 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [5980 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [196 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [73.0 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [971 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [547 kB] Fetched 24.6 MB in 6s (4142 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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu gcc-14-base gcc-powerpc64le-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-powerpc64le-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 175 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 84.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.3 [8106 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.1build1 [225 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnsl-dev ppc64el 1.3.0-3build3 [80.3 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnsl2 ppc64el 1.3.0-3build3 [48.9 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1build1 [102 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-6ubuntu2 [185 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libkrb5-3 ppc64el 1.20.1-6ubuntu2 [432 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libk5crypto3 ppc64el 1.20.1-6ubuntu2 [108 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libkrb5support0 ppc64el 1.20.1-6ubuntu2 [38.6 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el libacl1 ppc64el 2.3.2-1build1 [21.4 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el libapparmor1 ppc64el 4.0.0-beta3-0ubuntu3 [55.1 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libcap-ng0 ppc64el 0.8.5-1 [16.0 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el libaudit1 ppc64el 1:3.1.2-2.1build1 [52.9 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu6 [155 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcap2 ppc64el 1:2.66-5ubuntu2 [35.6 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4build1 [145 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcrypt1 ppc64el 1:4.4.36-4build1 [110 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgpg-error0 ppc64el 1.47-3build2 [88.4 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgcrypt20 ppc64el 1.10.3-2build1 [748 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblzma5 ppc64el 5.6.1+really5.4.5-1 [160 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main ppc64el libzstd1 ppc64el 1.5.5+dfsg2-2build1 [397 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu7 [64.5 kB] Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el liblz4-1 ppc64el 1.9.4-2 [105 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpcre2-8-0 ppc64el 10.42-4ubuntu2 [265 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el libselinux1 ppc64el 3.5-2ubuntu2 [101 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu6 [169 kB] Get:29 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el perl-modules-5.38 all 5.38.2-4 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-7 [868 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgdbm6t64 ppc64el 1.23-5.1build1 [42.0 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1build1 [6982 B] Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-4 [4938 kB] Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el perl ppc64el 5.38.2-4 [231 kB] Get:35 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el perl-base ppc64el 5.38.2-4 [1906 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu5 [16.1 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtext-iconv-perl ppc64el 1.7-8build3 [13.7 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build3 [9536 B] Get:39 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libnss-nisplus ppc64el 1.3-5build1 [27.5 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libnss-nis ppc64el 3.1-0ubuntu7 [30.8 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu8.1 [21.3 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu7 [82.4 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu8.1 [2104 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu8.1 [3275 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu8.1 [751 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main ppc64el openssl ppc64el 3.0.13-0ubuntu3 [1025 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu8 [2351 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu4 [376 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu3 [2125 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main ppc64el systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main ppc64el systemd ppc64el 255.4-1ubuntu8 [3771 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu8 [526 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libapt-pkg6.0t64 ppc64el 2.9.2 [1063 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2build1 [226 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2build1 [208 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main ppc64el libp11-kit0 ppc64el 0.25.3-4ubuntu2 [312 kB] Get:58 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libunistring5 ppc64el 1.2-1 [562 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu3.1 [1057 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el apt ppc64el 2.9.2 [1430 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el apt-utils ppc64el 2.9.2 [231 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-7ubuntu1 [57.8 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpam-modules ppc64el 1.5.3-7ubuntu1 [325 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main ppc64el bzip2 ppc64el 1.0.8-5.1 [37.6 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbz2-1.0 ppc64el 1.0.8-5.1 [48.7 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc-14-base ppc64el 14-20240412-0ubuntu1 [47.6 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgcc-s1 ppc64el 14-20240412-0ubuntu1 [39.3 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main ppc64el libstdc++6 ppc64el 14-20240412-0ubuntu1 [893 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main ppc64el libudev1 ppc64el 255.4-1ubuntu8 [201 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxxhash0 ppc64el 0.8.2-2build1 [31.3 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu2 [72.8 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgmp10 ppc64el 2:6.3.0+dfsg-2ubuntu6 [282 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main ppc64el libffi8 ppc64el 3.4.6-1build1 [27.9 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main ppc64el libidn2-0 ppc64el 2.3.7-2build1 [69.9 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtasn1-6 ppc64el 4.19.0-3build1 [55.1 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu3 [11.3 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main ppc64el base-passwd ppc64el 3.6.3build1 [53.0 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main ppc64el libassuan0 ppc64el 2.5.6-1build1 [43.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.3-1 [803 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main ppc64el gpg ppc64el 2.4.4-2ubuntu17 [706 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main ppc64el libreadline8t64 ppc64el 8.2-4build1 [182 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main ppc64el readline-common all 8.2-4build1 [56.5 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main ppc64el libncursesw6 ppc64el 6.4+20240113-1ubuntu2 [186 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtinfo6 ppc64el 6.4+20240113-1ubuntu2 [130 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu17 [275 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu17 [115 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu5 [38.8 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main ppc64el init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnpth0t64 ppc64el 1.6-3.1build1 [8914 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main ppc64el gpgv ppc64el 2.4.4-2ubuntu17 [198 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main ppc64el ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu3 [62.5 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main ppc64el debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main ppc64el debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpam0g ppc64el 1.5.3-7ubuntu1 [75.7 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main ppc64el libargon2-1 ppc64el 0~20190702+dfsg-4build1 [27.5 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu3 [182 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main ppc64el libjson-c5 ppc64el 0.17-1build1 [44.7 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu6 [39.6 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu6 [171 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main ppc64el mount ppc64el 2.39.3-9ubuntu6 [125 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu4 [22.9 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main ppc64el libkeyutils1 ppc64el 1.6.3-3build1 [11.0 kB] Get:104 http://ftpmaster.internal/ubuntu oracular/main ppc64el linux-libc-dev ppc64el 6.8.0-31.31 [1588 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main ppc64el base-files ppc64el 13.1ubuntu1 [74.1 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main ppc64el debianutils ppc64el 5.17build1 [90.5 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main ppc64el bash ppc64el 5.2.21-2ubuntu4 [977 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu6 [99.1 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main ppc64el coreutils ppc64el 9.4-3ubuntu6 [1524 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main ppc64el tar ppc64el 1.35+dfsg-3build1 [309 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu10 [1339 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main ppc64el dash ppc64el 0.5.12-6ubuntu5 [108 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main ppc64el diffutils ppc64el 1:3.10-1build1 [202 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main ppc64el findutils ppc64el 4.9.0-5build1 [330 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main ppc64el grep ppc64el 3.11-4build1 [174 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main ppc64el gzip ppc64el 1.12-1ubuntu3 [115 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main ppc64el hostname ppc64el 3.23+nmu2ubuntu2 [11.3 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main ppc64el login ppc64el 1:4.13+dfsg1-4ubuntu3 [205 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main ppc64el ncurses-bin ppc64el 6.4+20240113-1ubuntu2 [202 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main ppc64el sed ppc64el 4.9-2build1 [210 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main ppc64el util-linux ppc64el 2.39.3-9ubuntu6 [1195 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main ppc64el ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main ppc64el sysvinit-utils ppc64el 3.08-6ubuntu3 [35.8 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu4 [23.0 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu4 [270 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu4 [663 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main ppc64el optipng ppc64el 0.7.8+ds-1build2 [118 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpng16-16t64 ppc64el 1.6.43-5build1 [242 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main ppc64el init ppc64el 1.66ubuntu1 [6190 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu6 [79.3 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu6 [33.8 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main ppc64el libattr1 ppc64el 1:2.5.2-1build1 [12.6 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmd0 ppc64el 1.1.0-2build1 [30.5 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsepol2 ppc64el 3.5-2build1 [388 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsemanage2 ppc64el 3.5-1build5 [115 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main ppc64el passwd ppc64el 1:4.13+dfsg1-4ubuntu3 [878 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu3 [68.7 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu4 [18.0 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main ppc64el mawk ppc64el 1.3.4.20240123-1build1 [139 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main ppc64el procps ppc64el 2:4.0.4-4ubuntu3 [736 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main ppc64el sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main ppc64el ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main ppc64el krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el bash-completion all 1:2.12.0-1 [204 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu6 [78.6 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgpm2 ppc64el 1.20.7-11 [15.9 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main ppc64el libip4tc2 ppc64el 1.8.10-3ubuntu2 [27.0 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main ppc64el libjansson4 ppc64el 2.14-2build2 [40.4 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main ppc64el psmisc ppc64el 23.7-1build1 [192 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main ppc64el xz-utils ppc64el 5.6.1+really5.4.5-1 [276 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main ppc64el advancecomp ppc64el 2.5-1build1 [244 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf0 ppc64el 2.42-4ubuntu2 [112 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf-nobfd0 ppc64el 2.42-4ubuntu2 [112 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-4ubuntu2 [2473 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbinutils ppc64el 2.42-4ubuntu2 [699 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils ppc64el 2.42-4ubuntu2 [3080 B] Get:160 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-common ppc64el 2.42-4ubuntu2 [217 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsframe1 ppc64el 2.42-4ubuntu2 [16.0 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/main ppc64el libubsan1 ppc64el 14-20240412-0ubuntu1 [1196 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/main ppc64el g++-13 ppc64el 13.2.0-23ubuntu4 [14.5 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/main ppc64el libstdc++-13-dev ppc64el 13.2.0-23ubuntu4 [2512 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB] Get:166 http://ftpmaster.internal/ubuntu oracular/main ppc64el libitm1 ppc64el 14-20240412-0ubuntu1 [32.4 kB] Get:167 http://ftpmaster.internal/ubuntu oracular/main ppc64el libatomic1 ppc64el 14-20240412-0ubuntu1 [10.7 kB] Get:168 http://ftpmaster.internal/ubuntu oracular/main ppc64el libasan8 ppc64el 14-20240412-0ubuntu1 [2971 kB] Get:169 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblsan0 ppc64el 14-20240412-0ubuntu1 [1327 kB] Get:170 http://ftpmaster.internal/ubuntu oracular/main ppc64el libquadmath0 ppc64el 14-20240412-0ubuntu1 [158 kB] Get:171 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc-13 ppc64el 13.2.0-23ubuntu4 [482 kB] Get:172 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgcc-13-dev ppc64el 13.2.0-23ubuntu4 [1580 kB] Get:173 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtsan2 ppc64el 14-20240412-0ubuntu1 [2709 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcc1-0 ppc64el 14-20240412-0ubuntu1 [48.1 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main ppc64el cpp-13 ppc64el 13.2.0-23ubuntu4 [1038 B] Get:176 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc-13-base ppc64el 13.2.0-23ubuntu4 [49.0 kB] Get:177 http://ftpmaster.internal/ubuntu oracular/main ppc64el libisl23 ppc64el 0.26-3build1 [886 kB] Get:178 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmpfr6 ppc64el 4.2.1-1build1 [350 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmpc3 ppc64el 1.3.1-1build1 [62.1 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu4 [20.6 MB] Get:181 http://ftpmaster.internal/ubuntu oracular/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu4 [12.2 MB] Get:182 http://ftpmaster.internal/ubuntu oracular/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu4 [10.7 MB] Get:183 http://ftpmaster.internal/ubuntu oracular/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] Get:184 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] Get:185 http://ftpmaster.internal/ubuntu oracular/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] Get:186 http://ftpmaster.internal/ubuntu oracular/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] Get:187 http://ftpmaster.internal/ubuntu oracular/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] Get:188 http://ftpmaster.internal/ubuntu oracular/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] Get:189 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:190 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:191 http://ftpmaster.internal/ubuntu oracular/main ppc64el patch ppc64el 2.7.6-7build3 [124 kB] Get:192 http://ftpmaster.internal/ubuntu oracular/main ppc64el make ppc64el 4.3-4.1build2 [214 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main ppc64el lto-disabled-list all 47 [12.4 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main ppc64el libfakeroot ppc64el 1.34-1 [34.6 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/main ppc64el fakeroot ppc64el 1.34-1 [69.4 kB] Get:196 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblockfile-bin ppc64el 1.17-1build3 [11.7 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblockfile1 ppc64el 1.17-1build3 [7692 B] Get:198 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el lockfile-progs ppc64el 0.1.19+nmu1 [9026 B] Preconfiguring packages ... 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Unpacking perl-modules-5.38 (5.38.2-4) ... dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libdb5.3. libpam-modules:ppc64el depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14968 files and directories currently installed.) Removing libdb5.3:ppc64el (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:ppc64el. (Reading database ... 14962 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_ppc64el.deb ... Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-7) ... dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm6 (>= 1.21). libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). (Reading database ... 14968 files and directories currently installed.) Removing libgdbm6:ppc64el (1.23-3) ... 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Preparing to unpack .../perl-base_5.38.2-4_ppc64el.deb ... Unpacking perl-base (5.38.2-4) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-4) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../0-liblocale-gettext-perl_1.07-6ubuntu5_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu5) over (1.07-6) ... Preparing to unpack .../1-libtext-iconv-perl_1.7-8build3_ppc64el.deb ... Unpacking libtext-iconv-perl:ppc64el (1.7-8build3) over (1.7-8) ... Preparing to unpack .../2-libtext-charwidth-perl_0.04-11build3_ppc64el.deb ... Unpacking libtext-charwidth-perl:ppc64el (0.04-11build3) over (0.04-11) ... Preparing to unpack .../3-libnss-nisplus_1.3-5build1_ppc64el.deb ... Unpacking libnss-nisplus:ppc64el (1.3-5build1) over (1.3-0ubuntu6) ... Preparing to unpack .../4-libnss-nis_3.1-0ubuntu7_ppc64el.deb ... Unpacking libnss-nis:ppc64el (3.1-0ubuntu7) over (3.1-0ubuntu6) ... 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(both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_ppc64el.deb ... Unpacking libbz2-1.0:ppc64el (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:ppc64el (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:ppc64el. (Reading database ... 15652 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14-20240412-0ubuntu1_ppc64el.deb ... Unpacking gcc-14-base:ppc64el (14-20240412-0ubuntu1) ... 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Setting up libgdbm-compat4t64:ppc64el (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libsqlite3-0:ppc64el (3.45.3-1) ... Setting up binutils-common:ppc64el (2.42-4ubuntu2) ... Setting up linux-libc-dev:ppc64el (6.8.0-31.31) ... Setting up libctf-nobfd0:ppc64el (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu2) ... Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:ppc64el (2.42-4ubuntu2) ... Setting up libfakeroot:ppc64el (1.34-1) ... Setting up libjansson4:ppc64el (2.14-2build2) ... Setting up libkrb5support0:ppc64el (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-4ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri May 3 05:27:05 UTC 2024. Universal Time is now: Fri May 3 05:27:05 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.34-1) ... Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... Setting up gcc-13-base:ppc64el (13.2.0-23ubuntu4) ... Setting up make (4.3-4.1build2) ... Setting up libmpfr6:ppc64el (4.2.1-1build1) ... Setting up bash-completion (1:2.12.0-1) ... Installing new version of config file /etc/profile.d/bash_completion.sh ... Setting up xz-utils (5.6.1+really5.4.5-1) ... Setting up perl-modules-5.38 (5.38.2-4) ... Setting up libquadmath0:ppc64el (14-20240412-0ubuntu1) ... Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:ppc64el (1.6.43-5build1) ... Setting up libmpc3:ppc64el (1.3.1-1build1) ... Setting up libatomic1:ppc64el (14-20240412-0ubuntu1) ... Setting up patch (2.7.6-7build3) ... Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu4) ... Setting up libncursesw6:ppc64el (6.4+20240113-1ubuntu2) ... Setting up libk5crypto3:ppc64el (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu4) ... Setting up libubsan1:ppc64el (14-20240412-0ubuntu1) ... Setting up advancecomp (2.5-1build1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:ppc64el (1:4.4.36-4build1) ... Setting up libasan8:ppc64el (14-20240412-0ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:ppc64el (1.20.1-6ubuntu2) ... Setting up liblockfile1:ppc64el (1.17-1build3) ... Setting up libperl5.38t64:ppc64el (5.38.2-4) ... Setting up libtsan2:ppc64el (14-20240412-0ubuntu1) ... Setting up libbinutils:ppc64el (2.42-4ubuntu2) ... Setting up libisl23:ppc64el (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8.1) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-23ubuntu4) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:ppc64el (14-20240412-0ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up liblsan0:ppc64el (14-20240412-0ubuntu1) ... Setting up libitm1:ppc64el (14-20240412-0ubuntu1) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libctf0:ppc64el (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-4) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19+nmu1) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:ppc64el (8.2-4build1) ... Setting up libgcc-13-dev:ppc64el (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:ppc64el (2.39-0ubuntu8.1) ... Setting up binutils-powerpc64le-linux-gnu (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:ppc64el (13.2.0-23ubuntu4) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.1build1) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up libnsl2:ppc64el (1.3.0-3build3) ... Setting up libnss-nisplus:ppc64el (1.3-5build1) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:ppc64el (3.1-0ubuntu7) ... Setting up libnsl-dev:ppc64el (1.3.0-3build3) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15877 files and directories currently installed.) Purging configuration files for libssl3:ppc64el (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... 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-28286490 ppc64el oracular-proposed -c chroot:build-PACKAGEBUILD-28286490 --arch=ppc64el --dist=oracular-proposed --nolog phast_1.6+dfsg-5.dsc Initiating build PACKAGEBUILD-28286490 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:55:42 UTC 2024 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-ppc64el-012.buildd +==============================================================================+ | phast 1.6+dfsg-5 (ppc64el) Fri, 03 May 2024 05:27:16 +0000 | +==============================================================================+ Package: phast Version: 1.6+dfsg-5 Source Version: 1.6+dfsg-5 Distribution: oracular-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28286490/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/phast-HbGm3V/resolver-FU7cTg' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phast_1.6+dfsg-5.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/phast-HbGm3V/phast-1.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-HbGm3V' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man, 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 [415 B] Get:5 copy:/<>/apt_archive ./ Packages [498 B] Fetched 1870 B in 0s (93.3 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: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1t64 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsub-override-perl libtmglib-dev libtmglib3 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 liblapack-doc 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 debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libgfortran5 libicu74 liblapack-dev liblapack3 liblapacke liblapacke-dev libmagic-mgc libmagic1t64 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 32.5 MB of archives. After this operation, 133 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [722 B] Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libelf1t64 ppc64el 0.191-1 [68.0 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libicu74 ppc64el 74.2-1ubuntu3 [11.3 MB] Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.3ubuntu3 [840 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmagic-mgc ppc64el 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libmagic1t64 ppc64el 1:5.45-3build1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el file ppc64el 1:5.45-3build1 [22.7 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el gettext-base ppc64el 0.21-14ubuntu2 [42.8 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libuchardet0 ppc64el 0.0.8-1build1 [79.3 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el groff-base ppc64el 1.23.0-4 [1106 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpipeline1 ppc64el 1.5.7-2 [26.9 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el man-db ppc64el 2.12.1-1 [1278 kB] Get:13 http://ftpmaster.internal/ubuntu oracular/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el autoconf all 2.71-3 [339 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el autopoint all 0.21-14ubuntu2 [422 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtool all 2.4.7-7build1 [166 kB] Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libdw1t64 ppc64el 0.191-1 [303 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el debugedit ppc64el 1:5.0-5build2 [51.4 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main ppc64el gettext ppc64el 0.21-14ubuntu2 [985 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main ppc64el debhelper all 13.14.1ubuntu5 [869 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/universe ppc64el help2man ppc64el 1.49.3 [201 kB] Get:33 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas-dev ppc64el 3.12.0-3build1 [301 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14-20240412-0ubuntu1 [574 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack-dev ppc64el 3.12.0-3build1 [6100 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtmglib3 ppc64el 3.12.0-3build1 [144 kB] Get:39 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapacke ppc64el 3.12.0-3build1 [465 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/main ppc64el libtmglib-dev ppc64el 3.12.0-3build1 [157 kB] Get:41 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapacke-dev ppc64el 3.12.0-3build1 [392 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpcre2-16-0 ppc64el 10.42-4ubuntu2 [247 kB] Get:43 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpcre2-32-0 ppc64el 10.42-4ubuntu2 [230 kB] Get:44 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpcre2-posix3 ppc64el 10.42-4ubuntu2 [7068 B] Get:45 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpcre2-dev ppc64el 10.42-4ubuntu2 [801 kB] Preconfiguring packages ... Fetched 32.5 MB in 2s (15.7 MB/s) Selecting previously unselected package libelf1t64:ppc64el. (Reading database ... 15877 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.191-1_ppc64el.deb ... Unpacking libelf1t64:ppc64el (0.191-1) ... Selecting previously unselected package libicu74:ppc64el. Preparing to unpack .../01-libicu74_74.2-1ubuntu3_ppc64el.deb ... Unpacking libicu74:ppc64el (74.2-1ubuntu3) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_ppc64el.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:ppc64el. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_ppc64el.deb ... Unpacking libmagic1t64:ppc64el (1:5.45-3build1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3build1_ppc64el.deb ... Unpacking file (1:5.45-3build1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14ubuntu2_ppc64el.deb ... Unpacking gettext-base (0.21-14ubuntu2) ... Selecting previously unselected package libuchardet0:ppc64el. Preparing to unpack .../07-libuchardet0_0.0.8-1build1_ppc64el.deb ... Unpacking libuchardet0:ppc64el (0.0.8-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-4_ppc64el.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../09-libpipeline1_1.5.7-2_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.1-1_ppc64el.deb ... Unpacking man-db (2.12.1-1) ... 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Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libmagic1t64:ppc64el (1:5.45-3build1) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up file (1:5.45-3build1) ... Setting up libpcre2-16-0:ppc64el (10.42-4ubuntu2) ... Setting up libelf1t64:ppc64el (0.191-1) ... Setting up libdw1t64:ppc64el (0.191-1) ... Setting up help2man (1.49.3) ... Setting up autotools-dev (20220109.1) ... Setting up libpcre2-32-0:ppc64el (10.42-4ubuntu2) ... Setting up libblas3:ppc64el (3.12.0-3build1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up autopoint (0.21-14ubuntu2) ... Setting up libgfortran5:ppc64el (14-20240412-0ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libicu74:ppc64el (74.2-1ubuntu3) ... Setting up libpcre2-posix3:ppc64el (10.42-4ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:ppc64el (0.0.8-1build1) ... Setting up debugedit (1:5.0-5build2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu3) ... Setting up libblas-dev:ppc64el (3.12.0-3build1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:ppc64el (3.12.0-3build1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up gettext (0.21-14ubuntu2) ... Setting up libpcre2-dev:ppc64el (10.42-4ubuntu2) ... Setting up libtool (2.4.7-7build1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:ppc64el (3.12.0-3build1) ... Setting up liblapack-dev:ppc64el (3.12.0-3build1) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up liblapacke:ppc64el (3.12.0-3build1) ... Setting up libtmglib-dev:ppc64el (3.12.0-3build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up liblapacke-dev:ppc64el (3.12.0-3build1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up debhelper (13.14.1ubuntu5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:55:42 UTC 2024 ppc64el (ppc64le) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.12.0-1 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-powerpc64le-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-powerpc64le-linux-gnu_13.2.0-23ubuntu4 cpp-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu4 g++-13-powerpc64le-linux-gnu_13.2.0-23ubuntu4 g++-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu4 gcc-13-base_13.2.0-23ubuntu4 gcc-13-powerpc64le-linux-gnu_13.2.0-23ubuntu4 gcc-14-base_14-20240412-0ubuntu1 gcc-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-4 gzip_1.12-1ubuntu3 help2man_1.49.3 hostname_3.23+nmu2ubuntu2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1build1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.9.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblas-dev_3.12.0-3build1 libblas3_3.12.0-3build1 libblkid1_2.39.3-9ubuntu6 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240412-0ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu10 libdw1t64_0.191-1 libelf1t64_0.191-1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu4 libgcc-s1_14-20240412-0ubuntu1 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgfortran5_14-20240412-0ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.3-1.1ubuntu3.1 libgomp1_14-20240412-0ubuntu1 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libitm1_14-20240412-0ubuntu1 libjansson4_2.14-2build2 libjson-c5_0.17-1build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 liblapack-dev_3.12.0-3build1 liblapack3_3.12.0-3build1 liblapacke_3.12.0-3build1 liblapacke-dev_3.12.0-3build1 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblsan0_14-20240412-0ubuntu1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncursesw6_6.4+20240113-1ubuntu2 libnettle8t64_3.9.1-2.2build1 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu7 libnss-nisplus_1.3-5build1 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-7ubuntu1 libpam-modules-bin_1.5.3-7ubuntu1 libpam-runtime_1.5.3-7ubuntu1 libpam0g_1.5.3-7ubuntu1 libpcre2-16-0_10.42-4ubuntu2 libpcre2-32-0_10.42-4ubuntu2 libpcre2-8-0_10.42-4ubuntu2 libpcre2-dev_10.42-4ubuntu2 libpcre2-posix3_10.42-4ubuntu2 libperl5.36_5.36.0-9ubuntu1 libperl5.38t64_5.38.2-4 libpipeline1_1.5.7-2 libpng16-16t64_1.6.43-5build1 libproc2-0_2:4.0.4-4ubuntu3 libquadmath0_14-20240412-0ubuntu1 libreadline8t64_8.2-4build1 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build5 libsemanage2_3.5-1build5 libsepol2_3.5-2build1 libsframe1_2.42-4ubuntu2 libsmartcols1_2.39.3-9ubuntu6 libsqlite3-0_3.45.3-1 libss2_1.47.0-2.4~exp1ubuntu4 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu8 libsystemd0_255.4-1ubuntu8 libtasn1-6_4.19.0-3build1 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu2 libtirpc-common_1.3.4+ds-1.3 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtmglib-dev_3.12.0-3build1 libtmglib3_3.12.0-3build1 libtool_2.4.7-7build1 libtsan2_14-20240412-0ubuntu1 libubsan1_14-20240412-0ubuntu1 libuchardet0_0.0.8-1build1 libudev1_255.4-1ubuntu8 libunistring2_1.0-2 libunistring5_1.2-1 libuuid1_2.39.3-9ubuntu6 libxml2_2.9.14+dfsg-1.3ubuntu3 libxxhash0_0.8.2-2build1 libzstd1_1.5.5+dfsg2-2build1 linux-libc-dev_6.8.0-31.31 lockfile-progs_0.1.19+nmu1 login_1:4.13+dfsg1-4ubuntu3 logsave_1.47.0-2.4~exp1ubuntu4 lto-disabled-list_47 m4_1.4.19-4build1 make_4.3-4.1build2 man-db_2.12.1-1 mawk_1.3.4.20240123-1build1 mount_2.39.3-9ubuntu6 ncurses-base_6.4+20240113-1ubuntu2 ncurses-bin_6.4+20240113-1ubuntu2 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu3 patch_2.7.6-7build3 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-4 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu8 systemd-dev_255.4-1ubuntu8 systemd-sysv_255.4-1ubuntu8 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phast Vcs-Git: https://salsa.debian.org/med-team/phast.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz b29ea018154c2ceb6f397cd966576ed689e70325 58636 phast_1.6+dfsg-5.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz 5a32f9b3bb33b4604a2ea6a096c7ce8d8a344e193e05d565c5f394921277d39d 58636 phast_1.6+dfsg-5.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz b70b9654d66ddaf8e939b022f1641c2d 58636 phast_1.6+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCZgKbmAAKCRAqJ5BL1yQ+ 2kidAQCID+4lGgZ7i/C6WWyB87kLVEZHPBj3/sgEf33brvldCAEAve1FYl2li/Jg i9KuL7Erft0G7VRxkT16TxcOMEmJbQQ= =KZWp -----END PGP SIGNATURE----- gpgv: Signature made Tue Mar 26 09:55:36 2024 UTC gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting phast in /<> dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying pcre2.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-28286490 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28286490 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28286490 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 phast dpkg-buildpackage: info: source version 1.6+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean cd src && make clean make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make clean ; done make[4]: Entering directory '/<>/src/lib/base' rm -f *.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' rm -f *.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' rm -f *.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' rm -f *.o make[4]: Leaving directory '/<>/src/lib/motif' rm -f /<>/src/lib/../../lib/* make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' rm -f *.o dless.help dlessP.help /<>/src/dless/../../bin/dless /<>/src/dless/../../bin/dlessP make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' rm -f *.o *.help /<>/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' rm -f *.o /<>/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' rm -f *.o *.help /<>/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' rm -f *.o /<>/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' rm -f *.o /<>/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' rm -f *.o *.help /<>/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' rm -f *.o /<>/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' rm -f *.o /<>/src/prequel/../../bin/pbsDecode /<>/src/prequel/../../bin/pbsEncode /<>/src/prequel/../../bin/pbsScoreMatrix /<>/src/prequel/../../bin/pbsTrain /<>/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' rm -f *.o *.help /<>/src/util/../../bin/all_dists /<>/src/util/../../bin/base_evolve /<>/src/util/../../bin/chooseLines /<>/src/util/../../bin/clean_genes /<>/src/util/../../bin/consEntropy /<>/src/util/../../bin/convert_coords /<>/src/util/../../bin/display_rate_matrix /<>/src/util/../../bin/draw_tree /<>/src/util/../../bin/eval_predictions /<>/src/util/../../bin/hmm_train /<>/src/util/../../bin/hmm_tweak /<>/src/util/../../bin/hmm_view /<>/src/util/../../bin/indelFit /<>/src/util/../../bin/indelHistory /<>/src/util/../../bin/maf_parse /<>/src/util/../../bin/makeHKY /<>/src/util/../../bin/modFreqs /<>/src/util/../../bin/msa_diff /<>/src/util/../../bin/msa_split /<>/src/util/../../bin/msa_view /<>/src/util/../../bin/phast /<>/src/util/../../bin/phastBias /<>/src/util/../../bin/refeature /<>/src/util/../../bin/stringiphy /<>/src/util/../../bin/treeGen /<>/src/util/../../bin/tree_doctor make[3]: Leaving directory '/<>/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/<>/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<>/src/$dir && make ; done make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make ; done make[4]: Entering directory '/<>/src/lib/base' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_misc.c: In function ‘make_name_hash’: phast_misc.c:672:46: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c:672:35: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~ phast_misc.c: In function ‘phast_fclose’: phast_misc.c:301:5: warning: pointer ‘f_5(D)’ used after ‘fclose’ [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to ‘fclose’ here 300 | fclose(f); | ^~~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of ‘pcre2_match_8’ differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:935:1: note: expected ‘PCRE2_SPTR8’ {aka ‘const unsigned char *’} but argument is of type ‘char *’ 935 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c: In function ‘str_re_match’: phast_stringsplus.c:532:30: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_search’: phast_stringsplus.c:538:28: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:504:52: warning: ‘ovector’ may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ phast_stringsplus.c:491:15: note: ‘ovector’ was declared here 491 | PCRE2_SIZE *ovector; | ^~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /<>/src/lib/base/../../../lib/libphast.a ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_local_alignment.c: In function ‘la_read_lav’: phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_local_alignment.c:50:44: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_maf.c: In function ‘maf_read_cats_subset’: phast_maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_msa.c: In function ‘msa_read_fasta’: phast_msa.c:264:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_msa.c:39: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:264:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^ phast_msa.c:257:40: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function ‘msa_read_seq_fasta’: phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:1929:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^ phast_msa.c: In function ‘msa_format_for_content’: phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2590:9: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2592 | fasta_re = str_re_new("^>.*"); | ^ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2593 | lav_re = str_re_new("^#:lav.*"); | ^ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2594 | maf_re = str_re_new("^##maf"); | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_multi_msa.c: In function ‘multimsa_new_from_files’: phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:54:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:36: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_sufficient_stats.c: In function ‘ss_from_msas’: phast_sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function ‘ss_read’: phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from /<>/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:661:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^ ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_bed.c: In function ‘gff_print_bed’: phast_bed.c:143:52: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_bed.c:15: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_bed.c:143:41: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_category_map.c: In function ‘cm_read’: phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:39:18: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:15: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_gff.c: In function ‘gff_read_set’: phast_gff.c:56:38: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_gff.c:13: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:56:25: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^ phast_gff.c: In function ‘gff_new_feature_genomic_pos’: phast_gff.c:272:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:272:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^ phast_gff.c: In function ‘gff_group’: phast_gff.c:688:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:688:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 688 | tag_re = str_re_new(tmpstr); | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_phylo_p_print.c: In function ‘print_feats_generic’: phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_phylo_p_print.c:752:39: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_motif.c: In function ‘mtf_print’: phast_motif.c:1411:21: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function ‘mtf_print_html’: phast_motif.c:1604:23: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_tfbs.c: In function ‘pwm_read’: phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:147:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^ phast_tfbs.c: In function ‘ms_read’: phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:229:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^ phast_tfbs.c:219:32: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/<>/src/lib/motif' make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/<>/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/exoniphy/../../lib -o /<>/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_leaves’ at ../lib/phylo/phast_trees.c:1285:3, inlined from ‘gp_set_patterns’ at ../lib/phylo_hmm/phast_gap_patterns.c:419:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘gp_set_patterns’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phastCons/../../lib -o /<>/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phastOdds/../../lib -o /<>/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/<>/src/phastMotif/../../lib -o /<>/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5, inlined from ‘mtf_free’ at ../lib/motif/phast_motif.c:1262:7: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘mtf_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloFit/../../lib -o /<>/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloBoot/../../lib -o /<>/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_free’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:521:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/phyloP/../../lib -o /<>/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:521:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/<>/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:405:3, inlined from ‘main’ at all_dists.c:101:17: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:408:3, inlined from ‘main’ at all_dists.c:101:17: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_free’ at ../lib/phylo/phast_trees.c:329:3, inlined from ‘tm_free’ at ../lib/phylo/phast_tree_model.c:289:5, inlined from ‘main’ at all_dists.c:102:7: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tm_new_from_file.constprop’ at ../lib/phylo/phast_tree_model.c:438:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_postorder’ at ../lib/phylo/phast_trees.c:630:5, inlined from ‘tl_compute_log_likelihood.constprop.isra’ at ../lib/phylo/phast_tree_likelihoods.c:192:23: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tl_compute_log_likelihood.constprop.isra’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tr_new_from_file’ at ../lib/phylo/phast_trees.c:55:12, inlined from ‘main’ at hmm_tweak.c:117:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tr_new_from_file’ at ../lib/phylo/phast_trees.c:55:12, inlined from ‘main’ at hmm_view.c:63:14: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes’ at ../lib/phylo/phast_trees.c:1318:3, inlined from ‘ih_expand’ at ../lib/phylo/phast_indel_history.c:82:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘ih_expand’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_new_from_string’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_new_from_string’ at ../lib/phylo/phast_trees.c:149:3, inlined from ‘tm_new_from_file’ at ../lib/phylo/phast_tree_model.c:438:14, inlined from ‘main’ at modFreqs.c:44:9: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition msa_view.c: In function ‘fill_with_Ns’: msa_view.c:361:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from msa_view.c:14: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ msa_view.c:361:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3, inlined from ‘tr_create_copy’ at ../lib/phylo/phast_trees.c:433:3, inlined from ‘main’ at treeGen.c:135:16: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘main’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/phast-1.6+dfsg-5 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition tree_doctor.c: In function ‘main’: tree_doctor.c:348:19: warning: the comparison will always evaluate as ‘true’ for the address of ‘name’ will never be NULL [-Waddress] 348 | if (n->name != NULL && n->name[0] != '\0' && | ^~ In file included from /<>/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /<>/src/../include/phast/trees.h:47:8: note: ‘name’ declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at ../lib/phylo/phast_trees.c:165:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_set_nnodes’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_preorder’ at ../lib/phylo/phast_trees.c:563:5: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_preorder’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘stk_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/stacks.h:110:42, inlined from ‘tr_partition_nodes.constprop’ at ../lib/phylo/phast_trees.c:1318:3: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tr_partition_nodes.constprop’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:497:26, inlined from ‘lst_push_ptr’ at /usr/src/phast-1.6+dfsg-5/src/../include/phast/lists.h:534:4, inlined from ‘tm_add_alt_mod’ at ../lib/phylo/phast_tree_model.c:859:2: ../lib/base/phast_misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 461 | void *retval = realloc(ptr, size); | ^ /usr/include/stdlib.h: In function ‘tm_add_alt_mod’: /usr/include/stdlib.h:683:14: note: in a call to allocation function ‘realloc’ declared here 683 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd test && PATH=/<>/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/<>/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o PHYLIP > hmrc.ph msa_view hmrc.ph -i PHYLIP > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm msa_view hmrc.mpm --in-format MPM > hmrc.fa if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa -o SS > hmrc_short_a.ss msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa msa_view --seqs human,cow hmrc.fa > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi msa_view hmrc.ss --summary -i SS > hmrc_summary if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi -e Passed all tests. make[2]: Leaving directory '/<>/test' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j4 install DESTDIR=/<>/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' (cd src; make install DESTDIR=/<>/debian/phast ) make[2]: Entering directory '/<>/src' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p /<>/debian/phast/usr/bin/ mkdir -p /<>/debian/phast/usr/share/phast/data/ mkdir -p /<>/debian/phast/usr/share/man/man1/ cp ../bin/* /<>/debian/phast/usr/bin/ cp -R ../data/* /<>/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /<>/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/phast/usr/bin/clean_genes: Unknown DWARF DW_FORM_0x1f20 56a46691156f6c5f73361de44aa6071c142b23d4 debugedit: debian/phast/usr/bin/msa_diff: Unknown DWARF DW_FORM_0x1f20 81dc09661531055c771d3d5ebe7dca3f3fd00e1c debugedit: debian/phast/usr/bin/all_dists: Unknown DWARF DW_FORM_0x1f20 f23578e52bdb6ddcf41fdc6a3a55b76e47e12a49 debugedit: debian/phast/usr/bin/draw_tree: Unknown DWARF DW_FORM_0x1f20 8274514e28b7d3c1330b881ec9a0facdb3f7e16e debugedit: debian/phast/usr/bin/phyloFit: Unknown DWARF DW_FORM_0x1f20 7058524e572e5eb4a1de8cbdbcd00d6db3d016b5 debugedit: debian/phast/usr/bin/modFreqs: Unknown DWARF DW_FORM_0x1f20 fb99b61c264aba54dd61f125440c6f757a66b469 debugedit: debian/phast/usr/bin/eval_predictions: Unknown DWARF DW_FORM_0x1f20 88d99924fe5b30a66afb1659a74e836930ef90e7 debugedit: debian/phast/usr/bin/maf_parse: Unknown DWARF DW_FORM_0x1f20 5f46517fa4291f07d7a197e0dca80b29bf166e4d debugedit: debian/phast/usr/bin/stringiphy: Unknown DWARF DW_FORM_0x1f20 4972f256f44477b59d4dafefb94acf498fbe4e72 debugedit: debian/phast/usr/bin/refeature: Unknown DWARF DW_FORM_0x1f20 4069541ae42db4edb6b6ec997193f3f3537ebcd6 debugedit: debian/phast/usr/bin/treeGen: Unknown DWARF DW_FORM_0x1f20 bdb88a3caf5b84530f8de8e8784a34923ab3f08d debugedit: debian/phast/usr/bin/phyloP: Unknown DWARF DW_FORM_0x1f20 f02d64a9427d3a41880136b0321b89e6647ff131 debugedit: debian/phast/usr/bin/phast: Unknown DWARF DW_FORM_0x1f20 52610c766dd01e9549a4ecf1899b6464433f704f debugedit: debian/phast/usr/bin/phastMotif: Unknown DWARF DW_FORM_0x1f20 94b4711265509ab71790e60a83ce1ccefb6a7fb1 debugedit: debian/phast/usr/bin/indelFit: Unknown DWARF DW_FORM_0x1f20 9e0fc70617160884ec50e9d509f7b54d7f689eb5 debugedit: debian/phast/usr/bin/hmm_tweak: Unknown DWARF DW_FORM_0x1f20 d9072a5a9d1ff1213ceb32f3430422671a1f2345 debugedit: debian/phast/usr/bin/display_rate_matrix: Unknown DWARF DW_FORM_0x1f20 52bad927853ae5cf91af7e487cc4e303cafc0b7d debugedit: debian/phast/usr/bin/tree_doctor: Unknown DWARF DW_FORM_0x1f20 c96d9225af91a76ff48821ab28145093eb537672 debugedit: debian/phast/usr/bin/makeHKY: Unknown DWARF DW_FORM_0x1f20 2d4956efc4fbc20db8081846e9e75bf5e47487e4 debugedit: debian/phast/usr/bin/phastBias: Unknown DWARF DW_FORM_0x1f20 efcf0ca230e27d4ebf0d0f071b0a9b1d4c2ed58d debugedit: debian/phast/usr/bin/hmm_train: Unknown DWARF DW_FORM_0x1f21 5b9cc0fde56bafe058961cde3cab17c54e8f3b6f debugedit: debian/phast/usr/bin/consEntropy: Unknown DWARF DW_FORM_0x1f20 086b010b3c13f5666ce1e975fac6ff37b7322a9d debugedit: debian/phast/usr/bin/phyloBoot: Unknown DWARF DW_FORM_0x1f20 7a2c08cdf20ffd0ae02075a0c0b765b4424b0629 debugedit: debian/phast/usr/bin/phastOdds: Unknown DWARF DW_FORM_0x1f20 238fefe73458801341e508dc784b0f61a6f66d86 debugedit: debian/phast/usr/bin/msa_split: Unknown DWARF DW_FORM_0x1f20 d9d638a18e30b8d1e54e0cd57391a9f6c0cbc7ec debugedit: debian/phast/usr/bin/phastCons: Unknown DWARF DW_FORM_0x1f20 5f2ed619c090f94ce36e2d095531f4088ba5af9a debugedit: debian/phast/usr/bin/msa_view: Unknown DWARF DW_FORM_0x1f20 6449cc2dcc7bb9a93f0f7c210bb33aa73934d17f debugedit: debian/phast/usr/bin/base_evolve: Unknown DWARF DW_FORM_0x1f20 2fda40e9af3340e523d7ddf0c9b032dc13c406d2 debugedit: debian/phast/usr/bin/chooseLines: Unknown DWARF DW_FORM_0x1f20 7ecd55339b9258c0de0a98114021a7682571d280 debugedit: debian/phast/usr/bin/exoniphy: Unknown DWARF DW_FORM_0x1f20 993c5ab1003fcb974704ec8e677de1a4ca692c35 debugedit: debian/phast/usr/bin/convert_coords: Unknown DWARF DW_FORM_0x1f20 3a7b72e011589a96b3d742a73c2aee67f03bf9a9 debugedit: debian/phast/usr/bin/indelHistory: Unknown DWARF DW_FORM_0x1f20 322cf462f7c073c651522fd14015b77321ab689f debugedit: debian/phast/usr/bin/hmm_view: Unknown DWARF DW_FORM_0x1f20 f05b3715718159771be830b37931ef0dbdd76c1a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing phast (in debian/phast); do_strip: , oemstrip: pkgstriptranslations: processing phast-dbgsym (in debian/.debhelper/phast/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/phast/DEBIAN/control, package phast, directory debian/phast pkgstripfiles: Running PNG optimization (using 4 cpus) for package phast ... pkgstripfiles: No PNG files. dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-5_ppc64el.deb'. pkgstripfiles: processing control file: debian/.debhelper/phast/dbgsym-root/DEBIAN/control, package phast-dbgsym, directory debian/.debhelper/phast/dbgsym-root dpkg-deb: building package 'phast-dbgsym' in 'debian/.debhelper/scratch-space/build-phast/phast-dbgsym_1.6+dfsg-5_ppc64el.deb'. Renaming phast-dbgsym_1.6+dfsg-5_ppc64el.deb to phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb dpkg-genbuildinfo --build=any -O../phast_1.6+dfsg-5_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../phast_1.6+dfsg-5_ppc64el.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 2024-05-03T05:32:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.6+dfsg-5_ppc64el.changes: --------------------------------- Format: 1.8 Date: Tue, 26 Mar 2024 15:19:11 +0530 Source: phast Binary: phast Built-For-Profiles: noudeb Architecture: ppc64el Version: 1.6+dfsg-5 Distribution: oracular-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: phast - phylogenetic analysis with space/time models Closes: 1066451 Changes: phast (1.6+dfsg-5) unstable; urgency=medium . * Team Upload. * Add patch to fix FTBFS due to -Werror-implicit-function-declaration (Closes: #1066451) * Added B-D on lapacke-dev for porting functions to lapack equivalents Checksums-Sha1: 18b8ae995bcb4e3076cf003241dc398c82ec3ec5 6798246 phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb cd40fa624f0f556dfc3a2fd4f3da5b658ae21c2f 6393 phast_1.6+dfsg-5_ppc64el.buildinfo d6c349207d9af5f0f2682257e3080037a10ff50e 2773610 phast_1.6+dfsg-5_ppc64el.deb Checksums-Sha256: f8a953cc316aa0c81cccf94ce4ff6173f15e83b74166f4687cb707541a3a52af 6798246 phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb d5d3cb6b43eaf5de0d620278c67b987c84545de048badf096c6dd42a26cab206 6393 phast_1.6+dfsg-5_ppc64el.buildinfo 9d5b30bfecc73b1eaa717846b94fecca2966e9bd3b0a356a58ae253396c493bf 2773610 phast_1.6+dfsg-5_ppc64el.deb Files: db0ef21c96c54b9c057d148e02b23b38 6798246 debug optional phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb 08140b32a42a6644f927ed8ea18f6684 6393 science optional phast_1.6+dfsg-5_ppc64el.buildinfo 21e174eb9108d475929bc86bbb8b621e 2773610 science optional phast_1.6+dfsg-5_ppc64el.deb /<>/phast_1.6+dfsg-5_ppc64el.changes.new could not be renamed to /<>/phast_1.6+dfsg-5_ppc64el.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: ppc64el Version: 1.6+dfsg-5 Checksums-Md5: db0ef21c96c54b9c057d148e02b23b38 6798246 phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb 21e174eb9108d475929bc86bbb8b621e 2773610 phast_1.6+dfsg-5_ppc64el.deb Checksums-Sha1: 18b8ae995bcb4e3076cf003241dc398c82ec3ec5 6798246 phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb d6c349207d9af5f0f2682257e3080037a10ff50e 2773610 phast_1.6+dfsg-5_ppc64el.deb Checksums-Sha256: f8a953cc316aa0c81cccf94ce4ff6173f15e83b74166f4687cb707541a3a52af 6798246 phast-dbgsym_1.6+dfsg-5_ppc64el.ddeb 9d5b30bfecc73b1eaa717846b94fecca2966e9bd3b0a356a58ae253396c493bf 2773610 phast_1.6+dfsg-5_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Fri, 03 May 2024 05:32:26 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu2), autotools-dev (= 20220109.1), base-files (= 13.1ubuntu1), base-passwd (= 3.6.3build1), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-powerpc64le-linux-gnu (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu6), bsdutils (= 1:2.39.3-9ubuntu6), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3ubuntu6), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu4), cpp-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu4), cpp-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86ubuntu1), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1build1), dpkg (= 1.22.6ubuntu10), dpkg-dev (= 1.22.6ubuntu10), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5build1), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu4), g++-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu4), g++-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu4), gcc-13-base (= 13.2.0-23ubuntu4), gcc-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu4), gcc-14-base (= 14-20240412-0ubuntu1), gcc-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu2), gettext-base (= 0.21-14ubuntu2), grep (= 3.11-4build1), groff-base (= 1.23.0-4), gzip (= 1.12-1ubuntu3), help2man (= 1.49.3), hostname (= 3.23+nmu2ubuntu2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1build1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240412-0ubuntu1), libatomic1 (= 14-20240412-0ubuntu1), libattr1 (= 1:2.5.2-1build1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblas-dev (= 3.12.0-3build1), libblas3 (= 3.12.0-3build1), libblkid1 (= 2.39.3-9ubuntu6), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8.1), libc-dev-bin (= 2.39-0ubuntu8.1), libc6 (= 2.39-0ubuntu8.1), libc6-dev (= 2.39-0ubuntu8.1), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5ubuntu2), libcc1-0 (= 14-20240412-0ubuntu1), libcrypt-dev (= 1:4.4.36-4build1), libcrypt1 (= 1:4.4.36-4build1), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu10), libdw1t64 (= 0.191-1), libelf1t64 (= 0.191-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu4), libgcc-s1 (= 14-20240412-0ubuntu1), libgcrypt20 (= 1.10.3-2build1), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran5 (= 14-20240412-0ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu6), libgomp1 (= 14-20240412-0ubuntu1), libgpg-error0 (= 1.47-3build2), libicu74 (= 74.2-1ubuntu3), libisl23 (= 0.26-3build1), libitm1 (= 14-20240412-0ubuntu1), libjansson4 (= 2.14-2build2), liblapack-dev (= 3.12.0-3build1), liblapack3 (= 3.12.0-3build1), liblapacke (= 3.12.0-3build1), liblapacke-dev (= 3.12.0-3build1), liblocale-gettext-perl (= 1.07-6ubuntu5), liblsan0 (= 14-20240412-0ubuntu1), liblz4-1 (= 1.9.4-2), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2build1), libmount1 (= 2.39.3-9ubuntu6), libmpc3 (= 1.3.1-1build1), libmpfr6 (= 4.2.1-1build1), libpam-modules (= 1.5.3-7ubuntu1), libpam-modules-bin (= 1.5.3-7ubuntu1), libpam-runtime (= 1.5.3-7ubuntu1), libpam0g (= 1.5.3-7ubuntu1), libpcre2-16-0 (= 10.42-4ubuntu2), libpcre2-32-0 (= 10.42-4ubuntu2), libpcre2-8-0 (= 10.42-4ubuntu2), libpcre2-dev (= 10.42-4ubuntu2), libpcre2-posix3 (= 10.42-4ubuntu2), libperl5.38t64 (= 5.38.2-4), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14-20240412-0ubuntu1), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu6), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu4), libstdc++6 (= 14-20240412-0ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu8), libtinfo6 (= 6.4+20240113-1ubuntu2), libtmglib-dev (= 3.12.0-3build1), libtmglib3 (= 3.12.0-3build1), libtool (= 2.4.7-7build1), libtsan2 (= 14-20240412-0ubuntu1), libubsan1 (= 14-20240412-0ubuntu1), libuchardet0 (= 0.0.8-1build1), libudev1 (= 255.4-1ubuntu8), libunistring5 (= 1.2-1), libuuid1 (= 2.39.3-9ubuntu6), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libzstd1 (= 1.5.5+dfsg2-2build1), linux-libc-dev (= 6.8.0-31.31), login (= 1:4.13+dfsg1-4ubuntu3), lto-disabled-list (= 47), m4 (= 1.4.19-4build1), make (= 4.3-4.1build2), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1build1), ncurses-base (= 6.4+20240113-1ubuntu2), ncurses-bin (= 6.4+20240113-1ubuntu2), patch (= 2.7.6-7build3), perl (= 5.38.2-4), perl-base (= 5.38.2-4), perl-modules-5.38 (= 5.38.2-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), util-linux (= 2.39.3-9ubuntu6), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711446551" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast_1.6+dfsg-5_ppc64el.deb ---------------------------- new Debian package, version 2.0. size 2773610 bytes: control archive=5572 bytes. 1193 bytes, 23 lines control 14785 bytes, 195 lines md5sums Package: phast Version: 1.6+dfsg-5 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 10733 Depends: libc6 (>= 2.34), liblapack3 | liblapack.so.3, libpcre2-8-0 (>= 10.22) Section: science Priority: optional Homepage: http://compgen.cshl.edu/phast/ Description: phylogenetic analysis with space/time models PHAST is a software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. . PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison). drwxr-xr-x root/root 0 2024-03-26 09:49 ./ drwxr-xr-x root/root 0 2024-03-26 09:49 ./usr/ drwxr-xr-x root/root 0 2024-03-26 09:49 ./usr/bin/ -rwxr-xr-x root/root 133504 2024-03-26 09:49 ./usr/bin/all_dists -rwxr-xr-x root/root 135296 2024-03-26 09:49 ./usr/bin/base_evolve -rwxr-xr-x root/root 67840 2024-03-26 09:49 ./usr/bin/chooseLines -rwxr-xr-x root/root 205944 2024-03-26 09:49 ./usr/bin/clean_genes -rwxr-xr-x root/root 135224 2024-03-26 09:49 ./usr/bin/consEntropy -rwxr-xr-x root/root 133376 2024-03-26 09:49 ./usr/bin/convert_coords -rwxr-xr-x root/root 133384 2024-03-26 09:49 ./usr/bin/display_rate_matrix -rwxr-xr-x root/root 67840 2024-03-26 09:49 ./usr/bin/draw_tree -rwxr-xr-x root/root 67840 2024-03-26 09:49 ./usr/bin/eval_predictions -rwxr-xr-x root/root 275104 2024-03-26 09:49 ./usr/bin/exoniphy -rwxr-xr-x root/root 133376 2024-03-26 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./usr/share/phast/data/exoniphy/models-gc2 -rw-r--r-- root/root 549 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-gc3 -rw-r--r-- root/root 549 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-gc4 -rw-r--r-- root/root 549 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-gc5 -rw-r--r-- root/root 523 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns -rw-r--r-- root/root 539 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns-gc1 -rw-r--r-- root/root 539 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns-gc2 -rw-r--r-- root/root 539 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns-gc3 -rw-r--r-- root/root 539 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns-gc4 -rw-r--r-- root/root 539 2024-03-26 09:49 ./usr/share/phast/data/exoniphy/models-no-cns-gc5 drwxr-xr-x root/root 0 2024-03-26 09:49 ./usr/share/phast/data/phastCons/ -rw-r--r-- root/root 103302 2024-03-26 09:49 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2024-03-26 09:49 ./usr/share/phast/data/phastCons/simple-coding.hmm +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 105108 Build-Time: 295 Distribution: oracular-proposed Host Architecture: ppc64el Install-Time: 13 Job: phast_1.6+dfsg-5.dsc Machine Architecture: ppc64el Package: phast Package-Time: 310 Source-Version: 1.6+dfsg-5 Space: 105108 Status: successful Version: 1.6+dfsg-5 -------------------------------------------------------------------------------- Finished at 2024-05-03T05:32:26Z Build needed 00:05:10, 105108k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=ppc64el PACKAGEBUILD-28286490 Scanning for processes to kill in build PACKAGEBUILD-28286490