sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | phast 1.6+dfsg-6 (amd64) Tue, 13 Aug 2024 09:11:25 +0000 | +==============================================================================+ Package: phast Version: 1.6+dfsg-6 Source Version: 1.6+dfsg-6 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.oznRuqQEW3... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/phast-lgMbIA/resolver-7NNqJ2' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [198 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.8 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [9877 kB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [9961 kB] Fetched 30.8 MB in 8s (3991 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bash cpp-14 cpp-14-aarch64-linux-gnu g++-14 g++-14-aarch64-linux-gnu gcc-14 gcc-14-aarch64-linux-gnu gcc-14-base libapt-pkg6.0t64 libasan8 libatomic1 libcc1-0 libgcc-14-dev libgcc-s1 libgomp1 libhwasan0 libitm1 liblsan0 libselinux1 libstdc++-14-dev libstdc++6 libsystemd0 libtsan2 libubsan1 libudev1 linux-libc-dev 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 58.2 MB of archives. After this operation, 77.8 kB of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 bash arm64 5.2.21-2.1+b1 [1456 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libcc1-0 arm64 14.2.0-2 [41.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 gcc-14-base arm64 14.2.0-2 [46.0 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1 arm64 14.2.0-2 [54.0 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libgomp1 arm64 14.2.0-2 [123 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 libitm1 arm64 14.2.0-2 [24.2 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libatomic1 arm64 14.2.0-2 [10.1 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libasan8 arm64 14.2.0-2 [2577 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 liblsan0 arm64 14.2.0-2 [1162 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libtsan2 arm64 14.2.0-2 [2386 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libubsan1 arm64 14.2.0-2 [1040 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libhwasan0 arm64 14.2.0-2 [1443 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 gcc-14 arm64 14.2.0-2 [511 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 g++-14 arm64 14.2.0-2 [19.0 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-2 [10.1 MB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libstdc++-14-dev arm64 14.2.0-2 [2261 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libgcc-14-dev arm64 14.2.0-2 [2363 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-2 [17.7 MB] Get:19 http://mirror.einval.org/debian unstable/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-2 [9164 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-14 arm64 14.2.0-2 [1280 B] Get:21 http://mirror.einval.org/debian unstable/main arm64 libstdc++6 arm64 14.2.0-2 [638 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libsystemd0 arm64 256.4-3 [355 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libudev1 arm64 256.4-3 [136 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg6.0t64 arm64 2.9.8 [921 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 apt arm64 2.9.8 [1329 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libselinux1 arm64 3.5-2+b4 [70.8 kB] Get:27 http://mirror.einval.org/debian unstable/main amd64 linux-libc-dev all 6.10.4-1 [2369 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.2 MB in 1s (86.3 MB/s) (Reading database ... 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NOTICE: 'phast' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phast.git Please use: git clone https://salsa.debian.org/med-team/phast.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1870 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main phast 1.6+dfsg-6 (dsc) [2218 B] Get:2 http://mirror.einval.org/debian unstable/main phast 1.6+dfsg-6 (tar) [1809 kB] Get:3 http://mirror.einval.org/debian unstable/main phast 1.6+dfsg-6 (diff) [59.2 kB] Fetched 1870 kB in 0s (6591 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phast-lgMbIA/phast-1.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-lgMbIA' 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, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [825 B] Get:5 copy:/<>/apt_archive ./ Packages [840 B] Fetched 2274 B in 0s (128 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... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-14-base:amd64 gcc-14-cross-base gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1t64 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-14-dev:amd64 libgcc-14-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblapacke:amd64 liblapacke-dev:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64 libpcre2-dev:amd64 libpcre2-posix3:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-14-dev:amd64 libstdc++-14-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtmglib-dev:amd64 libtmglib3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales cpp-14-doc cpp-doc dh-make binutils-multiarch gcc-14-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libstdc++-14-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-14-base:amd64 gcc-14-cross-base gcc-14-x86-64-linux-gnu gcc-14-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl libdebian-dpkgcross-perl libelf1t64 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-14-dev:amd64 libgcc-14-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblapacke:amd64 liblapacke-dev:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64 libpcre2-dev:amd64 libpcre2-posix3:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-14-dev:amd64 libstdc++-14-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtmglib-dev:amd64 libtmglib3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils ucf 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 486 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-6 [96.0 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.12.1-3 [1397 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 gcc-14-x86-64-linux-gnu-base arm64 14.2.0-1cross1 [45.9 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-14-x86-64-linux-gnu arm64 14.2.0-1cross1 [10.4 MB] Get:21 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:14.1.0-2 [4800 B] Get:22 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.43-2 [2439 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14.2.0-1cross1 [41.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 14.2.0-1cross1 [72.8 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 14.2.0-1cross1 [129 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 14.2.0-1cross1 [25.3 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 14.2.0-1cross1 [9020 B] Get:29 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 14.2.0-1cross1 [2716 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 14.2.0-1cross1 [1204 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 14.2.0-1cross1 [2450 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.39-4cross1 [1502 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 14.2.0-1cross1 [667 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 14.2.0-1cross1 [1074 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 14.2.0-1cross1 [1485 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 14.2.0-1cross1 [145 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libgcc-14-dev-amd64-cross all 14.2.0-1cross1 [2668 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 gcc-14-x86-64-linux-gnu arm64 14.2.0-1cross1 [20.0 MB] Get:39 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:14.1.0-2 [1452 B] Get:40 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.39-4cross1 [1920 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libstdc++-14-dev-amd64-cross all 14.2.0-1cross1 [2342 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 g++-14-x86-64-linux-gnu arm64 14.2.0-1cross1 [11.2 MB] Get:43 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:14.1.0-2 [1204 B] Get:44 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-3 [44.8 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg-3+b1 [609 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-4 [299 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.10 [3488 B] Get:60 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.16 [88.6 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:66 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.16 [891 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.35.1-1.1 [29.6 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.35.1-1.1 [74.0 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 gcc-14-base amd64 14.2.0-2 [46.0 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 14.2.0-2 [72.8 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.39-6 [2781 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 14.2.0-2 [2724 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 14.2.0-2 [9288 B] Get:80 http://mirror.einval.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:81 http://mirror.einval.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.39-6 [1924 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 14.2.0-2 [137 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 14.2.0-2 [25.9 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 14.2.0-2 [1205 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 14.2.0-2 [2461 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 14.2.0-2 [714 kB] Get:90 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 14.2.0-2 [1075 kB] Get:91 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 14.2.0-2 [1489 kB] Get:92 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 14.2.0-2 [145 kB] Get:93 http://mirror.einval.org/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-2 [2672 kB] Get:94 http://mirror.einval.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-2 [837 kB] Get:95 http://mirror.einval.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:96 http://mirror.einval.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:97 http://mirror.einval.org/debian unstable/main amd64 libtmglib3 amd64 3.12.0-3 [127 kB] Get:98 http://mirror.einval.org/debian unstable/main amd64 liblapacke amd64 3.12.0-3 [379 kB] Get:99 http://mirror.einval.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.0-3 [130 kB] Get:100 http://mirror.einval.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.0-3 [348 kB] Get:101 http://mirror.einval.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get:102 http://mirror.einval.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get:103 http://mirror.einval.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:104 http://mirror.einval.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get:105 http://mirror.einval.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get:106 http://mirror.einval.org/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-2 [2343 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 114 MB in 2s (68.9 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11868 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.2-6_arm64.deb ... Unpacking bsdextrautils (2.40.2-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.12.1-3_arm64.deb ... Unpacking man-db (2.12.1-3) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package gcc-14-x86-64-linux-gnu-base:arm64. Preparing to unpack .../017-gcc-14-x86-64-linux-gnu-base_14.2.0-1cross1_arm64.deb ... Unpacking gcc-14-x86-64-linux-gnu-base:arm64 (14.2.0-1cross1) ... Selecting previously unselected package cpp-14-x86-64-linux-gnu. Preparing to unpack .../018-cpp-14-x86-64-linux-gnu_14.2.0-1cross1_arm64.deb ... Unpacking cpp-14-x86-64-linux-gnu (14.2.0-1cross1) ... Selecting previously unselected package cpp-x86-64-linux-gnu. Preparing to unpack .../019-cpp-x86-64-linux-gnu_4%3a14.1.0-2_arm64.deb ... Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2) ... Selecting previously unselected package cross-config. Preparing to unpack .../020-cross-config_2.6.20_all.deb ... Unpacking cross-config (2.6.20) ... Selecting previously unselected package binutils-x86-64-linux-gnu. Preparing to unpack .../021-binutils-x86-64-linux-gnu_2.43-2_arm64.deb ... Unpacking binutils-x86-64-linux-gnu (2.43-2) ... Selecting previously unselected package gcc-14-cross-base. Preparing to unpack .../022-gcc-14-cross-base_14.2.0-1cross1_all.deb ... Unpacking gcc-14-cross-base (14.2.0-1cross1) ... Selecting previously unselected package libgcc-s1-amd64-cross. Preparing to unpack .../023-libgcc-s1-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libgcc-s1-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libgomp1-amd64-cross. Preparing to unpack .../024-libgomp1-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libgomp1-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libitm1-amd64-cross. Preparing to unpack .../025-libitm1-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libitm1-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libatomic1-amd64-cross. Preparing to unpack .../026-libatomic1-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libatomic1-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libasan8-amd64-cross. Preparing to unpack .../027-libasan8-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libasan8-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package liblsan0-amd64-cross. Preparing to unpack .../028-liblsan0-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking liblsan0-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libtsan2-amd64-cross. Preparing to unpack .../029-libtsan2-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libtsan2-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libc6-amd64-cross. Preparing to unpack .../030-libc6-amd64-cross_2.39-4cross1_all.deb ... Unpacking libc6-amd64-cross (2.39-4cross1) ... Selecting previously unselected package libstdc++6-amd64-cross. Preparing to unpack .../031-libstdc++6-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libstdc++6-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libubsan1-amd64-cross. Preparing to unpack .../032-libubsan1-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libubsan1-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libhwasan0-amd64-cross. Preparing to unpack .../033-libhwasan0-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libhwasan0-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libquadmath0-amd64-cross. Preparing to unpack .../034-libquadmath0-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libquadmath0-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package libgcc-14-dev-amd64-cross. Preparing to unpack .../035-libgcc-14-dev-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libgcc-14-dev-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package gcc-14-x86-64-linux-gnu. Preparing to unpack .../036-gcc-14-x86-64-linux-gnu_14.2.0-1cross1_arm64.deb ... Unpacking gcc-14-x86-64-linux-gnu (14.2.0-1cross1) ... Selecting previously unselected package gcc-x86-64-linux-gnu. Preparing to unpack .../037-gcc-x86-64-linux-gnu_4%3a14.1.0-2_arm64.deb ... Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2) ... Selecting previously unselected package libc6-dev-amd64-cross. Preparing to unpack .../038-libc6-dev-amd64-cross_2.39-4cross1_all.deb ... Unpacking libc6-dev-amd64-cross (2.39-4cross1) ... Selecting previously unselected package libstdc++-14-dev-amd64-cross. Preparing to unpack .../039-libstdc++-14-dev-amd64-cross_14.2.0-1cross1_all.deb ... Unpacking libstdc++-14-dev-amd64-cross (14.2.0-1cross1) ... Selecting previously unselected package g++-14-x86-64-linux-gnu. Preparing to unpack .../040-g++-14-x86-64-linux-gnu_14.2.0-1cross1_arm64.deb ... Unpacking g++-14-x86-64-linux-gnu (14.2.0-1cross1) ... Selecting previously unselected package g++-x86-64-linux-gnu. Preparing to unpack .../041-g++-x86-64-linux-gnu_4%3a14.1.0-2_arm64.deb ... Unpacking g++-x86-64-linux-gnu (4:14.1.0-2) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../042-libconfig-inifiles-perl_3.000003-3_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-3) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../043-libio-string-perl_1.08-4_all.deb ... 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Setting up libdebhelper-perl (13.16) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up gcc-14-cross-base (14.2.0-1cross1) ... Setting up file (1:5.45-3) ... Setting up libyaml-perl (1.31-1) ... Setting up libgomp1-amd64-cross (14.2.0-1cross1) ... Setting up libfakeroot:arm64 (1.35.1-1.1) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up fakeroot (1.35.1-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libitm1-amd64-cross (14.2.0-1cross1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up libatomic1-amd64-cross (14.2.0-1cross1) ... Setting up libquadmath0-amd64-cross (14.2.0-1cross1) ... Setting up autopoint (0.22.5-2) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-1cross1) ... Setting up libc6-amd64-cross (2.39-4cross1) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libgcc-s1-amd64-cross (14.2.0-1cross1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libxml2:arm64 (2.12.7+dfsg-3+b1) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up binutils-x86-64-linux-gnu (2.43-2) ... Setting up libstdc++6-amd64-cross (14.2.0-1cross1) ... Setting up cpp-x86-64-linux-gnu (4:14.1.0-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libasan8-amd64-cross (14.2.0-1cross1) ... Setting up liblsan0-amd64-cross (14.2.0-1cross1) ... Setting up libc6-dev-amd64-cross (2.39-4cross1) ... Setting up libtsan2-amd64-cross (14.2.0-1cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libhwasan0-amd64-cross (14.2.0-1cross1) ... Setting up libubsan1-amd64-cross (14.2.0-1cross1) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgcc-14-dev-amd64-cross (14.2.0-1cross1) ... Setting up groff-base (1.23.0-5) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-1cross1) ... Setting up libstdc++-14-dev-amd64-cross (14.2.0-1cross1) ... Setting up gcc-x86-64-linux-gnu (4:14.1.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-14-x86-64-linux-gnu (14.2.0-1cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-4) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-x86-64-linux-gnu (4:14.1.0-2) ... Setting up debhelper (13.16) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-amd64 (12.10) ... Setting up libgcc-s1:amd64 (14.2.0-2) ... Setting up libc6:amd64 (2.39-6) ... Setting up libhwasan0:amd64 (14.2.0-2) ... Setting up libasan8:amd64 (14.2.0-2) ... Setting up libtsan2:amd64 (14.2.0-2) ... Setting up libstdc++6:amd64 (14.2.0-2) ... Setting up liblsan0:amd64 (14.2.0-2) ... Setting up libitm1:amd64 (14.2.0-2) ... Setting up libcrypt1:amd64 (1:4.4.36-4) ... Setting up libgomp1:amd64 (14.2.0-2) ... Setting up libpcre2-16-0:amd64 (10.42-4+b1) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libquadmath0:amd64 (14.2.0-2) ... Setting up libatomic1:amd64 (14.2.0-2) ... Setting up libpcre2-8-0:amd64 (10.42-4+b1) ... Setting up libgfortran5:amd64 (14.2.0-2) ... Setting up libubsan1:amd64 (14.2.0-2) ... Setting up libpcre2-posix3:amd64 (10.42-4+b1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up libc6-dev:amd64 (2.39-6) ... Setting up libgcc-14-dev:amd64 (14.2.0-2) ... Setting up libstdc++-14-dev:amd64 (14.2.0-2) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up libtmglib3:amd64 (3.12.0-3) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up liblapacke:amd64 (3.12.0-3) ... Setting up libtmglib-dev:amd64 (3.12.0-3) ... Setting up liblapacke-dev:amd64 (3.12.0-3) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (13.5) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64) Toolchain package versions: binutils_2.43-2 dpkg-dev_1.22.11 g++-14_14.2.0-2 gcc-14_14.2.0-2 libc6-dev_2.39-6 libstdc++-14-dev_14.2.0-2 libstdc++-14-dev-amd64-cross_14.2.0-1cross1 libstdc++6_14.2.0-2 libstdc++6-amd64-cross_14.2.0-1cross1 linux-libc-dev_6.10.4-1 Package versions: apt_2.9.8 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.21-2.1+b1 binutils_2.43-2 binutils-aarch64-linux-gnu_2.43-2 binutils-common_2.43-2 binutils-x86-64-linux-gnu_2.43-2 bsdextrautils_2.40.2-6 bsdutils_1:2.40.2-6 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-14_14.2.0-2 cpp-14-aarch64-linux-gnu_14.2.0-2 cpp-14-x86-64-linux-gnu_14.2.0-1cross1 cpp-aarch64-linux-gnu_4:14.1.0-2 cpp-x86-64-linux-gnu_4:14.1.0-2 cross-config_2.6.20 crossbuild-essential-amd64_12.10 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dpkg_1.22.11 dpkg-cross_2.6.20 dpkg-dev_1.22.11 dwz_0.15-1+b1 fakeroot_1.35.1-1.1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-14_14.2.0-2 g++-14-aarch64-linux-gnu_14.2.0-2 g++-14-x86-64-linux-gnu_14.2.0-1cross1 g++-aarch64-linux-gnu_4:14.1.0-2 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-14_14.2.0-2 gcc-14-aarch64-linux-gnu_14.2.0-2 gcc-14-base_14.2.0-2 gcc-14-cross-base_14.2.0-1cross1 gcc-14-x86-64-linux-gnu_14.2.0-1cross1 gcc-14-x86-64-linux-gnu-base_14.2.0-1cross1 gcc-aarch64-linux-gnu_4:14.1.0-2 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 help2man_1.49.3 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-2 libasan8-amd64-cross_14.2.0-1cross1 libatomic1_14.2.0-2 libatomic1-amd64-cross_14.2.0-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43-2 libblas-dev_3.12.0-3 libblas3_3.12.0-3 libblkid1_2.40.2-6 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc6_2.39-6 libc6-amd64-cross_2.39-4cross1 libc6-dev_2.39-6 libc6-dev-amd64-cross_2.39-4cross1 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcc1-0_14.2.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-3 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.43-2 libctf0_2.43-2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.11 libelf1t64_0.191-2 libfakeroot_1.35.1-1.1 libffi8_3.4.6-1 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.14.0-1 libfile-which-perl_1.27-2 libgcc-14-dev_14.2.0-2 libgcc-14-dev-amd64-cross_14.2.0-1cross1 libgcc-s1_14.2.0-2 libgcc-s1-amd64-cross_14.2.0-1cross1 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-2 libgomp1-amd64-cross_14.2.0-1cross1 libgpg-error0_1.50-3 libgprofng0_2.43-2 libhogweed6t64_3.10-1 libhwasan0_14.2.0-2 libhwasan0-amd64-cross_14.2.0-1cross1 libicu72_72.1-5 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14.2.0-2 libitm1-amd64-cross_14.2.0-1cross1 libjansson4_2.14-2+b2 liblapack-dev_3.12.0-3 liblapack3_3.12.0-3 liblapacke_3.12.0-3 liblapacke-dev_3.12.0-3 liblocale-gettext-perl_1.07-7 liblsan0_14.2.0-2 liblsan0-amd64-cross_14.2.0-1cross1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-6 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libnettle8t64_3.10-1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-16-0_10.42-4+b1 libpcre2-32-0_10.42-4+b1 libpcre2-8-0_10.42-4+b1 libpcre2-dev_10.42-4+b1 libpcre2-posix3_10.42-4+b1 libperl5.38t64_5.38.2-5 libpipeline1_1.5.7-2 libquadmath0_14.2.0-2 libquadmath0-amd64-cross_14.2.0-1cross1 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b4 libsframe1_2.43-2 libsmartcols1_2.40.2-6 libssl3t64_3.3.1-2 libstdc++-14-dev_14.2.0-2 libstdc++-14-dev-amd64-cross_14.2.0-1cross1 libstdc++6_14.2.0-2 libstdc++6-amd64-cross_14.2.0-1cross1 libsystemd0_256.4-3 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtmglib-dev_3.12.0-3 libtmglib3_3.12.0-3 libtool_2.4.7-7 libtsan2_14.2.0-2 libtsan2-amd64-cross_14.2.0-1cross1 libubsan1_14.2.0-2 libubsan1-amd64-cross_14.2.0-1cross1 libuchardet0_0.0.8-1+b1 libudev1_256.4-3 libunistring5_1.2-1 libuuid1_2.40.2-6 libxml-libxml-perl_2.0207+dfsg+really+2.0134-4 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libyaml-perl_1.31-1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.4-1 login_1:4.16.0-2+really2.40.2-6 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-3 mawk_1.3.4.20240622-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 patch_2.7.6-7 perl_5.38.2-5 perl-base_5.38.2-5 perl-modules-5.38_5.38.2-5 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sysvinit-utils_3.10-1 tar_1.35+dfsg-3 ucf_3.0043+nmu1 util-linux_2.40.2-6 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.7.0 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 3d222e3f22a904910f4f732143da1fcb759d9573 59204 phast_1.6+dfsg-6.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz bb1615d418e5b718c7ea1b9ecdef1d4fea54d1f38c18a10b9d53401ef460755a 59204 phast_1.6+dfsg-6.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz c7d85106e1e9f1afa300e6f0895ccc0f 59204 phast_1.6+dfsg-6.debian.tar.xz Dgit: c8e4e0f7a6923b7596177679f43f17cc3bdb9afd debian archive/debian/1.6+dfsg-6 https://git.dgit.debian.org/phast -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmaqnokUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoDjQ//W0UPexRQcQGcxlE9XSWKEPvGt/gv jGsCCLDU+d301nIMbqr+jdn8KJpakzT5q16d6oaZ53yWzOCHSgq7fawDluw/BX3j wS/e7y7IhHX10MKLDpWiAv7nu1BBphRXEiNjWduJEe/n9Qomwzf/Hl8jouZ/SWgV VuGMJW1XeHvA0BX4LSmWfMWvOc4nR9+4uh01V/c4Mu2kN4N/llgvysWWZWLuymE1 RmnuV+k1xNbGQBjPYt6Fr+kVgGpqL8BQ/L9MW2fAWwysxwgYCbFrLjyZC/hAyJ/2 1GfPU4WNfUJErbGAAmCcrBUCG2aO+DnErre+vYYIffGiFN+fVNnaySchR5ik+Ur6 1HBLEGzfMh2Xk+i01Y7sPi9G6UXXlLc/QaZk4Q20e66DBRL37o/Ant/o5aVfecOo 6ol1vz1343aY2vuceDmxUUqo31DoPxfomkzPCTgEkfOeiwte8SuA1pTyIjzeJdj6 Tl6mYnatU3TGTzt9t5m4098ziPmLqJljKiy3LpUXNUEusvH0yQRkqL9sejqoWfCl AhX0xHVF6/45y5hNEvt/oVnRZJqGRUSwlr58C0bsqE5m6gtiRYLEMJEcnzf83yI0 yKnHsLeWpt6gLAw+BtTOAyvzy/pqIEqw0ibGgU+zPQi2QUIq7y+9127tPRt/eYAo NpDWd7nT9la+fV8= =CgqX -----END PGP SIGNATURE----- gpgv: Signature made Wed Jul 31 20:28:57 2024 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-6.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-6.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 dpkg-source: info: applying gcc-14.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc 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' 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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c: In function ‘phast_fclose’: phast_misc.c:301:5: warning: pointer ‘f’ used after ‘fclose’ [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to ‘fclose’ here 300 | fclose(f); | ^~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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: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; | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, | ^~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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)); | ^~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ 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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/exoniphy/../../lib -o /<>/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/phastCons/../../lib -o /<>/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/phastOdds/../../lib -o /<>/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -L/<>/src/phastMotif/../../lib -o /<>/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/phyloFit/../../lib -o /<>/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/phyloBoot/../../lib -o /<>/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/phyloP/../../lib -o /<>/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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]; | ^~~~~~~ x86_64-linux-gnu-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,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 */ | ^~~~ x86_64-linux-gnu-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/util' mkdir -p ../doc/man/ Generating man pages... ../debian/help2man_wrapper: 1: ../bin/all_dists: Exec format error ../debian/help2man_wrapper: 1: ../bin/base_evolve: Exec format error ../debian/help2man_wrapper: 1: ../bin/chooseLines: Exec format error ../debian/help2man_wrapper: 1: ../bin/clean_genes: Exec format error ../debian/help2man_wrapper: 1: ../bin/consEntropy: Exec format error ../debian/help2man_wrapper: 1: ../bin/convert_coords: Exec format error ../debian/help2man_wrapper: 1: ../bin/display_rate_matrix: Exec format error ../debian/help2man_wrapper: 1: ../bin/draw_tree: Exec format error ../debian/help2man_wrapper: 1: ../bin/eval_predictions: Exec format error ../debian/help2man_wrapper: 1: ../bin/exoniphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_train: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_tweak: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelHistory: Exec format error ../debian/help2man_wrapper: 1: ../bin/maf_parse: Exec format error ../debian/help2man_wrapper: 1: ../bin/makeHKY: Exec format error ../debian/help2man_wrapper: 1: ../bin/modFreqs: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_diff: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_split: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/phast: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastBias: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastCons: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastMotif: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastOdds: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloBoot: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloP: Exec format error ../debian/help2man_wrapper: 1: ../bin/refeature: Exec format error ../debian/help2man_wrapper: 1: ../bin/stringiphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/treeGen: Exec format error ../debian/help2man_wrapper: 1: ../bin/tree_doctor: Exec format error Done. make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j1 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' 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 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-6_amd64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=any -O../phast_1.6+dfsg-6_amd64.buildinfo dpkg-genchanges --build=any -O../phast_1.6+dfsg-6_amd64.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 2024-08-13T09:18:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.6+dfsg-6_amd64.changes: ------------------------------- Format: 1.8 Date: Wed, 31 Jul 2024 22:24:23 +0200 Source: phast Binary: phast phast-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 1.6+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phast - phylogenetic analysis with space/time models Closes: 1075383 Changes: phast (1.6+dfsg-6) unstable; urgency=medium . * gcc-14.patch: fix build failure with gcc 14. (Closes: #1075383) * d/control: add myself to uploaders. * d/control: declare compliance to standards version 4.7.0. * d/p/clapack.patch: convert e acute to UTF-8. Checksums-Sha1: 35a7521d47ffb0022b95168e4aa142374316bbe1 28066952 phast-dbgsym_1.6+dfsg-6_amd64.deb 1aff5c04a6355ec7acb6dc3e1ec33fab67d68b89 5205 phast_1.6+dfsg-6_amd64.buildinfo b63b7b2db83a55640610f5eff2d78b1b6cae9489 3040528 phast_1.6+dfsg-6_amd64.deb Checksums-Sha256: 1b5182494241848217f0f648822c5972be2cb25794c7850db7e85f9f28771753 28066952 phast-dbgsym_1.6+dfsg-6_amd64.deb 7986515e1a6960e82b41f7a01fee1f168996cec43eac4b7401c12a8343cd0f27 5205 phast_1.6+dfsg-6_amd64.buildinfo 216439c410d2a75e11d2686d46ce1d35001d947ab60a8de505a8969f996ad2be 3040528 phast_1.6+dfsg-6_amd64.deb Files: 2950b698540351f1b06b26d5e720f2b3 28066952 debug optional phast-dbgsym_1.6+dfsg-6_amd64.deb 6515170e205064aa5ad85d279dfde998 5205 science optional phast_1.6+dfsg-6_amd64.buildinfo 6d099a3c427eb3e2940e72e8ac117ded 3040528 science optional phast_1.6+dfsg-6_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: amd64 Version: 1.6+dfsg-6 Checksums-Md5: 2950b698540351f1b06b26d5e720f2b3 28066952 phast-dbgsym_1.6+dfsg-6_amd64.deb 6d099a3c427eb3e2940e72e8ac117ded 3040528 phast_1.6+dfsg-6_amd64.deb Checksums-Sha1: 35a7521d47ffb0022b95168e4aa142374316bbe1 28066952 phast-dbgsym_1.6+dfsg-6_amd64.deb b63b7b2db83a55640610f5eff2d78b1b6cae9489 3040528 phast_1.6+dfsg-6_amd64.deb Checksums-Sha256: 1b5182494241848217f0f648822c5972be2cb25794c7850db7e85f9f28771753 28066952 phast-dbgsym_1.6+dfsg-6_amd64.deb 216439c410d2a75e11d2686d46ce1d35001d947ab60a8de505a8969f996ad2be 3040528 phast_1.6+dfsg-6_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Tue, 13 Aug 2024 09:18:49 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.21-2.1+b1), binutils (= 2.43-2), binutils-aarch64-linux-gnu (= 2.43-2), binutils-common (= 2.43-2), bsdextrautils (= 2.40.2-6), bsdutils (= 1:2.40.2-6), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-14 (= 14.2.0-2), cpp-14-aarch64-linux-gnu (= 14.2.0-2), cpp-aarch64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-2), g++-14-aarch64-linux-gnu (= 14.2.0-2), g++-aarch64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-14 (= 14.2.0-2), gcc-14-aarch64-linux-gnu (= 14.2.0-2), gcc-14-base (= 14.2.0-2), gcc-aarch64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), help2man (= 1.49.3), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-2), libatomic1 (= 14.2.0-2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43-2), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.2-6), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-2), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.43-2), libctf0 (= 2.43-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-14-dev (= 14.2.0-2), libgcc-s1 (= 14.2.0-2), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-2), libgprofng0 (= 2.43-2), libhwasan0 (= 14.2.0-2), libicu72 (= 72.1-5), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-2), libjansson4 (= 2.14-2+b2), liblapack-dev (= 3.12.0-3), liblapack3 (= 3.12.0-3), liblapacke (= 3.12.0-3), liblapacke-dev (= 3.12.0-3), liblocale-gettext-perl (= 1.07-7), liblsan0 (= 14.2.0-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-6), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-16-0 (= 10.42-4+b1), libpcre2-32-0 (= 10.42-4+b1), libpcre2-8-0 (= 10.42-4+b1), libpcre2-dev (= 10.42-4+b1), libpcre2-posix3 (= 10.42-4+b1), libperl5.38t64 (= 5.38.2-5), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.2.0-2), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b4), libsframe1 (= 2.43-2), libsmartcols1 (= 2.40.2-6), libssl3t64 (= 3.3.1-2), libstdc++-14-dev (= 14.2.0-2), libstdc++6 (= 14.2.0-2), libsystemd0 (= 256.4-3), libtinfo6 (= 6.5-2), libtmglib-dev (= 3.12.0-3), libtmglib3 (= 3.12.0-3), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-2), libubsan1 (= 14.2.0-2), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-3), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-6), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.4-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-3), mawk (= 1.3.4.20240622-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.38.2-5), perl-base (= 5.38.2-5), perl-modules-5.38 (= 5.38.2-5), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-1), tar (= 1.35+dfsg-3), util-linux (= 2.40.2-6), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1722457463" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast-dbgsym_1.6+dfsg-6_amd64.deb --------------------------------- new Debian package, version 2.0. size 28066952 bytes: control archive=2080 bytes. 1682 bytes, 12 lines control 3580 bytes, 34 lines md5sums Package: phast-dbgsym Source: phast Version: 1.6+dfsg-6 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 29416 Depends: phast (= 1.6+dfsg-6) Section: debug Priority: optional Description: debug symbols for phast Build-Ids: 08a1dd000aa7997769ae609b418d34731f4cc8be 0ac4de9a8ed1e0cd16dc12b18b87be4e31f61992 17689c7739ee40acdaea3d7c0627c7297117b804 1d79369460f1922288df824704c9f650cc6cef1c 26f0ca09984be35804b77daf9a3dc4ff92bcc49c 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root/root 0 2024-07-31 20:24 ./usr/share/doc/phast-dbgsym -> phast phast_1.6+dfsg-6_amd64.deb -------------------------- new Debian package, version 2.0. size 3040528 bytes: control archive=5528 bytes. 1112 bytes, 22 lines control 14785 bytes, 195 lines md5sums Package: phast Version: 1.6+dfsg-6 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 25696 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. . 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629 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/cftr25_hybrid.nh -rw-r--r-- root/root 680372 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/default-indels-no-cns.hmm -rw-r--r-- root/root 732444 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/default-indels.hmm -rw-r--r-- root/root 14434 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/default-no-cns.hmm -rw-r--r-- root/root 15378 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/default.hmm -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-1.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-2.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-3.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-4.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-5.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-6.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-1.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-2.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-3.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-4.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-5.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-6.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.cds3'ss.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-1.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-2.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-3.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-1.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-2.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-3.mod -rw-r--r-- root/root 392 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-4.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.start-1.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.start-2.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.start-3.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.stop-1.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.stop-2.mod -rw-r--r-- root/root 363 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/hky.stop-3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc4.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc5.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod -rw-r--r-- root/root 62237 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod -rw-r--r-- root/root 62237 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.cns.mod -rw-r--r-- root/root 49950 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod -rw-r--r-- root/root 49950 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod -rw-r--r-- root/root 49950 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod -rw-r--r-- root/root 49950 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod -rw-r--r-- root/root 49950 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc5.mod -rw-r--r-- root/root 49949 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod -rw-r--r-- root/root 529 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models -rw-r--r-- root/root 549 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-gc1 -rw-r--r-- root/root 549 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-gc2 -rw-r--r-- root/root 549 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-gc3 -rw-r--r-- root/root 549 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-gc4 -rw-r--r-- root/root 549 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-gc5 -rw-r--r-- root/root 523 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns -rw-r--r-- root/root 539 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns-gc1 -rw-r--r-- root/root 539 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns-gc2 -rw-r--r-- root/root 539 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns-gc3 -rw-r--r-- root/root 539 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns-gc4 -rw-r--r-- root/root 539 2024-07-31 20:24 ./usr/share/phast/data/exoniphy/models-no-cns-gc5 drwxr-xr-x root/root 0 2024-07-31 20:24 ./usr/share/phast/data/phastCons/ -rw-r--r-- root/root 103302 2024-07-31 20:24 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2024-07-31 20:24 ./usr/share/phast/data/phastCons/simple-coding.hmm lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1407 B] Get:5 copy:/<>/apt_archive ./ Packages [1458 B] Fetched 3480 B in 0s (195 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8t64 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8t64 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 12.6 MB of archives. After this operation, 52.9 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.3.1-2 [1346 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.66-1 [31.6 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1+b1 [48.0 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.43-8 [112 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.0-1 [843 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.43-8 [477 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.16.0-1 [2936 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b5 [63.8 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b1 [10.6 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-1 [12.1 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-1 [16.0 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b3 [22.3 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.64-1 [43.5 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.64-2+b3 [120 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1 [97.2 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.66-1 [217 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://mirror.einval.org/debian unstable/main arm64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b3 [35.2 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.46-1+b2 [13.6 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.38-1 [127 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b3 [31.2 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b3 [97.6 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.84-1 [23.7 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b3 [28.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libnumber-compare-perl all 0.03-3 [6332 B] Get:62 http://mirror.einval.org/debian unstable/main arm64 libtext-glob-perl all 0.11-3 [7676 B] Get:63 http://mirror.einval.org/debian unstable/main arm64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 6.46-1 [79.7 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:78 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1+b1 [328 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.088-1 [222 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.15~pre1-1 [37.7 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3 [48.9 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2+b1 [33.2 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:101 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.11-1 [141 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3+b2 [11.2 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.27-1+b2 [12.3 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.146-1 [56.2 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b3 [17.4 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b2 [11.4 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.636-1+b2 [41.6 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b2 [95.4 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b2 [97.6 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:114 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.44-1 [62.7 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.29-2 [26.6 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b3 [24.4 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b3 [8680 B] Get:118 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b2 [13.1 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2 [171 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b3 [72.2 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2+b2 [19.9 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.18-1 [114 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.89+ds-1+b1 [33.2 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.11-2 [58.9 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:130 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.118.0 [1055 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.6 MB in 0s (47.0 MB/s) Selecting previously unselected package netbase. (Reading database ... 17482 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.1-2_arm64.deb ... Unpacking openssl (3.3.1-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.66-1_arm64.deb ... Unpacking diffstat (1.66-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../005-libassuan0_2.5.6-1+b1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.6-1+b1) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../006-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package gpgconf. Preparing to unpack .../007-gpgconf_2.2.43-8_arm64.deb ... Unpacking gpgconf (2.2.43-8) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../008-libsqlite3-0_3.46.0-1_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.46.0-1) ... Selecting previously unselected package gpg. Preparing to unpack .../009-gpg_2.2.43-8_arm64.deb ... Unpacking gpg (2.2.43-8) ... Selecting previously unselected package iso-codes. Preparing to unpack .../010-iso-codes_4.16.0-1_all.deb ... Unpacking iso-codes (4.16.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../011-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../012-libapt-pkg-perl_0.1.40+b5_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40+b5) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-3+b1_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.004-1_all.deb ... Unpacking libdynaloader-functions-perl (0.004-1) ... Selecting previously unselected package libdevel-callchecker-perl:arm64. Preparing to unpack .../015-libdevel-callchecker-perl_0.009-1_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.009-1) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b3_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b3) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.64-1_arm64.deb ... Unpacking libvariable-magic-perl (0.64-1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.28-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.28-1) ... Selecting previously unselected package libberkeleydb-perl:arm64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b3_arm64.deb ... Unpacking libberkeleydb-perl:arm64 (0.64-2+b3) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.24-1_all.deb ... Unpacking libhtml-tagset-perl (3.24-1) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../026-liburi-perl_5.28-1_all.deb ... Unpacking liburi-perl (5.28-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../027-libhtml-parser-perl_3.83-1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.83-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../028-libcgi-pm-perl_4.66-1_all.deb ... Unpacking libcgi-pm-perl (4.66-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../029-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../030-libclass-inspector-perl_1.36-3_all.deb ... Unpacking libclass-inspector-perl (1.36-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../031-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../032-libclass-xsaccessor-perl_1.19-4+b3_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b3) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../033-libclone-perl_0.46-1+b2_arm64.deb ... Unpacking libclone-perl:arm64 (0.46-1+b2) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../034-libconfig-tiny-perl_2.30-1_all.deb ... Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../035-libparams-util-perl_1.102-3_arm64.deb ... Unpacking libparams-util-perl (1.102-3) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../036-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../037-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../038-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../039-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:arm64. Preparing to unpack .../040-libcpanel-json-xs-perl_4.38-1_arm64.deb ... Unpacking libcpanel-json-xs-perl:arm64 (4.38-1) ... Selecting previously unselected package libdevel-stacktrace-perl. 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Preparing to unpack .../129-lintian_2.118.0_all.deb ... Unpacking lintian (2.118.0) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:amd64. Preparing to unpack .../130-sbuild-build-depends-lintian-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b5) ... Setting up liblz1:arm64 (1.15~pre1-1) ... Setting up libberkeleydb-perl:arm64 (0.64-2+b3) ... Setting up plzip (1.11-2) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2+b2) ... Setting up libmouse-perl:arm64 (2.5.11-1) ... Setting up libdata-messagepack-perl (1.02-1+b3) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-1) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.46-1+b2) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libsub-identify-perl (0.14-3+b2) ... Setting up libcpanel-json-xs-perl:arm64 (4.38-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdevel-size-perl (0.84-1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:arm64 (3.46.0-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.89+ds-1+b1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:arm64 (2.10-3) ... Setting up libtime-moment-perl (0.44-2+b3) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:arm64 (2.5.6-1+b1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b2) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b3) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfile-find-rule-perl (0.34-3) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1+b2) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.66-1) ... Setting up libvariable-magic-perl (0.64-1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b1) ... Setting up libparams-util-perl (1.102-3) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:arm64 (0.27-1+b2) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.636-1+b2) ... Setting up libpath-tiny-perl (0.146-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b3) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.3.1-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b3) ... Setting up libperlio-gzip-perl (0.20-1+b3) ... Setting up readline-common (8.2-4) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b2) ... Setting up libmarkdown2:arm64 (2.2.7-2+b1) ... Setting up liburi-perl (5.28-1) ... Setting up iso-codes (4.16.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b3) ... Setting up libnet-ssleay-perl:arm64 (1.94-1+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1+b2) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.44-1) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsyntax-keyword-try-perl (0.29-2) ... Setting up libhtml-parser-perl:arm64 (3.83-1) ... Setting up gpgconf (2.2.43-8) ... Setting up libio-socket-ssl-perl (2.088-1) ... Setting up gpg (2.2.43-8) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b3) ... Setting up libcgi-pm-perl (4.66-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.28-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.77-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.18-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up lintian (2.118.0) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... Processing triggers for man-db (2.12.1-3) ... Not building database; man-db/auto-update is not 'true'. 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. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 212580 Build-Time: 337 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 51 Job: phast_1.6+dfsg-6 Lintian: pass Machine Architecture: arm64 Package: phast Package-Time: 446 Source-Version: 1.6+dfsg-6 Space: 212580 Status: successful Version: 1.6+dfsg-6 -------------------------------------------------------------------------------- Finished at 2024-08-13T09:18:51Z Build needed 00:07:26, 212580k disk space