sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | phast 1.7+dfsg-3 (i386) Mon, 03 Nov 2025 14:16:28 +0000 | +==============================================================================+ Package: phast Version: 1.7+dfsg-3 Source Version: 1.7+dfsg-3 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.FLs4Urshxn... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/phast-hsdzhY/resolver-9MFe6c' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [207 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.2 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.1 MB] Get:4 http://mirror.einval.org/debian unstable/main i386 Packages [9957 kB] Fetched 31.5 MB in 7s (4312 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... 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 1.7+dfsg-3 (dsc) [1494 B] Get:2 http://mirror.einval.org/debian unstable/main phast 1.7+dfsg-3 (tar) [1810 kB] Get:3 http://mirror.einval.org/debian unstable/main phast 1.7+dfsg-3 (diff) [58.9 kB] Fetched 1870 kB in 0s (22.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phast-hsdzhY/phast-1.7+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-hsdzhY' 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-i386:arm64, libc-dev:i386, libstdc++-dev:i386 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-i386:arm64, libc-dev:i386, libstdc++-dev:i386 dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 998:999 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [822 B] Get:5 copy:/<>/apt_archive ./ Packages [836 B] Fetched 2267 B in 0s (104 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-i686-linux-gnu bsdextrautils cpp-15-i686-linux-gnu cpp-i686-linux-gnu crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-i686-linux-gnu g++-i686-linux-gnu gcc-15-base:i386 gcc-15-cross-base gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libblas-dev:i386 libblas3:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgcc-15-dev:i386 libgcc-15-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5:i386 libgomp1:i386 libgomp1-i386-cross libitm1:i386 libitm1-i386-cross liblapack-dev:i386 liblapack3:i386 liblapacke:i386 liblapacke-dev:i386 liblocale-gettext-perl libmagic-mgc libmagic1t64 libpcre2-16-0:i386 libpcre2-32-0:i386 libpcre2-8-0:i386 libpcre2-dev:i386 libpcre2-posix3:i386 libpipeline1 libquadmath0:i386 libquadmath0-i386-cross libstdc++-15-dev:i386 libstdc++-15-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libtmglib-dev:i386 libtmglib3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-i386-cross m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc:i386 glibc-doc:i386 libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386 manpages-dev:i386 libstdc++-15-doc:i386 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:i386 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-15-i686-linux-gnu cpp-i686-linux-gnu crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-15-i686-linux-gnu g++-i686-linux-gnu gcc-15-base:i386 gcc-15-cross-base gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base gcc-i686-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libblas-dev:i386 libblas3:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgcc-15-dev:i386 libgcc-15-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5:i386 libgomp1:i386 libgomp1-i386-cross libitm1:i386 libitm1-i386-cross liblapack-dev:i386 liblapack3:i386 liblapacke:i386 liblapacke-dev:i386 liblocale-gettext-perl libmagic-mgc libmagic1t64 libpcre2-16-0:i386 libpcre2-32-0:i386 libpcre2-8-0:i386 libpcre2-dev:i386 libpcre2-posix3:i386 libpipeline1 libquadmath0:i386 libquadmath0-i386-cross libstdc++-15-dev:i386 libstdc++-15-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libtmglib-dev:i386 libtmglib3:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-i386-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:i386 sensible-utils 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 99.3 MB of archives. After this operation, 410 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+b1 [15.2 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 gcc-15-i686-linux-gnu-base arm64 15.2.0-7cross1 [53.5 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 cpp-15-i686-linux-gnu arm64 15.2.0-7cross1 [11.3 MB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-i686-linux-gnu arm64 4:15.2.0-4 [5288 B] Get:21 http://mirror.einval.org/debian unstable/main arm64 binutils-i686-linux-gnu arm64 2.45-8 [1508 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-7cross1 [48.9 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libc6-i386-cross all 2.41-11cross1 [1424 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-i386-cross all 15.2.0-7cross1 [87.0 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libgomp1-i386-cross all 15.2.0-7cross1 [139 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libitm1-i386-cross all 15.2.0-7cross1 [27.5 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libatomic1-i386-cross all 15.2.0-7cross1 [7496 B] Get:28 http://mirror.einval.org/debian unstable/main arm64 libasan8-i386-cross all 15.2.0-7cross1 [2642 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-i386-cross all 15.2.0-7cross1 [734 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libubsan1-i386-cross all 15.2.0-7cross1 [1080 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-i386-cross all 15.2.0-7cross1 [229 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-i386-cross all 15.2.0-7cross1 [2621 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 gcc-15-i686-linux-gnu arm64 15.2.0-7cross1 [21.8 MB] Get:34 http://mirror.einval.org/debian unstable/main arm64 gcc-i686-linux-gnu arm64 4:15.2.0-4 [1444 B] Get:35 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-i386-cross all 6.12.38-1cross1 [2470 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-i386-cross all 2.41-11cross1 [1806 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-i386-cross all 15.2.0-7cross1 [2489 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 g++-15-i686-linux-gnu arm64 15.2.0-7cross1 [12.3 MB] Get:39 http://mirror.einval.org/debian unstable/main arm64 g++-i686-linux-gnu arm64 4:15.2.0-4 [1192 B] Get:40 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-i386 all 12.12 [3544 B] Get:41 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:47 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.37.1.2-1 [29.7 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.37.1.2-1 [75.4 kB] Get:57 http://mirror.einval.org/debian unstable/main i386 gcc-15-base i386 15.2.0-7 [53.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get:59 http://mirror.einval.org/debian unstable/main i386 libgcc-s1 i386 15.2.0-7 [87.0 kB] Get:60 http://mirror.einval.org/debian unstable/main i386 libc6 i386 2.41-12 [2720 kB] Get:61 http://mirror.einval.org/debian unstable/main i386 libasan8 i386 15.2.0-7 [2651 kB] Get:62 http://mirror.einval.org/debian unstable/main i386 libatomic1 i386 15.2.0-7 [7744 B] Get:63 http://mirror.einval.org/debian unstable/main i386 libblas3 i386 3.12.1-7 [149 kB] Get:64 http://mirror.einval.org/debian unstable/main i386 libblas-dev i386 3.12.1-7 [161 kB] Get:65 http://mirror.einval.org/debian unstable/main i386 libcrypt1 i386 1:4.4.38-1 [95.7 kB] Get:66 http://mirror.einval.org/debian unstable/main i386 libcrypt-dev i386 1:4.4.38-1 [126 kB] Get:67 http://mirror.einval.org/debian unstable/main i386 libc6-dev i386 2.41-12 [1809 kB] Get:68 http://mirror.einval.org/debian unstable/main i386 libgomp1 i386 15.2.0-7 [142 kB] Get:69 http://mirror.einval.org/debian unstable/main i386 libitm1 i386 15.2.0-7 [28.0 kB] Get:70 http://mirror.einval.org/debian unstable/main i386 libstdc++6 i386 15.2.0-7 [781 kB] Get:71 http://mirror.einval.org/debian unstable/main i386 libubsan1 i386 15.2.0-7 [1081 kB] Get:72 http://mirror.einval.org/debian unstable/main i386 libquadmath0 i386 15.2.0-7 [229 kB] Get:73 http://mirror.einval.org/debian unstable/main i386 libgcc-15-dev i386 15.2.0-7 [2625 kB] Get:74 http://mirror.einval.org/debian unstable/main i386 libgfortran5 i386 15.2.0-7 [729 kB] Get:75 http://mirror.einval.org/debian unstable/main i386 liblapack3 i386 3.12.1-7 [2160 kB] Get:76 http://mirror.einval.org/debian unstable/main i386 liblapack-dev i386 3.12.1-7 [4394 kB] Get:77 http://mirror.einval.org/debian unstable/main i386 libtmglib3 i386 3.12.1-7 [120 kB] Get:78 http://mirror.einval.org/debian unstable/main i386 liblapacke i386 3.12.1-7 [376 kB] Get:79 http://mirror.einval.org/debian unstable/main i386 libtmglib-dev i386 3.12.1-7 [125 kB] Get:80 http://mirror.einval.org/debian unstable/main i386 liblapacke-dev i386 3.12.1-7 [382 kB] Get:81 http://mirror.einval.org/debian unstable/main i386 libpcre2-16-0 i386 10.46-1 [278 kB] Get:82 http://mirror.einval.org/debian unstable/main i386 libpcre2-32-0 i386 10.46-1 [267 kB] Get:83 http://mirror.einval.org/debian unstable/main i386 libpcre2-8-0 i386 10.46-1 [296 kB] Get:84 http://mirror.einval.org/debian unstable/main i386 libpcre2-posix3 i386 10.46-1 [64.0 kB] Get:85 http://mirror.einval.org/debian unstable/main i386 libpcre2-dev i386 10.46-1 [857 kB] Get:86 http://mirror.einval.org/debian unstable/main i386 libstdc++-15-dev i386 15.2.0-7 [2507 kB] Preconfiguring packages ... Fetched 99.3 MB in 1s (88.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12024 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. 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Unpacking sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Setting up binutils-i686-linux-gnu (2.45-8) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up file (1:5.46-5) ... Setting up libfakeroot:arm64 (1.37.1.2-1) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up fakeroot (1.37.1.2-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up linux-libc-dev-i386-cross (6.12.38-1cross1) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up gcc-15-i686-linux-gnu-base:arm64 (15.2.0-7cross1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libc6-i386-cross (2.41-11cross1) ... Setting up gcc-15-cross-base (15.2.0-7cross1) ... Setting up gcc-15-base:i386 (15.2.0-7) ... Setting up libquadmath0-i386-cross (15.2.0-7cross1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up libatomic1-i386-cross (15.2.0-7cross1) ... Setting up cpp-15-i686-linux-gnu (15.2.0-7cross1) ... Setting up libgomp1-i386-cross (15.2.0-7cross1) ... Setting up libc6-dev-i386-cross (2.41-11cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up libgcc-s1-i386-cross (15.2.0-7cross1) ... Setting up dh-autoreconf (21) ... Setting up libitm1-i386-cross (15.2.0-7cross1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up cpp-i686-linux-gnu (4:15.2.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasan8-i386-cross (15.2.0-7cross1) ... Setting up libstdc++6-i386-cross (15.2.0-7cross1) ... Setting up debhelper (13.28) ... Setting up libubsan1-i386-cross (15.2.0-7cross1) ... Setting up libgcc-15-dev-i386-cross (15.2.0-7cross1) ... Setting up libstdc++-15-dev-i386-cross (15.2.0-7cross1) ... Setting up gcc-15-i686-linux-gnu (15.2.0-7cross1) ... Setting up g++-15-i686-linux-gnu (15.2.0-7cross1) ... Setting up gcc-i686-linux-gnu (4:15.2.0-4) ... Setting up g++-i686-linux-gnu (4:15.2.0-4) ... Setting up crossbuild-essential-i386 (12.12) ... Setting up libgcc-s1:i386 (15.2.0-7) ... Setting up libc6:i386 (2.41-12) ... Setting up libasan8:i386 (15.2.0-7) ... Setting up libstdc++6:i386 (15.2.0-7) ... Setting up libitm1:i386 (15.2.0-7) ... Setting up libcrypt1:i386 (1:4.4.38-1) ... Setting up libgomp1:i386 (15.2.0-7) ... Setting up libpcre2-16-0:i386 (10.46-1) ... Setting up libpcre2-32-0:i386 (10.46-1) ... Setting up libblas3:i386 (3.12.1-7) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libquadmath0:i386 (15.2.0-7) ... Setting up libatomic1:i386 (15.2.0-7) ... Setting up libpcre2-8-0:i386 (10.46-1) ... Setting up libgfortran5:i386 (15.2.0-7) ... Setting up libubsan1:i386 (15.2.0-7) ... Setting up libpcre2-posix3:i386 (10.46-1) ... Setting up libcrypt-dev:i386 (1:4.4.38-1) ... Setting up libc6-dev:i386 (2.41-12) ... Setting up libblas-dev:i386 (3.12.1-7) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up liblapack3:i386 (3.12.1-7) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libgcc-15-dev:i386 (15.2.0-7) ... Setting up libpcre2-dev:i386 (10.46-1) ... Setting up libtmglib3:i386 (3.12.1-7) ... Setting up libstdc++-15-dev:i386 (15.2.0-7) ... Setting up liblapack-dev:i386 (3.12.1-7) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up liblapacke:i386 (3.12.1-7) ... Setting up libtmglib-dev:i386 (3.12.1-7) ... Setting up liblapacke-dev:i386 (3.12.1-7) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-37-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) arm64 (aarch64) Toolchain package versions: binutils_2.45-8 dpkg-dev_1.22.21 g++-15_15.2.0-7 gcc-15_15.2.0-7 libc6-dev_2.41-12 libstdc++-15-dev_15.2.0-7 libstdc++-15-dev-i386-cross_15.2.0-7cross1 libstdc++6_15.2.0-7 libstdc++6-i386-cross_15.2.0-7cross1 linux-libc-dev_6.17.6-1 Package versions: apt_3.1.11 apt-utils_3.1.11 autoconf_2.72-3.1 automake_1:1.18.1-2 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.3-1 binutils_2.45-8 binutils-aarch64-linux-gnu_2.45-8 binutils-common_2.45-8 binutils-i686-linux-gnu_2.45-8 bsdextrautils_2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-7 cpp-15-aarch64-linux-gnu_15.2.0-7 cpp-15-i686-linux-gnu_15.2.0-7cross1 cpp-aarch64-linux-gnu_4:15.2.0-4 cpp-i686-linux-gnu_4:15.2.0-4 crossbuild-essential-i386_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 fakeroot_1.37.1.2-1 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-7 g++-15-aarch64-linux-gnu_15.2.0-7 g++-15-i686-linux-gnu_15.2.0-7cross1 g++-aarch64-linux-gnu_4:15.2.0-4 g++-i686-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-7 gcc-15-aarch64-linux-gnu_15.2.0-7 gcc-15-base_15.2.0-7 gcc-15-cross-base_15.2.0-7cross1 gcc-15-i686-linux-gnu_15.2.0-7cross1 gcc-15-i686-linux-gnu-base_15.2.0-7cross1 gcc-aarch64-linux-gnu_4:15.2.0-4 gcc-i686-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 help2man_1.49.3+b1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.11 libarchive-zip-perl_1.68-1 libasan8_15.2.0-7 libasan8-i386-cross_15.2.0-7cross1 libatomic1_15.2.0-7 libatomic1-i386-cross_15.2.0-7cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbinutils_2.45-8 libblas-dev_3.12.1-7 libblas3_3.12.1-7 libblkid1_2.41.2-4 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libc6-dev-i386-cross_2.41-11cross1 libc6-i386-cross_2.41-11cross1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-7 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-8 libctf0_2.45-8 libdb5.3t64_5.3.28+dfsg2-10 libdebconfclient0_0.280 libdebhelper-perl_13.28 libdpkg-perl_1.22.21 libelf1t64_0.194-1 libfakeroot_1.37.1.2-1 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-7 libgcc-15-dev-i386-cross_15.2.0-7cross1 libgcc-s1_15.2.0-7 libgcc-s1-i386-cross_15.2.0-7cross1 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgfortran5_15.2.0-7 libgmp10_2:6.3.0+dfsg-5 libgomp1_15.2.0-7 libgomp1-i386-cross_15.2.0-7cross1 libgprofng0_2.45-8 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-7 libisl23_0.27-1 libitm1_15.2.0-7 libitm1-i386-cross_15.2.0-7cross1 libjansson4_2.14-2+b3 liblapack-dev_3.12.1-7 liblapack3_3.12.1-7 liblapacke_3.12.1-7 liblapacke-dev_3.12.1-7 liblocale-gettext-perl_1.07-7+b1 liblsan0_15.2.0-7 liblz4-1_1.10.0-6 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libnettle8t64_3.10.2-1 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-16-0_10.46-1 libpcre2-32-0_10.46-1 libpcre2-8-0_10.46-1 libpcre2-dev_10.46-1 libpcre2-posix3_10.46-1 libperl5.40_5.40.1-6 libpipeline1_1.5.8-1 libquadmath0_15.2.0-7 libquadmath0-i386-cross_15.2.0-7cross1 libseccomp2_2.6.0-2 libselinux1_3.9-2 libsframe2_2.45-8 libsmartcols1_2.41.2-4 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-7 libstdc++-15-dev-i386-cross_15.2.0-7cross1 libstdc++6_15.2.0-7 libstdc++6-i386-cross_15.2.0-7cross1 libsystemd0_258.1-2 libtinfo6_6.5+20250216-2 libtmglib-dev_3.12.1-7 libtmglib3_3.12.1-7 libtool_2.5.4-7 libtsan2_15.2.0-7 libubsan1_15.2.0-7 libubsan1-i386-cross_15.2.0-7cross1 libuchardet0_0.0.8-2 libudev1_258.1-2 libunistring5_1.3-2 libuuid1_2.41.2-4 libxml2-16_2.15.1+dfsg-0.3 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.6-1 linux-libc-dev-i386-cross_6.12.38-1cross1 login_1:4.16.0-2+really2.41.2-4 login.defs_1:4.18.0-2 m4_1.4.20-2 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.4-1 patch_2.8-2 perl_5.40.1-6 perl-base_5.40.1-6 perl-modules-5.40_5.40.1-6 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1+b1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b1 sensible-utils_0.0.26 sqv_1.3.0-3 sysvinit-utils_3.15-5 tar_1.35+dfsg-3.1 util-linux_2.41.2-4 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.7+dfsg-3 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: 718957dc45971f6f249cecd243ada1efe4034eb5 1809648 phast_1.7+dfsg.orig.tar.xz abf8664fa05eca5968067a66a9ec30ba453716fe 58908 phast_1.7+dfsg-3.debian.tar.xz Checksums-Sha256: 56131c493daa49de2cb2031d620e056e7f10a361284798716274c0d006ff2c0e 1809648 phast_1.7+dfsg.orig.tar.xz 237cebccfa1ced69dad0c6bfe4dceefdc242977169b7e295f69ee43a70a41438 58908 phast_1.7+dfsg-3.debian.tar.xz Files: fb92e0faf0f68e257f20633a5832f530 1809648 phast_1.7+dfsg.orig.tar.xz b7bd056a2b03ec248e1dd7d7dfd32ef0 58908 phast_1.7+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaM3SFxIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtosJgD/VrXhuRFaqNB1DAlKit4YMNs10+6dlwVH jvomLQVgd8sA/A2vd1g8zrRQDnTln+Gb2DCq6oMD0UYpO+F61J+D7ugN =jkEn -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting phast in /<> dpkg-source: info: unpacking phast_1.7+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.7+dfsg-3.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 pcre2.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying make.patch dpkg-source: info: applying gcc-15.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.i386 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 -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.7+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-architecture: warning: specified GNU system type i686-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 i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean cd src && /usr/bin/make clean make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/lib' cat: /<>/src/lib/../version: No such file or directory for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && /usr/bin/make clean ; done make[4]: Entering directory '/<>/src/lib/base' cat: /<>/src/lib/base/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' cat: /<>/src/lib/msa/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' cat: /<>/src/lib/feature/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' cat: /<>/src/lib/hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' cat: /<>/src/lib/phylo/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' cat: /<>/src/lib/phylo_hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' cat: /<>/src/lib/motif/../version: No such file or directory 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' cat: /<>/src/dless/../version: No such file or directory 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' cat: /<>/src/exoniphy/../version: No such file or directory rm -f *.o *.help /<>/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' cat: /<>/src/phastCons/../version: No such file or directory rm -f *.o /<>/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' cat: /<>/src/phastOdds/../version: No such file or directory rm -f *.o *.help /<>/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' cat: /<>/src/phastMotif/../version: No such file or directory rm -f *.o /<>/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' cat: /<>/src/phyloFit/../version: No such file or directory rm -f *.o /<>/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' cat: /<>/src/phyloBoot/../version: No such file or directory rm -f *.o *.help /<>/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' cat: /<>/src/phyloP/../version: No such file or directory rm -f *.o /<>/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' cat: /<>/src/prequel/../version: No such file or directory 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' cat: /<>/src/util/../version: No such file or directory 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=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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:673:46: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 673 | 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); | ^~~~~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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:1011:1: note: expected ‘PCRE2_SPTR8’ {aka ‘const unsigned char *’} but argument is of type ‘char *’ 1011 | 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; | ^~~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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, | ^~~~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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)); | ^~ i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/dless/../..\" -fno-strict-aliasing -c phast_bd_phylo_hmm.c -o phast_bd_phylo_hmm.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition i686-linux-gnu-gcc -L/<>/src/dless/../../lib -o /<>/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition dlessP.c: In function ‘do_p_values’: dlessP.c:199:45: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 199 | pcre2_compile_context *id_re = str_re_new(".*id \"([^\"]*)\""); | ^~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/trees.h:25, from /<>/src/../include/phast/tree_model.h:26, from /<>/src/../include/phast/bd_phylo_hmm.h:22, from dlessP.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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -L/<>/src/dless/../../lib -o /<>/src/dless/../../bin/dlessP dlessP.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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' i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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, | ^~~~~~~~~~~~~~~ i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c phast_simplex_grid.c -o phast_simplex_grid.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c phast_pbs_code.c -o phast_pbs_code.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition phast_pbs_code.c: In function ‘pbs_new_from_file’: phast_pbs_code.c:88:48: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 88 | pcre2_compile_context *nrows_re = str_re_new("##NROWS[[:space:]]*=[[:space:]]*([0-9]+)"), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/pbs_code.h:8, from phast_pbs_code.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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_pbs_code.c:89:32: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 89 | *dimension_re = str_re_new("##DIMENSION[[: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_pbs_code.c:90:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 90 | *nbytes_re = str_re_new("##NBYTES[[: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_pbs_code.c:91:31: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 91 | *codesize_re = str_re_new("##CODESIZE[[: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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-linux-gnu-gcc -L/<>/src/prequel/../../lib -o /<>/src/prequel/../../bin/pbsDecode pbsDecode.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition i686-linux-gnu-gcc -L/<>/src/prequel/../../lib -o /<>/src/prequel/../../bin/pbsEncode pbsEncode.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition i686-linux-gnu-gcc -L/<>/src/prequel/../../lib -o /<>/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition i686-linux-gnu-gcc -L/<>/src/prequel/../../lib -o /<>/src/prequel/../../bin/pbsTrain pbsTrain.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition prequel.c: In function ‘main’: prequel.c:285:32: warning: ‘.bin’ directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 285 | sprintf(out_fname, "%s.%s.bin", out_root, n->name); | ^~~~ In file included from /usr/i686-linux-gnu/include/stdio.h:970, from prequel.c:11: In function ‘sprintf’, inlined from ‘main’ at prequel.c:285:7: /usr/i686-linux-gnu/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 6 or more bytes (assuming 261) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function ‘main’: prequel.c:253:32: warning: ‘.fa’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 253 | sprintf(out_fname, "%s.%s.fa", out_root, n->name); | ^~~ In function ‘sprintf’, inlined from ‘main’ at prequel.c:253:7: /usr/i686-linux-gnu/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 5 or more bytes (assuming 260) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ prequel.c: In function ‘main’: prequel.c:203:32: warning: ‘.probs’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 203 | sprintf(out_fname, "%s.%s.probs", out_root, n->name); | ^~~~~~ In function ‘sprintf’, inlined from ‘main’ at prequel.c:203:7: /usr/i686-linux-gnu/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 8 or more bytes (assuming 263) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -L/<>/src/prequel/../../lib -o /<>/src/prequel/../../bin/prequel prequel.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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]; | ^~~~~~~ i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 i686-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 i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -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 */ | ^~~~ i686-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/dless: Exec format error ../debian/help2man_wrapper: 1: ../bin/dlessP: 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/pbsDecode: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsEncode: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsScoreMatrix: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsTrain: 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/prequel: 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-1.7\+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_1.7+dfsg-3_i386.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.7+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=any -O../phast_1.7+dfsg-3_i386.buildinfo dpkg-genchanges --build=any -O../phast_1.7+dfsg-3_i386.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 2025-11-03T14:23:56Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands | +------------------------------------------------------------------------------+ rm -Rf /<>/ ------------------------------------------ I: Finished running 'rm -Rf /<>/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.7+dfsg-3_i386.changes: ------------------------------ Format: 1.8 Date: Sat, 20 Sep 2025 03:01:50 +0530 Source: phast Binary: phast phast-dbgsym Built-For-Profiles: cross nocheck Architecture: i386 Version: 1.7+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: phast - phylogenetic analysis with space/time models Closes: 1097575 Changes: phast (1.7+dfsg-3) unstable; urgency=medium . * Team Upload. * Fixup FTBFS with gcc-15 (Closes: #1097575) Checksums-Sha1: f3b8b13bafced36aaccb4bd96a6e9a18704d7ffe 34406088 phast-dbgsym_1.7+dfsg-3_i386.deb b4d1451c55d3517e1313e57aae6895d9f91286bd 5116 phast_1.7+dfsg-3_i386.buildinfo 264e0ac3732d78a194df62441224039632d2d682 3644384 phast_1.7+dfsg-3_i386.deb Checksums-Sha256: 8f144954d483a3dbe5a95e19c181456f80f9f3ad416fc21f41b8b17f317f415c 34406088 phast-dbgsym_1.7+dfsg-3_i386.deb 069b1c426b251ead4b467651a7d9a4f9243f6d92eedcf1840e50aea6ca118887 5116 phast_1.7+dfsg-3_i386.buildinfo 1bbb783459f79bdc78d81285c70fb60fa65a425759252680c120b3ed85fd35ef 3644384 phast_1.7+dfsg-3_i386.deb Files: 8de4572930cd5864c5e97c1909836961 34406088 debug optional phast-dbgsym_1.7+dfsg-3_i386.deb 64658f02e42f1c412bbf74eb90d715e5 5116 science optional phast_1.7+dfsg-3_i386.buildinfo 23dcdbdd1f7e04bf5334131278641e8b 3644384 science optional phast_1.7+dfsg-3_i386.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: i386 Version: 1.7+dfsg-3 Checksums-Md5: 8de4572930cd5864c5e97c1909836961 34406088 phast-dbgsym_1.7+dfsg-3_i386.deb 23dcdbdd1f7e04bf5334131278641e8b 3644384 phast_1.7+dfsg-3_i386.deb Checksums-Sha1: f3b8b13bafced36aaccb4bd96a6e9a18704d7ffe 34406088 phast-dbgsym_1.7+dfsg-3_i386.deb 264e0ac3732d78a194df62441224039632d2d682 3644384 phast_1.7+dfsg-3_i386.deb Checksums-Sha256: 8f144954d483a3dbe5a95e19c181456f80f9f3ad416fc21f41b8b17f317f415c 34406088 phast-dbgsym_1.7+dfsg-3_i386.deb 1bbb783459f79bdc78d81285c70fb60fa65a425759252680c120b3ed85fd35ef 3644384 phast_1.7+dfsg-3_i386.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Mon, 03 Nov 2025 14:23:53 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-2), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.3-1), binutils (= 2.45-8), binutils-aarch64-linux-gnu (= 2.45-8), binutils-common (= 2.45-8), bsdextrautils (= 2.41.2-4), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-15 (= 15.2.0-7), cpp-15-aarch64-linux-gnu (= 15.2.0-7), cpp-aarch64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-7), g++-15-aarch64-linux-gnu (= 15.2.0-7), g++-aarch64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-15 (= 15.2.0-7), gcc-15-aarch64-linux-gnu (= 15.2.0-7), gcc-15-base (= 15.2.0-7), gcc-aarch64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.12-1), groff-base (= 1.23.0-9), gzip (= 1.13-1), help2man (= 1.49.3+b1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-7), libatomic1 (= 15.2.0-7), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1), libbinutils (= 2.45-8), libblas-dev (= 3.12.1-7), libblas3 (= 3.12.1-7), libblkid1 (= 2.41.2-4), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-7), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-8), libctf0 (= 2.45-8), libdb5.3t64 (= 5.3.28+dfsg2-10), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.28), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.194-1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-7), libgcc-s1 (= 15.2.0-7), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgfortran5 (= 15.2.0-7), libgmp10 (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-7), libgprofng0 (= 2.45-8), libhwasan0 (= 15.2.0-7), libisl23 (= 0.27-1), libitm1 (= 15.2.0-7), libjansson4 (= 2.14-2+b3), liblapack-dev (= 3.12.1-7), liblapack3 (= 3.12.1-7), liblapacke (= 3.12.1-7), liblapacke-dev (= 3.12.1-7), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 15.2.0-7), liblzma5 (= 5.8.1-2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-4), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-16-0 (= 10.46-1), libpcre2-32-0 (= 10.46-1), libpcre2-8-0 (= 10.46-1), libpcre2-dev (= 10.46-1), libpcre2-posix3 (= 10.46-1), libperl5.40 (= 5.40.1-6), libpipeline1 (= 1.5.8-1), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.9-2), libsframe2 (= 2.45-8), libsmartcols1 (= 2.41.2-4), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-7), libstdc++6 (= 15.2.0-7), libsystemd0 (= 258.1-2), libtinfo6 (= 6.5+20250216-2), libtmglib-dev (= 3.12.1-7), libtmglib3 (= 3.12.1-7), libtool (= 2.5.4-7), libtsan2 (= 15.2.0-7), libubsan1 (= 15.2.0-7), libuchardet0 (= 0.0.8-2), libudev1 (= 258.1-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-4), libxml2-16 (= 2.15.1+dfsg-0.3), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.6-1), m4 (= 1.4.20-2), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.40.1-6), perl-base (= 5.40.1-6), perl-modules-5.40 (= 5.40.1-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1+b1), sed (= 4.9-2+b1), sensible-utils (= 0.0.26), sysvinit-utils (= 3.15-5), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.2-4), xz-utils (= 5.8.1-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) 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="1758317510" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast-dbgsym_1.7+dfsg-3_i386.deb -------------------------------- new Debian package, version 2.0. size 34406088 bytes: control archive=2392 bytes. 1968 bytes, 12 lines control 4320 bytes, 41 lines md5sums Package: phast-dbgsym Source: phast Version: 1.7+dfsg-3 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 42116 Depends: phast (= 1.7+dfsg-3) Section: debug Priority: optional Description: debug symbols for phast Build-Ids: 014d946d4b7b5790b23ea0cc08c684521e5e2372 028466768dd6d1b037064bcd18b60fd9a0f81217 066d936b0cb88b4cccbe5aa202cb64c3438cfda6 125e4170bc110a5bf19096c58af5dab0cb47b5cb 157bc3439f96ee6a37fbbc8d33e756ac53aca0a0 1f2124a3878e5fee94d1372d8a8a6599451841b5 20c3ad77906734876e923e7b36e5ce4151c7e849 233664d756a34f2ee6c5a41cc96c819b892b1db5 243f0a46aac5790ae04744bfe075701c14fe5dbf 280b7da76bb0f36931a41ab5b66ee46c940724a2 2ea5e7e0055e3db915d30f956af503aa8109aacc 432f08ae8a850922f775e214687db27e4c7d0722 45a02c47b8d2bed7b84037b95072b3f611cd1a11 54c5a0ec907ea4c3c70e362b8eb523aad2219ca5 64f6ef1b776bfd6fcc29fb423b0cf88c39ade33f 6fd6c292d0b3f42060b7404b34fa95ad59de9d18 8781cd787ca157b1d15be862097b814dc627c555 9062145cf85e55afe7d2358dd380129dd3ac3306 91a0a0ad20d3f442e0e952de48c1b41f64d44593 9242a993a773a07412c2865a1844be2cb7b055d9 98e0e8294192be7ed8678a37d87f3ea7dd5ddd42 9ff5b35746237ed2e07056726dfe0a393800e794 a3091da547ecf5853373c4abb58b1af38a0986ec b194e3878b3427eb3b72454389cbf247da83b6c5 be08df02ab367ed514048a26add3b2aead2487d7 c36dd42f6834c6443fc5d264dcdd788e374ffd07 c50a56d575488503ee6b2472d8537a7caf95f1bb ceaba4ad3af40f54081fcf59dddda5eaa5baa5f0 ceb461e0ffd3531ee687decd68ebfef48c54c820 d0b7c3955ac510fa6d9649ff5693e9a7dd66eb28 d2bb03bae3e6cf7a3401051bb2c8f3aed8a70784 d3e4ce88a2643b39ad50cc484974fd54944de323 e156c1a5272f9b7793c9028fef45cecbaef81665 e335f31fd2987617d4deed5bdc618f5642154e4f 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libc6 (>= 2.38), liblapack3 | liblapack.so.3, libpcre2-8-0 (>= 10.22) Section: science Priority: optional Homepage: http://compgen.cshl.edu/phast/ Description: phylogenetic analysis with space/time models PHAST is a software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. . PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison). drwxr-xr-x root/root 0 2025-09-19 21:31 ./ drwxr-xr-x root/root 0 2025-09-19 21:31 ./usr/ drwxr-xr-x root/root 0 2025-09-19 21:31 ./usr/bin/ -rwxr-xr-x root/root 685676 2025-09-19 21:31 ./usr/bin/all_dists -rwxr-xr-x root/root 716148 2025-09-19 21:31 ./usr/bin/base_evolve -rwxr-xr-x root/root 681580 2025-09-19 21:31 ./usr/bin/chooseLines -rwxr-xr-x root/root 720964 2025-09-19 21:31 ./usr/bin/clean_genes -rwxr-xr-x root/root 683372 2025-09-19 21:31 ./usr/bin/consEntropy -rwxr-xr-x root/root 685676 2025-09-19 21:31 ./usr/bin/convert_coords -rwxr-xr-x root/root 697964 2025-09-19 21:31 ./usr/bin/display_rate_matrix -rwxr-xr-x root/root 809100 2025-09-19 21:31 ./usr/bin/dless -rwxr-xr-x root/root 867636 2025-09-19 21:31 ./usr/bin/dlessP -rwxr-xr-x root/root 681580 2025-09-19 21:31 ./usr/bin/draw_tree -rwxr-xr-x root/root 689772 2025-09-19 21:31 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./usr/share/phast/data/exoniphy/mammals/default.hmm -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-1.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-2.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-3.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-4.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-5.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-6.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-1.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-2.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-3.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-4.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-5.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.5'splice-6.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.cds3'ss.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-1.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-2.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-3.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-1.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-2.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-3.mod -rw-r--r-- root/root 392 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-4.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.start-1.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.start-2.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.start-3.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.stop-1.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.stop-2.mod -rw-r--r-- root/root 363 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/hky.stop-3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc4.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc5.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod -rw-r--r-- root/root 62237 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod -rw-r--r-- root/root 62237 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.cns.mod -rw-r--r-- root/root 49950 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod -rw-r--r-- root/root 49950 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod -rw-r--r-- root/root 49950 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod -rw-r--r-- root/root 49950 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod -rw-r--r-- root/root 49950 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc5.mod -rw-r--r-- root/root 49949 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod -rw-r--r-- root/root 529 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models -rw-r--r-- root/root 549 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-gc1 -rw-r--r-- root/root 549 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-gc2 -rw-r--r-- root/root 549 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-gc3 -rw-r--r-- root/root 549 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-gc4 -rw-r--r-- root/root 549 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-gc5 -rw-r--r-- root/root 523 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns -rw-r--r-- root/root 539 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns-gc1 -rw-r--r-- root/root 539 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns-gc2 -rw-r--r-- root/root 539 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns-gc3 -rw-r--r-- root/root 539 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns-gc4 -rw-r--r-- root/root 539 2025-09-19 21:31 ./usr/share/phast/data/exoniphy/models-no-cns-gc5 drwxr-xr-x root/root 0 2025-09-19 21:31 ./usr/share/phast/data/phastCons/ -rw-r--r-- root/root 103302 2025-09-19 21:31 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2025-09-19 21:31 ./usr/share/phast/data/phastCons/simple-coding.hmm lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: warning: root directory /<>/sbuild-build-depends-lintian-dummy has unusual owner or group 998:999 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [1404 B] Get:5 copy:/<>/apt_archive ./ Packages [1453 B] Fetched 3472 B in 0s (134 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: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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 libffi8 libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libglib2.0-0t64 libgnutls30t64 libgpg-error0 libgssapi-krb5-2 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 libidn2-0 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap2 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 libncursesw6 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libp11-kit0 libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libproc2-0 libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d 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 libtasn1-6 libterm-readkey-perl libtext-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip procps readline-common shared-mime-info t1utils ucf unzip Suggested packages: apt-config-icons isoquery libxml-parser-perl rng-tools low-memory-monitor gnutls-bin krb5-doc krb5-user libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl python3 readline-doc zip Recommended packages: gnupg libcgi-fast-perl libglib2.0-data xdg-user-dirs libgpg-error-l10n libhtml-format-perl libio-compress-brotli-perl krb5-locales libldap-common liblist-someutils-xs-perl libfreezethaw-perl libgpm2 libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl publicsuffix libsasl2-modules libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libbrotli1 libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcom-err2 libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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 libffi8 libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libglib2.0-0t64 libgnutls30t64 libgpg-error0 libgssapi-krb5-2 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 libidn2-0 libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libldap2 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 libncursesw6 libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libp11-kit0 libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libproc2-0 libpsl5t64 libreadline8t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libssh2-1t64 libstemmer0d 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 libtasn1-6 libterm-readkey-perl libtext-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip procps readline-common sbuild-build-depends-lintian-dummy:i386 shared-mime-info t1utils ucf unzip 0 upgraded, 176 newly installed, 0 to remove and 0 not upgraded. Need to get 23.1 MB of archives. After this operation, 95.4 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 6.5 [12.4 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.5+20250216-2 [124 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.3-3 [74.8 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.5.4-1 [1457 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get:10 http://mirror.einval.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:11 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0052 [43.3 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.86.1-1 [1436 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b3 [755 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get:26 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libfyaml0 arm64 0.9-2 [194 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libstemmer0d arm64 3.0.1-1 [126 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libxmlb2 arm64 0.3.24-2 [58.5 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libappstream5 arm64 1.1.1-1 [210 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 appstream arm64 1.1.1-1 [560 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.68-1 [32.8 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libgpg-error0 arm64 1.56-2 [84.0 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2 [59.1 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.2-2 [772 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.4.8-4 [121 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b1 [125 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-3 [22.9 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-8 [884 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.4.8-4 [573 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.18.0-1 [3125 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.42 [64.3 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b2 [10.6 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-2 [15.7 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b4 [22.3 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:63 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.64-1+b1 [43.9 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-2 [17.6 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.66-1 [115 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.34-2 [111 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b2 [97.5 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.71-1 [217 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:72 http://mirror.einval.org/debian unstable/main arm64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b5 [34.9 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b1 [13.7 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:82 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.40-1 [129 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-3 [31.1 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0003-1 [28.5 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b5 [97.7 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.85-1 [23.9 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b4 [28.2 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libnumber-compare-perl all 0.03-3 [6332 B] Get:102 http://mirror.einval.org/debian unstable/main arm64 libtext-glob-perl all 0.11-3 [7676 B] Get:103 http://mirror.einval.org/debian unstable/main arm64 libfile-find-rule-perl all 0.35-1 [25.9 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 7.01-1 [80.0 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.13-1 [32.6 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:119 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.095-1 [226 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.24-1 [23.2 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.81-1 [186 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.027-1 [11.8 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:130 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:132 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:133 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.15-3 [37.8 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get:135 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2.1 [33.1 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:137 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:138 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:139 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:140 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:141 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:142 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.11-1+b1 [141 kB] Get:143 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:144 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3+b3 [11.2 kB] Get:145 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.28-1 [12.1 kB] Get:146 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:147 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.148-1 [56.7 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b4 [17.4 kB] Get:149 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b3 [11.4 kB] Get:150 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.637-1 [41.5 kB] Get:151 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:152 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b3 [96.7 kB] Get:153 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b3 [99.0 kB] Get:154 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:155 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.49-1 [64.3 kB] Get:156 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.31-1 [27.2 kB] Get:157 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB] Get:158 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b4 [8772 B] Get:159 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.18-1 [13.2 kB] Get:160 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2+b1 [172 kB] Get:161 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:162 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b4 [72.0 kB] Get:163 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-3 [19.9 kB] Get:164 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.20-1 [117 kB] Get:165 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:166 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:167 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:168 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-6+b1 [300 kB] Get:169 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get:170 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.904.0+ds-1 [43.6 kB] Get:171 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.12-3 [60.0 kB] Get:172 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2+b1 [82.3 kB] Get:173 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.3-1 [74.4 kB] Get:174 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get:175 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get:176 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.127.0 [1066 kB] Preconfiguring packages ... Fetched 23.1 MB in 0s (61.1 MB/s) Selecting previously unselected package netbase. (Reading database ... 18303 files and directories currently installed.) Preparing to unpack .../000-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package libncursesw6:arm64. Preparing to unpack .../001-libncursesw6_6.5+20250216-2_arm64.deb ... Unpacking libncursesw6:arm64 (6.5+20250216-2) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-9_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-9_arm64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package readline-common. Preparing to unpack .../004-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.5.4-1_arm64.deb ... 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Setting up plzip (1.12-3) ... 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 libtext-charwidth-perl:arm64 (0.04-11+b4) ... Setting up libnpth0t64:arm64 (1.8-3) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libunicode-utf8-perl (0.62-3) ... Setting up libmouse-perl:arm64 (2.5.11-1+b1) ... Setting up libgpg-error0:arm64 (1.56-2) ... Setting up libdata-messagepack-perl (1.02-3) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-2) ... 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 (0.47-1+b1) ... Setting up libyaml-0-2:arm64 (0.2.5-2) ... Setting up libsub-identify-perl (0.14-3+b3) ... Setting up libcpanel-json-xs-perl:arm64 (4.40-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdevel-size-perl (0.85-1) ... Setting up unzip (6.0-29) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libsqlite3-0:arm64 (3.46.1-8) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.904.0+ds-1) ... Setting up libio-interactive-perl (1.027-1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libgcrypt20:arm64 (1.11.2-2) ... Setting up liblzo2-2:arm64 (2.10-3+b1) ... Setting up libtime-moment-perl (0.44-2+b4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b3) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libnet-netmask-perl (2.0003-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libfyaml0:arm64 (0.9-2) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up patchutils (0.4.3-1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b5) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libfile-find-rule-perl (0.35-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-4) ... Setting up libperlio-utf8-strict-perl (0.010-1+b3) ... Setting up t1utils (1.41-4+b1) ... Setting up diffstat (1.68-1) ... Setting up libproc2-0:arm64 (2:4.0.4-9) ... Setting up libvariable-magic-perl (0.64-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b2) ... Setting up libncursesw6:arm64 (6.5+20250216-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-2+b1) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:arm64 (0.28-1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:arm64 (0.637-1) ... Setting up libpath-tiny-perl (0.148-1) ... Setting up lzop (1.04-2+b1) ... Setting up libassuan9:arm64 (3.0.2-2) ... Setting up procps (2:4.0.4-9) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... 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 (6.5) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libstemmer0d:arm64 (3.0.1-1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.5.4-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b4) ... Setting up libperlio-gzip-perl (0.20-1+b4) ... Setting up readline-common (8.3-3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b3) ... Setting up libmarkdown2:arm64 (2.2.7-2.1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up liburi-perl (5.34-2) ... Setting up iso-codes (4.18.0-1) ... 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+b4) ... Setting up libnet-ssleay-perl:arm64 (1.94-3) ... Setting up libksba8:arm64 (1.6.7-2+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 libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnet-http-perl (6.24-1) ... Setting up libtext-markdown-discount-perl (0.18-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-2) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglib2.0-0t64:arm64 (2.86.1-1) ... No schema files found: doing nothing. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.49-1) ... Setting up shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up ucf (3.0052) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsyntax-keyword-try-perl (0.31-1) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b2) ... Setting up gpgconf (2.4.8-4) ... Setting up libio-socket-ssl-perl (2.095-1) ... Setting up gpg (2.4.8-4) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.01-1) ... Setting up libhtml-form-perl (6.13-1) ... Setting up libgnutls30t64:arm64 (3.8.10-3) ... 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 libxmlb2:arm64 (0.3.24-2) ... Setting up libparams-classify-perl:arm64 (0.015-2+b4) ... Setting up libcgi-pm-perl (4.71-1) ... Setting up libxml-sax-perl (1.02+dfsg-4) ... 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 libmodule-runtime-perl (0.018-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-6+b1) ... 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... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.60-1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... 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 libcurl3t64-gnutls:arm64 (8.17.0~rc3-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libappstream5:arm64 (1.1.1-1) ... Setting up appstream (1.1.1-1) ... ✔ Metadata cache was updated successfully. Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.28-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.81-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.20-1) ... Setting up lintian (2.127.0) ... Setting up sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20250419) ... 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: n/a Build-Time: 366 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 46 Job: phast_1.7+dfsg-3 Lintian: pass Machine Architecture: arm64 Package: phast Package-Time: 448 Source-Version: 1.7+dfsg-3 Space: n/a Status: successful Version: 1.7+dfsg-3 -------------------------------------------------------------------------------- Finished at 2025-11-03T14:23:56Z Build needed 00:07:28, no disk space