sbuild (Debian sbuild) 0.89.3+deb13u1 (16 August 2025) on mjolnir.einval.org +==============================================================================+ | phast 1.8+dfsg-1 (amd64) Sat, 10 Jan 2026 19:14:32 +0000 | +==============================================================================+ Package: phast Version: 1.8+dfsg-1 Source Version: 1.8+dfsg-1 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.cQbgrsTVdT... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 10 Jan 2026 19:14:49 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [187 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 amd64 Packages [10.2 MB] Fetched 31.7 MB in 7s (4296 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libcrypt-dev Use 'apt autoremove' to remove it. The following packages will be upgraded: apt apt-utils libapt-pkg7.0 libc-bin libc-dev-bin libc-gconv-modules-extra libc6 libc6-dev libzstd1 linux-libc-dev login.defs 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 10.8 MB of archives. After this operation, 137 kB of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 libc-dev-bin arm64 2.42-7 [59.8 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libc6-dev arm64 2.42-7 [1695 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libc-gconv-modules-extra arm64 2.42-7 [1158 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libc6 arm64 2.42-7 [1462 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 6.18.3-1 [2548 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 libzstd1 arm64 1.5.7+dfsg-3 [260 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg7.0 arm64 3.1.13 [1056 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 apt arm64 3.1.13 [1419 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 apt-utils arm64 3.1.13 [338 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libc-bin arm64 2.42-7 [574 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 login.defs all 1:4.19.0-4 [211 kB] Preconfiguring packages ... Fetched 10.8 MB in 0s (37.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12037 files and directories currently installed.) Preparing to unpack .../libc-dev-bin_2.42-7_arm64.deb ... Unpacking libc-dev-bin (2.42-7) over (2.42-6) ... Preparing to unpack .../libc6-dev_2.42-7_arm64.deb ... Unpacking libc6-dev:arm64 (2.42-7) over (2.42-6) ... Preparing to unpack .../libc-gconv-modules-extra_2.42-7_arm64.deb ... 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Setting up libc6-dev:arm64 (2.42-7) ... +------------------------------------------------------------------------------+ | Fetch source files Sat, 10 Jan 2026 19:15:13 +0000 | +------------------------------------------------------------------------------+ 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 1871 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main phast 1.8+dfsg-1 (dsc) [2218 B] Get:2 http://mirror.einval.org/debian unstable/main phast 1.8+dfsg-1 (tar) [1810 kB] Get:3 http://mirror.einval.org/debian unstable/main phast 1.8+dfsg-1 (diff) [58.9 kB] Fetched 1871 kB in 0s (22.4 MB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 10 Jan 2026 19:15:22 +0000 | +------------------------------------------------------------------------------+ 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, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-SJKJk0/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Sources [826 B] Get:5 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Packages [841 B] Fetched 2276 B in 0s (108 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 package was automatically installed and is no longer required: libcrypt-dev Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblapacke:amd64 liblapacke-dev:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64 libpcre2-dev:amd64 libpcre2-posix3:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtmglib-dev:amd64 libtmglib3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-amd64-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-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libstdc++-15-doc:amd64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblapack-dev:amd64 liblapack3:amd64 liblapacke:amd64 liblapacke-dev:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64 libpcre2-dev:amd64 libpcre2-posix3:amd64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtmglib-dev:amd64 libtmglib3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-amd64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 474 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 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 0.23.2-1 [242 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 1.23.0-10 [1130 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.3-3 [97.7 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-2 [40.3 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 1:1.18.1-3 [878 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.2-1 [772 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu-base arm64 15.2.0-7cross1 [53.5 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 cpp-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [11.3 MB] Get:20 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:15.2.0-4 [5296 B] Get:21 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.45.50.20251209-1 [1512 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 libgcc-s1-amd64-cross all 15.2.0-7cross1 [71.7 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 15.2.0-7cross1 [132 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 15.2.0-7cross1 [25.9 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 15.2.0-7cross1 [9228 B] Get:27 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 15.2.0-7cross1 [2770 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 15.2.0-7cross1 [1247 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 15.2.0-7cross1 [2479 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.42-4cross1 [1655 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 15.2.0-7cross1 [689 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 15.2.0-7cross1 [1106 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 15.2.0-7cross1 [1534 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 15.2.0-7cross1 [145 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-amd64-cross all 15.2.0-7cross1 [2706 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [21.8 MB] Get:37 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:15.2.0-4 [1448 B] Get:38 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.18.3-1 [12.3 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.42-4cross1 [2088 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-amd64-cross all 15.2.0-7cross1 [2423 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 g++-15-x86-64-linux-gnu arm64 15.2.0-7cross1 [12.3 MB] Get:42 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:15.2.0-4 [1200 B] Get:43 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:44 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.29 [92.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-9 [540 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:50 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-2+b1 [591 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.2-1 [1613 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.29 [943 kB] Get:58 http://mirror.einval.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-12 [54.1 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get:60 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-12 [71.5 kB] Get:61 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-7 [1124 kB] Get:62 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.42-7 [1891 kB] Get:63 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 15.2.0-12 [2779 kB] Get:64 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-12 [9524 B] Get:65 http://mirror.einval.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get:66 http://mirror.einval.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get:67 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.42-7 [2091 kB] Get:68 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-12 [140 kB] Get:69 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 15.2.0-12 [26.5 kB] Get:70 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-12 [1249 kB] Get:71 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-12 [2490 kB] Get:72 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-12 [737 kB] Get:73 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-12 [1108 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-12 [1538 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-12 [145 kB] Get:76 http://mirror.einval.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-12 [2717 kB] Get:77 http://mirror.einval.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-12 [862 kB] Get:78 http://mirror.einval.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get:79 http://mirror.einval.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get:80 http://mirror.einval.org/debian unstable/main amd64 libtmglib3 amd64 3.12.1-7 [143 kB] Get:81 http://mirror.einval.org/debian unstable/main amd64 liblapacke amd64 3.12.1-7 [441 kB] Get:82 http://mirror.einval.org/debian unstable/main amd64 libtmglib-dev amd64 3.12.1-7 [148 kB] Get:83 http://mirror.einval.org/debian unstable/main amd64 liblapacke-dev amd64 3.12.1-7 [440 kB] Get:84 http://mirror.einval.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get:85 http://mirror.einval.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.46-1 [268 kB] Get:86 http://mirror.einval.org/debian unstable/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:87 http://mirror.einval.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.46-1 [63.9 kB] Get:88 http://mirror.einval.org/debian unstable/main amd64 libpcre2-dev amd64 10.46-1 [853 kB] Get:89 http://mirror.einval.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-12 [2445 kB] Preconfiguring packages ... Fetched 111 MB in 2s (50.8 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12090 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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Setting up binutils-x86-64-linux-gnu (2.45.50.20251209-1) ... Setting up libstdc++6-amd64-cross (15.2.0-7cross1) ... Setting up cpp-x86-64-linux-gnu (4:15.2.0-4) ... Setting up automake (1:1.18.1-3) ... 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 (0.23.2-1) ... Setting up libtool (2.5.4-9) ... Setting up libasan8-amd64-cross (15.2.0-7cross1) ... Setting up liblsan0-amd64-cross (15.2.0-7cross1) ... Setting up libc6-dev-amd64-cross (2.42-4cross1) ... Setting up libtsan2-amd64-cross (15.2.0-7cross1) ... Setting up libgomp1-amd64-cross (15.2.0-7cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (21) ... Setting up libitm1-amd64-cross (15.2.0-7cross1) ... Setting up libatomic1-amd64-cross (15.2.0-7cross1) ... Setting up libhwasan0-amd64-cross (15.2.0-7cross1) ... Setting up libquadmath0-amd64-cross (15.2.0-7cross1) ... Setting up libubsan1-amd64-cross (15.2.0-7cross1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-15-dev-amd64-cross (15.2.0-7cross1) ... Setting up libstdc++-15-dev-amd64-cross (15.2.0-7cross1) ... Setting up debhelper (13.29) ... Setting up gcc-15-x86-64-linux-gnu (15.2.0-7cross1) ... Setting up g++-15-x86-64-linux-gnu (15.2.0-7cross1) ... Setting up gcc-x86-64-linux-gnu (4:15.2.0-4) ... Setting up g++-x86-64-linux-gnu (4:15.2.0-4) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (15.2.0-12) ... Setting up libc6:amd64 (2.42-7) ... Setting up libhwasan0:amd64 (15.2.0-12) ... Setting up libasan8:amd64 (15.2.0-12) ... Setting up libc6-dev:amd64 (2.42-7) ... Setting up libtsan2:amd64 (15.2.0-12) ... Setting up libstdc++6:amd64 (15.2.0-12) ... Setting up liblsan0:amd64 (15.2.0-12) ... Setting up libitm1:amd64 (15.2.0-12) ... Setting up libgomp1:amd64 (15.2.0-12) ... Setting up libpcre2-16-0:amd64 (10.46-1) ... Setting up libpcre2-32-0:amd64 (10.46-1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libquadmath0:amd64 (15.2.0-12) ... Setting up libatomic1:amd64 (15.2.0-12) ... Setting up libpcre2-8-0:amd64 (10.46-1) ... Setting up libgfortran5:amd64 (15.2.0-12) ... Setting up libubsan1:amd64 (15.2.0-12) ... Setting up libpcre2-posix3:amd64 (10.46-1) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libgcc-15-dev:amd64 (15.2.0-12) ... Setting up libpcre2-dev:amd64 (10.46-1) ... Setting up libtmglib3:amd64 (3.12.1-7) ... Setting up libstdc++-15-dev:amd64 (15.2.0-12) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up liblapacke:amd64 (3.12.1-7) ... Setting up libtmglib-dev:amd64 (3.12.1-7) ... Setting up liblapacke-dev:amd64 (3.12.1-7) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (14) ... Processing triggers for libc-bin (2.42-7) ... +------------------------------------------------------------------------------+ | Check architectures Sat, 10 Jan 2026 19:16:17 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sat, 10 Jan 2026 19:16:18 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) Toolchain package versions: binutils_2.45.50.20251209-1 dpkg-dev_1.23.3 g++-15_15.2.0-12 gcc-15_15.2.0-12 libc6-dev_2.42-7 libstdc++-15-dev_15.2.0-12 libstdc++-15-dev-amd64-cross_15.2.0-7cross1 libstdc++6_15.2.0-12 libstdc++6-amd64-cross_15.2.0-7cross1 linux-libc-dev_6.18.3-1 Package versions: apt_3.1.13 apt-utils_3.1.13 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45.50.20251209-1 binutils-aarch64-linux-gnu_2.45.50.20251209-1 binutils-common_2.45.50.20251209-1 binutils-x86-64-linux-gnu_2.45.50.20251209-1 bsdextrautils_2.41.3-3 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-12 cpp-15-aarch64-linux-gnu_15.2.0-12 cpp-15-x86-64-linux-gnu_15.2.0-7cross1 cpp-aarch64-linux-gnu_4:15.2.0-4 cpp-x86-64-linux-gnu_4:15.2.0-4 crossbuild-essential-amd64_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.29 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_1.23.3 dpkg-dev_1.23.3 dwz_0.16-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-12 g++-15-aarch64-linux-gnu_15.2.0-12 g++-15-x86-64-linux-gnu_15.2.0-7cross1 g++-aarch64-linux-gnu_4:15.2.0-4 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-12 gcc-15-aarch64-linux-gnu_15.2.0-12 gcc-15-base_15.2.0-12 gcc-15-cross-base_15.2.0-7cross1 gcc-15-x86-64-linux-gnu_15.2.0-7cross1 gcc-15-x86-64-linux-gnu-base_15.2.0-7cross1 gcc-aarch64-linux-gnu_4:15.2.0-4 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1 groff-base_1.23.0-10 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_3.1.13 libarchive-zip-perl_1.68-1 libasan8_15.2.0-12 libasan8-amd64-cross_15.2.0-7cross1 libatomic1_15.2.0-12 libatomic1-amd64-cross_15.2.0-7cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.45.50.20251209-1 libblas-dev_3.12.1-7 libblas3_3.12.1-7 libblkid1_2.41.3-3 libbz2-1.0_1.0.8-6 libc-bin_2.42-7 libc-dev-bin_2.42-7 libc-gconv-modules-extra_2.42-7 libc6_2.42-7 libc6-amd64-cross_2.42-4cross1 libc6-dev_2.42-7 libc6-dev-amd64-cross_2.42-4cross1 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-12 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45.50.20251209-1 libctf0_2.45.50.20251209-1 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.29 libdpkg-perl_1.23.3 libelf1t64_0.194-1 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-12 libgcc-15-dev-amd64-cross_15.2.0-7cross1 libgcc-s1_15.2.0-12 libgcc-s1-amd64-cross_15.2.0-7cross1 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgfortran5_15.2.0-12 libgmp10_2:6.3.0+dfsg-5 libgomp1_15.2.0-12 libgomp1-amd64-cross_15.2.0-7cross1 libgprofng0_2.45.50.20251209-1 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-12 libhwasan0-amd64-cross_15.2.0-7cross1 libisl23_0.27-1 libitm1_15.2.0-12 libitm1-amd64-cross_15.2.0-7cross1 libjansson4_2.14-2+b4 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_15.2.0-12 liblsan0-amd64-cross_15.2.0-7cross1 liblz4-1_1.10.0-6 liblzma5_5.8.2-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.3-3 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_5.40.1-7 libpipeline1_1.5.8-2 libquadmath0_15.2.0-12 libquadmath0-amd64-cross_15.2.0-7cross1 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsframe2_2.45.50.20251209-1 libsmartcols1_2.41.3-3 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-12 libstdc++-15-dev-amd64-cross_15.2.0-7cross1 libstdc++6_15.2.0-12 libstdc++6-amd64-cross_15.2.0-7cross1 libsystemd0_259-1 libtinfo6_6.6+20251231-1 libtmglib-dev_3.12.1-7 libtmglib3_3.12.1-7 libtool_2.5.4-9 libtsan2_15.2.0-12 libtsan2-amd64-cross_15.2.0-7cross1 libubsan1_15.2.0-12 libubsan1-amd64-cross_15.2.0-7cross1 libuchardet0_0.0.8-2 libudev1_259-1 libunistring5_1.3-2 libuuid1_2.41.3-3 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-3 linux-libc-dev_6.18.3-1 linux-libc-dev-amd64-cross_6.18.3-1 login_1:4.16.0-2+really2.41.3-3 login.defs_1:4.19.0-4 m4_1.4.20-2 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20250131-2 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 openssl-provider-legacy_3.5.4-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 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_1.3.0-5 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 util-linux_2.41.3-3 xz-utils_5.8.2-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b2 +------------------------------------------------------------------------------+ | Build Sat, 10 Jan 2026 19:16:19 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.8+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/phast Vcs-Git: https://salsa.debian.org/med-team/phast.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 6da744c1437952a6598686aa0bbb6b0985b58227 1809612 phast_1.8+dfsg.orig.tar.xz 6445ea4a67d7291a6c61adf6cc27a9c02fb94a3d 58940 phast_1.8+dfsg-1.debian.tar.xz Checksums-Sha256: 5b451481899265f167e7f3e6ba8c8fa7149101e554ba60465499405901c4b031 1809612 phast_1.8+dfsg.orig.tar.xz 3332c09a3929544c3e8a194efd13804cdd73176b3efb90d2566c2e1400341096 58940 phast_1.8+dfsg-1.debian.tar.xz Files: 3bf164f1bce6776f0d55994fd5ec72ba 1809612 phast_1.8+dfsg.orig.tar.xz 9b321ae2f7e895293dc7698b05153f56 58940 phast_1.8+dfsg-1.debian.tar.xz Dgit: 5e6cb5e46107c6ececceb18d4274afab118e733a debian archive/debian/1.8+dfsg-1 https://git.dgit.debian.org/phast -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmkYS2IUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpqChAAnzXmkuRT5z45UX0A8dUbLTgesXVa 5gpl0RoAJQ6YusEPSFdkUg1LaGHywNZmtZ2DIZerOpmr8OSfoLleJC3S/kXcQIEn WESeKuj3E+6QsszkPTDNLyda7H1rMrrSEo+H7HMY0D6adXq3NU2W/gb/EnsI7PTA rVDIZ5LBVeyRWZgW4uiZem9RdzqiN45LEUlkTYs0Ept2SAOxlRMsJcgcmDmRTUBv qZclklom6qY0tC1GLzyYylikiqlIM0lvsi+6n8n9/uKwWQredXxzvl/mHFFCC4fP jiLEAIt8DxBuK2Ud2KolqVmoJ56vR8CtFht+cS/wjo8w6YbtgBOmOh5c49+siNCi K52FwR0/mZfoFTzzNgA60j8yKaWHtTTJF4nEOlMCJouw1AeLNxIDPtMvlLmXT3Mz cmKfajjzl0JOu8D+adFU5ItxIxizCe2Q9XSRT2aU1ymC4JRsngdLAVOKDqPS6U91 g6NQgUYVpPLX26MUSPRU6XVM6lgYBuAiZdyvyrRPfLsc8cZ/K5Pc8w153kQr2Zvj faefv3BStUeeFb/mdYoufI/F3d3qaJX1W77ulYfv2MYOtg1yEGza7meEci4IJ81P Hdkv1Li/KSuu/8PgH6VcwXRR9axcpCLRGnGVDLkC8/XJXZFRyf0KylIA9bGBV1AG N+7NhIboWVS2dY8= =Oe2J -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./phast_1.8+dfsg-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./phast_1.8+dfsg-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting phast in /build/reproducible-path/phast-1.8+dfsg dpkg-source: info: unpacking phast_1.8+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.8+dfsg-1.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.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --jobs-try=1 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.8+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/phast-1.8+dfsg' dh_auto_clean cd src \ && /usr/bin/make clean make[2]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/../version: No such file or directory for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.8+dfsg/src/lib/$dir && /usr/bin/make clean ; done make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/base' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/base/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/msa' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/feature' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/motif' cat: /build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../version: No such file or directory rm -f *.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/motif' rm -f /build/reproducible-path/phast-1.8+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/dless' cat: /build/reproducible-path/phast-1.8+dfsg/src/dless/../version: No such file or directory rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.8+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.8+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/exoniphy' cat: /build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastCons' cat: /build/reproducible-path/phast-1.8+dfsg/src/phastCons/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.8+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastOdds' cat: /build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastMotif' cat: /build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloFit' cat: /build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot' cat: /build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloP' cat: /build/reproducible-path/phast-1.8+dfsg/src/phyloP/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.8+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/prequel' cat: /build/reproducible-path/phast-1.8+dfsg/src/prequel/../version: No such file or directory rm -f *.o /build/reproducible-path/phast-1.8+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.8+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.8+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.8+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.8+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/util' cat: /build/reproducible-path/phast-1.8+dfsg/src/util/../version: No such file or directory rm -f *.o *.help /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/tree_doctor make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc make[1]: Entering directory '/build/reproducible-path/phast-1.8+dfsg' 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 '/build/reproducible-path/phast-1.8+dfsg/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /build/reproducible-path/phast-1.8+dfsg/src/$dir && make ; done make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.8+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/base' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c: In function ‘phast_fclose’: phast_misc.c:301:5: warning: pointer ‘f’ used after ‘fclose’ [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to ‘fclose’ here 300 | fclose(f); | ^~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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; | ^~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/lib/base/../../../lib/libphast.a ar rs /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 '/build/reproducible-path/phast-1.8+dfsg/src/lib/base' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/msa' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition phast_maf.c: In function ‘maf_read_cats_subset’: phast_maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from phast_msa.c:39: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 '/build/reproducible-path/phast-1.8+dfsg/src/lib/msa' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/feature' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from phast_bed.c:15: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from phast_gff.c:13: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /build/reproducible-path/phast-1.8+dfsg/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 '/build/reproducible-path/phast-1.8+dfsg/src/lib/feature' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/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 '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/motif' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition phast_motif.c: In function ‘mtf_print’: phast_motif.c:1411:21: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function ‘mtf_print_html’: phast_motif.c:1604:23: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /build/reproducible-path/phast-1.8+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib/motif' make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/lib' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/dless/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/trees.h:25, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/tree_model.h:26, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/bd_phylo_hmm.h:22, from dlessP.c:17: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/dless/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/dless' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/exoniphy' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phastCons/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastCons' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastOdds' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phastMotif' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phastMotif' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloFit' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloBoot' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/phyloP/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/phyloP' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/pbs_code.h:8, from phast_pbs_code.c:14: /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/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 * /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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/x86_64-linux-gnu/include/stdio.h:970, from prequel.c:11: In function ‘sprintf’, inlined from ‘main’ at prequel.c:285:7: /usr/x86_64-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/x86_64-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/x86_64-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 ()); | ~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/prequel/../../lib -o /build/reproducible-path/phast-1.8+dfsg/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 -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src/prequel' make[3]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/gff.h:21, from /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/msa.h:19, from msa_view.c:14: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_compile_context *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: ‘PHAST_HOME’ redefined : note: this is the location of the previous definition x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.8+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.8+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.8+dfsg/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 /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /build/reproducible-path/phast-1.8+dfsg/src/../include/phast/trees.h:47:8: note: ‘name’ declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ x86_64-linux-gnu-gcc -L/build/reproducible-path/phast-1.8+dfsg/src/util/../../lib -o /build/reproducible-path/phast-1.8+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now -fcf-protection make[3]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/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 '/build/reproducible-path/phast-1.8+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j1 install DESTDIR=/build/reproducible-path/phast-1.8\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/phast-1.8+dfsg' (cd src; make install DESTDIR=/build/reproducible-path/phast-1.8+dfsg/debian/phast ) make[2]: Entering directory '/build/reproducible-path/phast-1.8+dfsg/src' mkdir -p /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/bin/ mkdir -p /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/bin/ cp -R ../data/* /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /build/reproducible-path/phast-1.8+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/phast-1.8+dfsg' dh_installexamples find debian/*/usr/share/doc/*/examples \ -type f \ -size +1k \ -exec xz \{\} \; make[1]: Leaving directory '/build/reproducible-path/phast-1.8+dfsg' 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_1.8+dfsg-1_amd64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.8+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../phast_1.8+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../phast_1.8+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2026-01-10T19:22:31Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands Sat, 10 Jan 2026 19:22:31 +0000 | +------------------------------------------------------------------------------+ rm -Rf /build/reproducible-path/phast-1.8+dfsg/ ----------------------------------------------- I: Finished running 'rm -Rf /build/reproducible-path/phast-1.8+dfsg/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 10 Jan 2026 19:22:33 +0000 | +------------------------------------------------------------------------------+ phast_1.8+dfsg-1_amd64.changes: ------------------------------- Format: 1.8 Date: Sat, 15 Nov 2025 10:32:38 +0100 Source: phast Binary: phast phast-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 1.8+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: phast - phylogenetic analysis with space/time models Changes: phast (1.8+dfsg-1) unstable; urgency=medium . * New upstream version 1.8+dfsg * d/control: declare compliance to standards version 4.7.2. * d/control: drop redundant Rules-Requires-Root: no. * d/rules: slight readability improvements. * d/watch convert to v5 Github template. 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+------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: amd64 Version: 1.8+dfsg-1 Checksums-Md5: 879417bcbac0788b8ddd54c91f305d04 37300236 phast-dbgsym_1.8+dfsg-1_amd64.deb 13f9c6bf44fea039999656d2bbe92d01 3563112 phast_1.8+dfsg-1_amd64.deb Checksums-Sha1: fddbcc0525af4de2935e6ff587e0d3f26da0bdd6 37300236 phast-dbgsym_1.8+dfsg-1_amd64.deb 82360e9c4a2b1a94585100920d0dd9db0a568797 3563112 phast_1.8+dfsg-1_amd64.deb Checksums-Sha256: f0392f4cd036d6cb30412118888d21a293012da8259d4ffab7269fceb1e99a1a 37300236 phast-dbgsym_1.8+dfsg-1_amd64.deb 1ba47062d78bbd19428e604c93adc021b1a64d0f806a7abbebcd16810948ad34 3563112 phast_1.8+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Sat, 10 Jan 2026 19:22:29 +0000 Build-Path: /build/reproducible-path/phast-1.8+dfsg Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-1), binutils (= 2.45.50.20251209-1), binutils-aarch64-linux-gnu (= 2.45.50.20251209-1), binutils-common (= 2.45.50.20251209-1), bsdextrautils (= 2.41.3-3), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-15 (= 15.2.0-12), cpp-15-aarch64-linux-gnu (= 15.2.0-12), cpp-aarch64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.29), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.3), dpkg-dev (= 1.23.3), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-12), g++-15-aarch64-linux-gnu (= 15.2.0-12), g++-aarch64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-15 (= 15.2.0-12), gcc-15-aarch64-linux-gnu (= 15.2.0-12), gcc-15-base (= 15.2.0-12), gcc-aarch64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), 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 (= 15.2.0-12), libatomic1 (= 15.2.0-12), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.45.50.20251209-1), libblas-dev (= 3.12.1-7), libblas3 (= 3.12.1-7), libblkid1 (= 2.41.3-3), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.42-7), libc-dev-bin (= 2.42-7), libc-gconv-modules-extra (= 2.42-7), libc6 (= 2.42-7), libc6-dev (= 2.42-7), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-12), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.45.50.20251209-1), libctf0 (= 2.45.50.20251209-1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.29), libdpkg-perl (= 1.23.3), libelf1t64 (= 0.194-1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-15-dev (= 15.2.0-12), libgcc-s1 (= 15.2.0-12), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgfortran5 (= 15.2.0-12), libgmp10 (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-12), libgprofng0 (= 2.45.50.20251209-1), libhwasan0 (= 15.2.0-12), libisl23 (= 0.27-1), libitm1 (= 15.2.0-12), libjansson4 (= 2.14-2+b4), 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 (= 15.2.0-12), liblzma5 (= 5.8.2-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.3-3), 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 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libquadmath0 (= 15.2.0-12), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsframe2 (= 2.45.50.20251209-1), libsmartcols1 (= 2.41.3-3), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-12), libstdc++6 (= 15.2.0-12), libsystemd0 (= 259-1), libtinfo6 (= 6.6+20251231-1), libtmglib-dev (= 3.12.1-7), libtmglib3 (= 3.12.1-7), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-12), libubsan1 (= 15.2.0-12), libuchardet0 (= 0.0.8-2), libudev1 (= 259-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.3-3), libxml2-16 (= 2.15.1+dfsg-2+b1), libzstd1 (= 1.5.7+dfsg-3), linux-libc-dev (= 6.18.3-1), m4 (= 1.4.20-2), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-2), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.3-1+b1), sed (= 4.9-2+b1), sensible-utils (= 0.0.26), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.3-3), xz-utils (= 5.8.2-1), zlib1g (= 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Installed-Size: 30429 Depends: 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. . 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2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-4.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.start-1.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.start-2.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.start-3.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.stop-1.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.stop-2.mod -rw-r--r-- root/root 363 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/hky.stop-3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc4.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc5.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod -rw-r--r-- root/root 62237 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod -rw-r--r-- root/root 62237 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.cns.mod -rw-r--r-- root/root 49950 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod -rw-r--r-- root/root 49950 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod -rw-r--r-- root/root 49950 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod -rw-r--r-- root/root 49950 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod -rw-r--r-- root/root 49950 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc5.mod -rw-r--r-- root/root 49949 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod -rw-r--r-- root/root 529 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models -rw-r--r-- root/root 549 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-gc1 -rw-r--r-- root/root 549 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-gc2 -rw-r--r-- root/root 549 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-gc3 -rw-r--r-- root/root 549 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-gc4 -rw-r--r-- root/root 549 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-gc5 -rw-r--r-- root/root 523 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns -rw-r--r-- root/root 539 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns-gc1 -rw-r--r-- root/root 539 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns-gc2 -rw-r--r-- root/root 539 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns-gc3 -rw-r--r-- root/root 539 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns-gc4 -rw-r--r-- root/root 539 2025-11-15 09:32 ./usr/share/phast/data/exoniphy/models-no-cns-gc5 drwxr-xr-x root/root 0 2025-11-15 09:32 ./usr/share/phast/data/phastCons/ -rw-r--r-- root/root 103302 2025-11-15 09:32 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2025-11-15 09:32 ./usr/share/phast/data/phastCons/simple-coding.hmm lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/build/reproducible-path/resolver-SJKJk0/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Release [615 B] Ign:3 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Sources [1408 B] Get:5 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ Packages [1459 B] Fetched 3482 B in 0s (132 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 package was automatically installed and is no longer required: libcrypt-dev Use 'apt autoremove' to remove it. 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-libmagic-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-libmagic-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:amd64 shared-mime-info t1utils ucf unzip 0 upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 23.4 MB of archives. After this operation, 96.7 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-SJKJk0/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [832 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 6.6+20251231-1 [125 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 3.5.2-3 [23.0 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.86.3-4 [1437 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+b9 [295 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 0.25.10-1 [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 3.8.11-3 [1400 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.22.1-2 [32.2 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b8 [24.9 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.22.1-2 [77.1 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 1.22.1-2 [315 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.22.1-2 [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 8.18.0-1 [365 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libfyaml0 arm64 0.9.2-1 [234 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 1.58-1 [84.5 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 1.11.2-3 [762 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 2.4.8-5 [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 2.4.8-5 [572 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.20.1-1 [3319 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 0.1.43 [64.6 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 0.66-2 [116 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 libfile-libmagic-perl arm64 1.23-2+b2 [30.9 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 7.01-1 [80.0 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.13-1 [32.6 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:120 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3 [323 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.098-1 [229 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.24-1 [23.2 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.81-1 [186 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.027-1 [11.8 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:130 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:132 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:133 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.15-5 [38.2 kB] Get:135 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b1 [49.6 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2.1 [33.1 kB] Get:137 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:138 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:139 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:140 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:141 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:142 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:143 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.6.1-1 [140 kB] Get:144 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:145 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-4 [10.9 kB] Get:146 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.28-1 [12.1 kB] Get:147 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:148 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.148-1 [56.7 kB] Get:149 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b4 [17.4 kB] Get:150 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b3 [11.4 kB] Get:151 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.637-1 [41.5 kB] Get:152 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:153 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b3 [96.7 kB] Get:154 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b3 [99.0 kB] Get:155 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:156 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.49-1 [64.3 kB] Get:157 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.31-1 [27.2 kB] Get:158 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b4 [24.5 kB] Get:159 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b4 [8772 B] Get:160 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.18-1 [13.2 kB] Get:161 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2+b1 [172 kB] Get:162 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:163 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.46-1 [77.1 kB] Get:164 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.63-1 [20.1 kB] Get:165 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.20-1 [117 kB] Get:166 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:167 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:168 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:169 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-7 [300 kB] Get:170 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2+b1 [47.8 kB] Get:171 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.904.0+ds-1 [43.6 kB] Get:172 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.12-4 [59.7 kB] Get:173 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2+b1 [82.3 kB] Get:174 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.3-1 [74.4 kB] Get:175 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4+b1 [57.6 kB] Get:176 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-29 [163 kB] Get:177 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.128.1 [1067 kB] Preconfiguring packages ... Fetched 23.4 MB in 2s (13.3 MB/s) Selecting previously unselected package netbase. (Reading database ... 18393 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_6.6+20251231-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.6+20251231-1) ... 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 ... Unpacking openssl (3.5.4-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../007-libtext-charwidth-perl_0.04-11+b4_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../008-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../009-ucf_3.0052_all.deb ... Moving old data out of the way Unpacking ucf (3.0052) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../010-libffi8_3.5.2-3_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-3) ... Selecting previously unselected package libglib2.0-0t64:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package gpgconf. Preparing to unpack .../045-gpgconf_2.4.8-5_arm64.deb ... Unpacking gpgconf (2.4.8-5) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../046-libksba8_1.6.7-2+b1_arm64.deb ... Unpacking libksba8:arm64 (1.6.7-2+b1) ... Selecting previously unselected package libnpth0t64:arm64. 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Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../069-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../070-libclass-inspector-perl_1.36-3_all.deb ... Unpacking libclass-inspector-perl (1.36-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../071-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../072-libclass-xsaccessor-perl_1.19-4+b5_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b5) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../073-libclone-perl_0.47-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.47-1+b1) ... 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Preparing to unpack .../095-libemail-address-xs-perl_1.05-1+b4_arm64.deb ... Unpacking libemail-address-xs-perl (1.05-1+b4) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../096-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../097-libipc-system-simple-perl_1.30-2_all.deb ... Unpacking libipc-system-simple-perl (1.30-2) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../098-libfile-basedir-perl_0.09-2_all.deb ... Unpacking libfile-basedir-perl (0.09-2) ... Selecting previously unselected package libnumber-compare-perl. Preparing to unpack .../099-libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../100-libtext-glob-perl_0.11-3_all.deb ... 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Setting up libberkeleydb-perl:arm64 (0.66-2) ... Setting up plzip (1.12-4) ... 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 (0.63-1) ... Setting up libmouse-perl:arm64 (2.6.1-1) ... Setting up libgpg-error0:arm64 (1.58-1) ... 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+b1) ... Setting up libsub-identify-perl (0.14-4) ... 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+b9) ... 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 (1.11.2-3) ... Setting up liblzo2-2:arm64 (2.10-3+b1) ... Setting up libtime-moment-perl (0.46-1) ... 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+b8) ... 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 (0.9.2-1) ... Setting up libkrb5support0:arm64 (1.22.1-2) ... 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 libfile-libmagic-perl (1.23-2+b2) ... Setting up libncursesw6:arm64 (6.6+20251231-1) ... Setting up libk5crypto3:arm64 (1.22.1-2) ... 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 (3.5.2-3) ... 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 (1.22.1-2) ... 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 (4.20.1-1) ... 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 (2.86.3-4) ... 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 (0.25.10-1) ... Setting up libgssapi-krb5-2:arm64 (1.22.1-2) ... 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 (2.4.8-5) ... Setting up libio-socket-ssl-perl (2.098-1) ... Setting up gpg (2.4.8-5) ... 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 (3.8.11-3) ... 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+2.0134-7) ... 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 (8.18.0-1) ... 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 (2.128.1) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for libc-bin (2.42-7) ... 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 Sat, 10 Jan 2026 19:24:05 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sat, 10 Jan 2026 19:24:05 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 10 Jan 2026 19:24:08 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 367 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 55 Job: phast_1.8+dfsg-1 Lintian: pass Machine Architecture: arm64 Package: phast Package-Time: 479 Source-Version: 1.8+dfsg-1 Space: n/a Status: successful Version: 1.8+dfsg-1 -------------------------------------------------------------------------------- Finished at 2026-01-10T19:22:31Z Build needed 00:07:59, no disk space