sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | phast 1.6+dfsg-4 (armel) Sat, 23 Dec 2023 18:17:54 +0000 | +==============================================================================+ Package: phast Version: 1.6+dfsg-4 Source Version: 1.6+dfsg-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-0f80300f-3edf-4ca4-a9be-f6f0d9e89108' with '<>' I: NOTICE: Log filtering will replace 'build/phast-OtJfeZ/resolver-ZOekYz' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [198 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-12-23-1406.17-F-2023-12-23-0204.41.pdiff [27.2 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-12-23-1406.17-F-2023-12-23-0204.41.pdiff [32.1 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-12-23-1406.17-F-2023-12-23-0204.41.pdiff [27.2 kB] Get:6 http://localhost:3142/debian sid/main armel Packages [9111 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-12-23-1406.17-F-2023-12-23-0204.41.pdiff [32.1 kB] Fetched 9495 kB in 3s (3619 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libcap-ng0 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 16.9 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://localhost:3142/debian sid/main amd64 libcap-ng0 amd64 0.8.4-1 [16.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.9 kB in 0s (0 B/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 ... 16231 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.4-1) over (0.8.3-3) ... Setting up libcap-ng0:amd64 (0.8.4-1) ... Processing triggers for libc-bin (2.37-13) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'phast' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phast.git Please use: git clone https://salsa.debian.org/med-team/phast.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1869 kB of source archives. Get:1 http://localhost:3142/debian sid/main phast 1.6+dfsg-4 (dsc) [2044 B] Get:2 http://localhost:3142/debian sid/main phast 1.6+dfsg-4 (tar) [1809 kB] Get:3 http://localhost:3142/debian sid/main phast 1.6+dfsg-4 (diff) [57.9 kB] Fetched 1869 kB in 0s (121 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phast-OtJfeZ/phast-1.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-OtJfeZ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre2-dev, help2man, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [809 B] Get:5 copy:/<>/apt_archive ./ Packages [824 B] Fetched 2242 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils cpp-13-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-base:armel gcc-13-arm-linux-gnueabi gcc-13-arm-linux-gnueabi-base gcc-13-base:armel gcc-13-cross-base-ports gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libblas-dev:armel libblas3:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armel libgcc-13-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu72 libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblapack-dev:armel liblapack3:armel liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armel libnsl2:armel libpcre2-16-0:armel libpcre2-32-0:armel libpcre2-8-0:armel libpcre2-dev:armel libpcre2-posix3:armel libpipeline1 libssl3:armel libstdc++-11-dev:armel libstdc++-13-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtirpc-dev:armel libtirpc3:armel libtmglib-dev:armel libtmglib3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armel-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc:armel glibc-doc:armel libc-l10n:armel locales:armel libnss-nis:armel libnss-nisplus:armel manpages-dev:armel krb5-doc:armel krb5-user:armel libstdc++-11-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:armel libarchive-cpio-perl krb5-locales:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdextrautils cpp-13-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-11-base:armel gcc-13-arm-linux-gnueabi gcc-13-arm-linux-gnueabi-base gcc-13-base:armel gcc-13-cross-base-ports gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:armel libasan8-armel-cross libatomic1:armel libatomic1-armel-cross libblas-dev:armel libblas3:armel libc6:armel libc6-armel-cross libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:armel libgcc-13-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgfortran5:armel libgomp1:armel libgomp1-armel-cross libgssapi-krb5-2:armel libicu72 libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel liblapack-dev:armel liblapack3:armel liblocale-gettext-perl libmagic-mgc libmagic1 libnsl-dev:armel libnsl2:armel libpcre2-16-0:armel libpcre2-32-0:armel libpcre2-8-0:armel libpcre2-dev:armel libpcre2-posix3:armel libpipeline1 libssl3:armel libstdc++-11-dev:armel libstdc++-13-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtirpc-dev:armel libtirpc3:armel libtmglib-dev:armel libtmglib3:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-armel-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:armel sensible-utils ucf 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 93.8 MB of archives. After this operation, 366 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB] Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2 [314 kB] Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2 [105 kB] Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2 [42.8 kB] Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-14 [161 kB] Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.8-1 [68.5 kB] Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.3-2 [89.1 kB] Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-1 [1402 kB] Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-14 [496 kB] Get:19 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabi amd64 2.41.50.20231214-1 [3222 kB] Get:20 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabi-base amd64 13.2.0-7cross2 [41.1 kB] Get:21 http://localhost:3142/debian sid/main amd64 cpp-13-arm-linux-gnueabi amd64 13.2.0-7cross2 [9284 kB] Get:22 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabi amd64 4:13.2.1-2 [3944 B] Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:24 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base-ports all 13.2.0-7cross2 [36.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libc6-armel-cross all 2.37-12cross1 [884 kB] Get:26 http://localhost:3142/debian sid/main amd64 libgcc-s1-armel-cross all 13.2.0-7cross2 [38.3 kB] Get:27 http://localhost:3142/debian sid/main amd64 libgomp1-armel-cross all 13.2.0-7cross2 [105 kB] Get:28 http://localhost:3142/debian sid/main amd64 libatomic1-armel-cross all 13.2.0-7cross2 [9120 B] Get:29 http://localhost:3142/debian sid/main amd64 libasan8-armel-cross all 13.2.0-7cross2 [2382 kB] Get:30 http://localhost:3142/debian sid/main amd64 libstdc++6-armel-cross all 13.2.0-7cross2 [534 kB] Get:31 http://localhost:3142/debian sid/main amd64 libubsan1-armel-cross all 13.2.0-7cross2 [965 kB] Get:32 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-armel-cross all 13.2.0-7cross2 [775 kB] Get:33 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabi amd64 13.2.0-7cross2 [18.2 MB] Get:34 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabi amd64 4:13.2.1-2 [1476 B] Get:35 http://localhost:3142/debian sid/main amd64 linux-libc-dev-armel-cross all 6.5.8-1cross1 [1975 kB] Get:36 http://localhost:3142/debian sid/main amd64 libc6-dev-armel-cross all 2.37-12cross1 [1292 kB] Get:37 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-armel-cross all 13.2.0-7cross2 [2215 kB] Get:38 http://localhost:3142/debian sid/main amd64 g++-13-arm-linux-gnueabi amd64 13.2.0-7cross2 [10.2 MB] Get:39 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabi amd64 4:13.2.1-2 [1180 B] Get:40 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:41 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:42 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:43 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b1 [692 kB] Get:44 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:45 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:46 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:47 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:48 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:49 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:50 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:51 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:52 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:54 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:55 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armel all 12.10 [3484 B] Get:56 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.9 [82.3 kB] Get:57 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:58 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:60 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get:61 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:62 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:63 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.190-1 [176 kB] Get:64 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:65 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-14 [1300 kB] Get:66 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:67 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:68 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.9 [956 kB] Get:69 http://localhost:3142/debian sid/main armel gcc-11-base armel 11.4.0-7 [40.3 kB] Get:70 http://localhost:3142/debian sid/main armel gcc-13-base armel 13.2.0-9 [41.5 kB] Get:71 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.3 [198 kB] Get:72 http://localhost:3142/debian sid/main armel libgcc-s1 armel 13.2.0-9 [38.3 kB] Get:73 http://localhost:3142/debian sid/main armel libc6 armel 2.37-13 [2140 kB] Get:74 http://localhost:3142/debian sid/main armel libasan6 armel 11.4.0-7 [1944 kB] Get:75 http://localhost:3142/debian sid/main armel libatomic1 armel 13.2.0-9 [9388 B] Get:76 http://localhost:3142/debian sid/main armel libblas3 armel 3.11.0-2 [181 kB] Get:77 http://localhost:3142/debian sid/main armel libblas-dev armel 3.11.0-2 [191 kB] Get:78 http://localhost:3142/debian sid/main armel libcrypt1 armel 1:4.4.36-2 [96.7 kB] Get:79 http://localhost:3142/debian sid/main armel libcrypt-dev armel 1:4.4.36-2 [126 kB] Get:80 http://localhost:3142/debian sid/main armel libkrb5support0 armel 1.20.1-5 [30.0 kB] Get:81 http://localhost:3142/debian sid/main armel libcom-err2 armel 1.47.0-2+b1 [19.4 kB] Get:82 http://localhost:3142/debian sid/main armel libk5crypto3 armel 1.20.1-5 [74.6 kB] Get:83 http://localhost:3142/debian sid/main armel libkeyutils1 armel 1.6.3-2 [7864 B] Get:84 http://localhost:3142/debian sid/main armel libssl3 armel 3.1.4-2 [1644 kB] Get:85 http://localhost:3142/debian sid/main armel libkrb5-3 armel 1.20.1-5 [285 kB] Get:86 http://localhost:3142/debian sid/main armel libgssapi-krb5-2 armel 1.20.1-5 [111 kB] Get:87 http://localhost:3142/debian sid/main armel libtirpc3 armel 1.3.4+ds-1 [69.4 kB] Get:88 http://localhost:3142/debian sid/main armel libnsl2 armel 1.3.0-3 [33.2 kB] Get:89 http://localhost:3142/debian sid/main armel libtirpc-dev armel 1.3.4+ds-1 [180 kB] Get:90 http://localhost:3142/debian sid/main armel libnsl-dev armel 1.3.0-3 [61.6 kB] Get:91 http://localhost:3142/debian sid/main armel libc6-dev armel 2.37-13 [1294 kB] Get:92 http://localhost:3142/debian sid/main armel libgomp1 armel 13.2.0-9 [107 kB] Get:93 http://localhost:3142/debian sid/main armel libstdc++6 armel 13.2.0-9 [580 kB] Get:94 http://localhost:3142/debian sid/main armel libubsan1 armel 13.2.0-9 [967 kB] Get:95 http://localhost:3142/debian sid/main armel libgcc-11-dev armel 11.4.0-7 [702 kB] Get:96 http://localhost:3142/debian sid/main armel libgfortran5 armel 13.2.0-9 [263 kB] Get:97 http://localhost:3142/debian sid/main armel liblapack3 armel 3.11.0-2 [2256 kB] Get:98 http://localhost:3142/debian sid/main armel liblapack-dev armel 3.11.0-2 [4457 kB] Get:99 http://localhost:3142/debian sid/main armel libpcre2-16-0 armel 10.42-4 [211 kB] Get:100 http://localhost:3142/debian sid/main armel libpcre2-32-0 armel 10.42-4 [201 kB] Get:101 http://localhost:3142/debian sid/main armel libpcre2-8-0 armel 10.42-4 [225 kB] Get:102 http://localhost:3142/debian sid/main armel libpcre2-posix3 armel 10.42-4 [55.1 kB] Get:103 http://localhost:3142/debian sid/main armel libpcre2-dev armel 10.42-4 [657 kB] Get:104 http://localhost:3142/debian sid/main armel libstdc++-11-dev armel 11.4.0-7 [1989 kB] Get:105 http://localhost:3142/debian sid/main armel libtmglib3 armel 3.11.0-2 [123 kB] Get:106 http://localhost:3142/debian sid/main armel libtmglib-dev armel 3.11.0-2 [128 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.8 MB in 0s (193 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 16231 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-6_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-2_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.45-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-2_amd64.deb ... Unpacking file (1:5.45-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-14_amd64.deb ... Unpacking gettext-base (0.21-14) ... 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Setting up gcc-13-cross-base-ports (13.2.0-7cross2) ... Setting up libelf1:amd64 (0.190-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b1) ... Setting up liblocale-gettext-perl (1.07-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14) ... Setting up cpp-13-arm-linux-gnueabi (13.2.0-7cross2) ... Setting up libgomp1-armel-cross (13.2.0-7cross2) ... Setting up libtool (2.4.7-7) ... Setting up libgcc-s1-armel-cross (13.2.0-7cross2) ... Setting up libstdc++6-armel-cross (13.2.0-7cross2) ... Setting up libatomic1-armel-cross (13.2.0-7cross2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up cpp-arm-linux-gnueabi (4:13.2.1-2) ... Setting up libubsan1-armel-cross (13.2.0-7cross2) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libasan8-armel-cross (13.2.0-7cross2) ... Setting up libgcc-13-dev-armel-cross (13.2.0-7cross2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up gcc-13-arm-linux-gnueabi (13.2.0-7cross2) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libstdc++-13-dev-armel-cross (13.2.0-7cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-arm-linux-gnueabi (4:13.2.1-2) ... Setting up g++-13-arm-linux-gnueabi (13.2.0-7cross2) ... Setting up debhelper (13.11.9) ... Setting up g++-arm-linux-gnueabi (4:13.2.1-2) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-armel (12.10) ... Setting up libgcc-s1:armel (13.2.0-9) ... Setting up libc6:armel (2.37-13) ... Setting up libstdc++6:armel (13.2.0-9) ... Setting up libkeyutils1:armel (1.6.3-2) ... Setting up libcrypt1:armel (1:4.4.36-2) ... Setting up libcom-err2:armel (1.47.0-2+b1) ... Setting up libgomp1:armel (13.2.0-9) ... Setting up libpcre2-16-0:armel (10.42-4) ... Setting up libasan6:armel (11.4.0-7) ... Setting up libkrb5support0:armel (1.20.1-5) ... Setting up libpcre2-32-0:armel (10.42-4) ... Setting up libblas3:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabi/libblas.so.3 (libblas.so.3-arm-linux-gnueabi) in auto mode Setting up libatomic1:armel (13.2.0-9) ... Setting up libpcre2-8-0:armel (10.42-4) ... Setting up libk5crypto3:armel (1.20.1-5) ... Setting up libgfortran5:armel (13.2.0-9) ... Setting up libubsan1:armel (13.2.0-9) ... Setting up libpcre2-posix3:armel (10.42-4) ... Setting up libgcc-11-dev:armel (11.4.0-7) ... Setting up libcrypt-dev:armel (1:4.4.36-2) ... Setting up libblas-dev:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/blas/libblas.so to provide /usr/lib/arm-linux-gnueabi/libblas.so (libblas.so-arm-linux-gnueabi) in auto mode Setting up liblapack3:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabi/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabi) in auto mode Setting up libssl3:armel (3.1.4-2) ... Setting up libtmglib3:armel (3.11.0-2) ... Setting up liblapack-dev:armel (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabi/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabi/liblapack.so (liblapack.so-arm-linux-gnueabi) in auto mode Setting up libkrb5-3:armel (1.20.1-5) ... Setting up libtmglib-dev:armel (3.11.0-2) ... Setting up libgssapi-krb5-2:armel (1.20.1-5) ... Setting up libtirpc3:armel (1.3.4+ds-1) ... Setting up libtirpc-dev:armel (1.3.4+ds-1) ... Setting up libnsl2:armel (1.3.0-3) ... Setting up libnsl-dev:armel (1.3.0-3) ... Setting up libc6-dev:armel (2.37-13) ... Setting up libpcre2-dev:armel (10.42-4) ... Setting up libstdc++-11-dev:armel (11.4.0-7) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.37-13) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41.50.20231214-1 dpkg-dev_1.22.2 g++-11_11.4.0-7 g++-13_13.2.0-9 gcc-11_11.4.0-7 gcc-13_13.2.0-9 libc6-dev_2.37-13 libstdc++-11-dev_11.4.0-7 libstdc++-13-dev_13.2.0-9 libstdc++-13-dev-armel-cross_13.2.0-7cross2 libstdc++6_13.2.0-9 libstdc++6-armel-cross_13.2.0-7cross2 linux-libc-dev_6.6.8-1 Package versions: adduser_3.137 apt_2.7.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41.50.20231214-1 binutils-arm-linux-gnueabi_2.41.50.20231214-1 binutils-common_2.41.50.20231214-1 binutils-x86-64-linux-gnu_2.41.50.20231214-1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.4-2+b1 cpp_4:13.2.0-2 cpp-11_11.4.0-7 cpp-13_13.2.0-9 cpp-13-arm-linux-gnueabi_13.2.0-7cross2 cpp-arm-linux-gnueabi_4:13.2.1-2 cross-config_2.6.20 crossbuild-essential-armel_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debian-archive-keyring_2023.4 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.2 dpkg-cross_2.6.20 dpkg-dev_1.22.2 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-2 g++-11_11.4.0-7 g++-13_13.2.0-9 g++-13-arm-linux-gnueabi_13.2.0-7cross2 g++-arm-linux-gnueabi_4:13.2.1-2 gcc_4:13.2.0-2 gcc-11_11.4.0-7 gcc-11-base_11.4.0-7 gcc-12-base_12.3.0-13 gcc-13_13.2.0-9 gcc-13-arm-linux-gnueabi_13.2.0-7cross2 gcc-13-arm-linux-gnueabi-base_13.2.0-7cross2 gcc-13-base_13.2.0-9 gcc-13-cross-base-ports_13.2.0-7cross2 gcc-9-base_9.5.0-4 gcc-arm-linux-gnueabi_4:13.2.1-2 gettext_0.21-14 gettext-base_0.21-14 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.7 libarchive-zip-perl_1.68-1 libasan6_11.4.0-7 libasan8_13.2.0-9 libasan8-armel-cross_13.2.0-7cross2 libatomic1_13.2.0-9 libatomic1-armel-cross_13.2.0-7cross2 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41.50.20231214-1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.3-2 libbz2-1.0_1.0.8-5+b1 libc-bin_2.37-13 libc-dev-bin_2.37-13 libc6_2.37-13 libc6-armel-cross_2.37-12cross1 libc6-dev_2.37-13 libc6-dev-armel-cross_2.37-12cross1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4 libcc1-0_13.2.0-9 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41.50.20231214-1 libctf0_2.41.50.20231214-1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.2 libelf1_0.190-1 libext2fs2_1.47.0-2+b1 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-11-dev_11.4.0-7 libgcc-13-dev_13.2.0-9 libgcc-13-dev-armel-cross_13.2.0-7cross2 libgcc-s1_13.2.0-9 libgcc-s1-armel-cross_13.2.0-7cross2 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-9 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-9 libgomp1-armel-cross_13.2.0-7cross2 libgpg-error0_1.47-3 libgprofng0_2.41.50.20231214-1 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhwasan0_13.2.0-9 libicu72_72.1-4 libidn2-0_2.3.4-1+b1 libio-string-perl_1.08-4 libisl23_0.26-3 libitm1_13.2.0-9 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 liblocale-gettext-perl_1.07-6 liblsan0_13.2.0-9 liblz4-1_1.9.4-1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libnettle8_3.9.1-2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-16-0_10.42-4 libpcre2-32-0_10.42-4 libpcre2-8-0_10.42-4 libpcre2-dev_10.42-4 libpcre2-posix3_10.42-4 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libquadmath0_13.2.0-9 libseccomp2_2.5.4-2+b1 libselinux1_3.5-1+b1 libsemanage-common_3.5-1 libsemanage2_3.5-1+b1 libsepol2_3.5-2 libsframe1_2.41.50.20231214-1 libsmartcols1_2.39.3-2 libss2_1.47.0-2+b1 libssl3_3.1.4-2 libstdc++-11-dev_11.4.0-7 libstdc++-13-dev_13.2.0-9 libstdc++-13-dev-armel-cross_13.2.0-7cross2 libstdc++6_13.2.0-9 libstdc++6-armel-cross_13.2.0-7cross2 libsub-override-perl_0.10-1 libsystemd0_255-1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtmglib-dev_3.11.0-2 libtmglib3_3.11.0-2 libtool_2.4.7-7 libtsan0_11.4.0-7 libtsan2_13.2.0-9 libubsan1_13.2.0-9 libubsan1-armel-cross_13.2.0-7cross2 libuchardet0_0.0.8-1 libudev1_255-1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3+b1 libxxhash0_0.8.2-2 libyaml-perl_1.30-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.8-1 linux-libc-dev-armel-cross_6.5.8-1cross1 login_1:4.13+dfsg1-3 logsave_1.47.0-2+b1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 mount_2.39.3-2 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-10 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.4 tzdata_2023c-11 ucf_3.0043+nmu1 usrmerge_38 util-linux_2.39.3-2 util-linux-extra_2.39.3-2 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: phast Binary: phast Architecture: any Version: 1.6+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://compgen.cshl.edu/phast/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/phast Vcs-Git: https://salsa.debian.org/med-team/phast.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man Package-List: phast deb science optional arch=any Checksums-Sha1: 5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz c0f74aa42bbb46eebe231f0adcb642694330bedf 57936 phast_1.6+dfsg-4.debian.tar.xz Checksums-Sha256: 7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz 7f5b1adf0df0a8290be8f07117762b2bea42720e2e9b2752e54f680b187f0678 57936 phast_1.6+dfsg-4.debian.tar.xz Files: b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz 2a268ec20d4b5b60d354fae365dc5c3e 57936 phast_1.6+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWFuT0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHOIA//eyCfPTB2qbw4E7fYvodojc5OvGnTMOR2 6nI+MSWImaD5neTkVstxYQENwrQ4npV9J8jbYn2RgnIqobH22HGP4d7RBAP86mq6 543imwc1jaDZBvYB8cxR6wG+mSjZT1OnfSZ+K/2ITLvlY6v2Fu9kjAzLADLqVf4a k9+JnI0dFAjdMsP4bws+G2yAwdyIKfaiYxlZH7padlKzLWXKT0OtW37Ircy1ARMJ 8IJIKtw7iBq3Dou/sqA8OR4D271shnsw3wMZJGS+OjdMo/13J7rEOyLKd/S9weyJ T6gerJHYXoxZ2UhAFFRfmNleG93S8pCn/FDoN+THv03U1FBb0Uj7WNapgkqe1GH0 fq7o69yU7OnHAtOM58WKgxTDSbBtNfGV9jcQekWcn7kkH2dvex0xno0iFqlb7Tyy fFpmueyHVb9mWfT5FPgSKJEFqYpqKsLDJn9PDgoeyf/zGk0fE0IybVCgcbZ1NGQC oOS9QJaNT6Qs51iDk9HRQKWx0iSOsDCnXCtjThNiUuOLBCFaA+0PrAXrc+gm7GGk hu5P8NgbK6AGrOXwSh+LezURWSwbGbnN6YcjqYawNyVQ3wwWP3qsXJofRr5A28/W u1C9T0KAw9/hslivACVzYXWGIIK4XBR7hYAqnojwsVBWAAsSPVLnf6GkXoaYNMhx 2XWe92QzcyI= =iVmf -----END PGP SIGNATURE----- gpgv: Signature made Fri Dec 22 16:28:45 2023 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting phast in /<> dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.6+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.patch dpkg-source: info: applying pcre2.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.r3M3u8zr9R/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-0f80300f-3edf-4ca4-a9be-f6f0d9e89108 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.6+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean cd src && make clean make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make clean ; done make[4]: Entering directory '/<>/src/lib/base' rm -f *.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' rm -f *.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' rm -f *.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' rm -f *.o make[4]: Leaving directory '/<>/src/lib/motif' rm -f /<>/src/lib/../../lib/* make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' rm -f *.o dless.help dlessP.help /<>/src/dless/../../bin/dless /<>/src/dless/../../bin/dlessP make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' rm -f *.o *.help /<>/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' rm -f *.o /<>/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' rm -f *.o *.help /<>/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' rm -f *.o /<>/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' rm -f *.o /<>/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' rm -f *.o *.help /<>/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' rm -f *.o /<>/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' rm -f *.o /<>/src/prequel/../../bin/pbsDecode /<>/src/prequel/../../bin/pbsEncode /<>/src/prequel/../../bin/pbsScoreMatrix /<>/src/prequel/../../bin/pbsTrain /<>/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' rm -f *.o *.help /<>/src/util/../../bin/all_dists /<>/src/util/../../bin/base_evolve /<>/src/util/../../bin/chooseLines /<>/src/util/../../bin/clean_genes /<>/src/util/../../bin/consEntropy /<>/src/util/../../bin/convert_coords /<>/src/util/../../bin/display_rate_matrix /<>/src/util/../../bin/draw_tree /<>/src/util/../../bin/eval_predictions /<>/src/util/../../bin/hmm_train /<>/src/util/../../bin/hmm_tweak /<>/src/util/../../bin/hmm_view /<>/src/util/../../bin/indelFit /<>/src/util/../../bin/indelHistory /<>/src/util/../../bin/maf_parse /<>/src/util/../../bin/makeHKY /<>/src/util/../../bin/modFreqs /<>/src/util/../../bin/msa_diff /<>/src/util/../../bin/msa_split /<>/src/util/../../bin/msa_view /<>/src/util/../../bin/phast /<>/src/util/../../bin/phastBias /<>/src/util/../../bin/refeature /<>/src/util/../../bin/stringiphy /<>/src/util/../../bin/treeGen /<>/src/util/../../bin/tree_doctor make[3]: Leaving directory '/<>/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc make[1]: Entering directory '/<>' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/<>/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<>/src/$dir && make ; done make[3]: Entering directory '/<>/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/src/lib/$dir && make ; done make[4]: Entering directory '/<>/src/lib/base' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_eigen.c: In function ‘mat_diagonalize’: phast_eigen.c:62:3: warning: implicit declaration of function ‘dgeev_’ [-Wimplicit-function-declaration] 62 | dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl, | ^~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_markov_matrix.c: In function ‘mm_exp_higham’: phast_markov_matrix.c:288:5: warning: implicit declaration of function ‘dgebal_’ [-Wimplicit-function-declaration] 288 | dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info); | ^~~~~~~ phast_markov_matrix.c:403:3: warning: implicit declaration of function ‘dgesv_’ [-Wimplicit-function-declaration] 403 | dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info); | ^~~~~~ phast_markov_matrix.c:428:5: warning: implicit declaration of function ‘dgebak_’ [-Wimplicit-function-declaration] 428 | dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info); | ^~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_matrix.c: In function ‘mat_invert’: phast_matrix.c:263:3: warning: implicit declaration of function ‘dgetrf_’ [-Wimplicit-function-declaration] 263 | dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info); | ^~~~~~~ phast_matrix.c:273:3: warning: implicit declaration of function ‘dgetri_’ [-Wimplicit-function-declaration] 273 | dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info); | ^~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_misc.c: In function ‘make_name_hash’: phast_misc.c:672:46: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from phast_misc.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_misc.c:672:35: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*"); | ^~~~~~~~~~ phast_misc.c: In function ‘phast_fclose’: phast_misc.c:301:5: warning: pointer ‘f’ used after ‘fclose’ [-Wuse-after-free] 301 | unregister_open_file(f); | ^~~~~~~~~~~~~~~~~~~~~~~ phast_misc.c:300:5: note: call to ‘fclose’ here 300 | fclose(f); | ^~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of ‘pcre2_match_8’ differ in signedness [-Wpointer-sign] 501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL); | ~^~~~~~~ | | | char * In file included from phast_stringsplus.c:16: /usr/include/pcre2.h:935:1: note: expected ‘PCRE2_SPTR8’ {aka ‘const unsigned char *’} but argument is of type ‘char *’ 935 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ phast_stringsplus.c: In function ‘str_re_match’: phast_stringsplus.c:532:30: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_search’: phast_stringsplus.c:538:28: warning: passing argument 2 of ‘str_re_match_sub’ from incompatible pointer type [-Wincompatible-pointer-types] 538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx); | ^~ | | | pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *} phast_stringsplus.c:488:45: note: expected ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} but argument is of type ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} 488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp, | ^ phast_stringsplus.c: In function ‘str_re_match_sub’: phast_stringsplus.c:504:52: warning: ‘ovector’ may be used uninitialized [-Wmaybe-uninitialized] 504 | if (first_match != NULL) (*first_match) = ovector[0]; | ~~~~~~~^~~ phast_stringsplus.c:491:15: note: ‘ovector’ was declared here 491 | PCRE2_SIZE *ovector; | ^~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar: creating /<>/src/lib/base/../../../lib/libphast.a ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o ar rs /<>/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o make[4]: Leaving directory '/<>/src/lib/base' make[4]: Entering directory '/<>/src/lib/msa' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_local_alignment.c: In function ‘la_read_lav’: phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/local_alignment.h:36, from phast_local_alignment.c:32: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_local_alignment.c:50:44: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{"); | ^~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_maf.c: In function ‘maf_read_cats_subset’: phast_maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_msa.c: In function ‘msa_read_fasta’: phast_msa.c:264:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_msa.c:39: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:264:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)"); | ^ phast_msa.c:257:40: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ phast_msa.c: In function ‘msa_read_seq_fasta’: phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:1929:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 1929 | descrip_re = str_re_new("^[[:space:]]*>"); | ^ phast_msa.c: In function ‘msa_format_for_content’: phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2590:9: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2591:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)"); | ^ phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2592 | fasta_re = str_re_new("^>.*"); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2592:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2592 | fasta_re = str_re_new("^>.*"); | ^ phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2593 | lav_re = str_re_new("^#:lav.*"); | ^~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2593:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2593 | lav_re = str_re_new("^#:lav.*"); | ^ phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 2594 | maf_re = str_re_new("^##maf"); | ^~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_msa.c:2594:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 2594 | maf_re = str_re_new("^##maf"); | ^ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_multi_msa.c: In function ‘multimsa_new_from_files’: phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_multi_msa.c:37: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:54:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~ phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:55:36: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_multi_msa.c:56:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)"); | ^~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_sufficient_stats.c: In function ‘ss_from_msas’: phast_sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ phast_sufficient_stats.c: In function ‘ss_read’: phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from /<>/src/../include/phast/sufficient_stats.h:20, from phast_sufficient_stats.c:11: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:661:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:662:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:663:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:664:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)"); | ^ phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:665:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)"); | ^ phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:666:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)"); | ^ phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:667:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:668:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)"); | ^ phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:669:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)"); | ^ phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_sufficient_stats.c:670:12: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 670 | order_re = str_re_new("TUPLE_IDX_ORDER:"); | ^ ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o ar rs /<>/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o make[4]: Leaving directory '/<>/src/lib/msa' make[4]: Entering directory '/<>/src/lib/feature' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_bed.c: In function ‘gff_print_bed’: phast_bed.c:143:52: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_bed.c:15: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_bed.c:143:41: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_category_map.c: In function ‘cm_read’: phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/category_map.h:92, from phast_category_map.c:10: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:39:18: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?"); | ^ phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:40:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)"); | ^ phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:41:13: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:42:14: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$"); | ^ phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_category_map.c:43:15: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$"); | ^ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_gff.c: In function ‘gff_read_set’: phast_gff.c:56:38: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from phast_gff.c:13: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:56:25: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?"); | ^ phast_gff.c: In function ‘gff_new_feature_genomic_pos’: phast_gff.c:272:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:272:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?"); | ^ phast_gff.c: In function ‘gff_group’: phast_gff.c:688:23: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 688 | tag_re = str_re_new(tmpstr); | ^~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_gff.c:688:10: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 688 | tag_re = str_re_new(tmpstr); | ^ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o ar rs /<>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o make[4]: Leaving directory '/<>/src/lib/feature' make[4]: Entering directory '/<>/src/lib/hmm' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o ar rs /<>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o make[4]: Leaving directory '/<>/src/lib/hmm' make[4]: Entering directory '/<>/src/lib/phylo' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_phylo_p_print.c: In function ‘print_feats_generic’: phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_phylo_p_print.c:17: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_phylo_p_print.c:752:39: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)"); | ^~~~~~~~~~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o ar rs /<>/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o make[4]: Leaving directory '/<>/src/lib/phylo' make[4]: Entering directory '/<>/src/lib/phylo_hmm' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o ar rs /<>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o make[4]: Leaving directory '/<>/src/lib/phylo_hmm' make[4]: Entering directory '/<>/src/lib/motif' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_motif.c: In function ‘mtf_print’: phast_motif.c:1411:21: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~ phast_motif.c: In function ‘mtf_print_html’: phast_motif.c:1604:23: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~ arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phast_tfbs.c: In function ‘pwm_read’: phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from phast_tfbs.c:16: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:147:11: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)"); | ^ phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:148:17: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*"); | ^ phast_tfbs.c: In function ‘ms_read’: phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ phast_tfbs.c:229:16: warning: assignment to ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)"); | ^ phast_tfbs.c:219:32: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o ar rs /<>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o make[4]: Leaving directory '/<>/src/lib/motif' make[3]: Leaving directory '/<>/src/lib' make[3]: Entering directory '/<>/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/<>/src/dless/../../bin/dless'. Stop. make[3]: Leaving directory '/<>/src/dless' make[3]: Entering directory '/<>/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/exoniphy/../../lib -o /<>/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/exoniphy' make[3]: Entering directory '/<>/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/phastCons/../../lib -o /<>/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastCons' make[3]: Entering directory '/<>/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/phastOdds/../../lib -o /<>/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastOdds' make[3]: Entering directory '/<>/src/phastMotif' arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ arm-linux-gnueabi-gcc -L/<>/src/phastMotif/../../lib -o /<>/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phastMotif' make[3]: Entering directory '/<>/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/phyloFit/../../lib -o /<>/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phyloFit' make[3]: Entering directory '/<>/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/phyloBoot/../../lib -o /<>/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phyloBoot' make[3]: Entering directory '/<>/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/phyloP/../../lib -o /<>/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/phyloP' make[3]: Entering directory '/<>/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition make[3]: *** No rule to make target 'simplex_grid.o', needed by '/<>/src/prequel/../../bin/pbsDecode'. Stop. make[3]: Leaving directory '/<>/src/prequel' make[3]: Entering directory '/<>/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh treeGen.help_src > treeGen.help arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition msa_view.c: In function ‘fill_with_Ns’: msa_view.c:361:49: warning: pointer targets in passing argument 1 of ‘str_re_new’ differ in signedness [-Wpointer-sign] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | char * In file included from /<>/src/../include/phast/gff.h:21, from /<>/src/../include/phast/msa.h:19, from msa_view.c:14: /<>/src/../include/phast/stringsplus.h:386:45: note: expected ‘const unsigned char *’ but argument is of type ‘char *’ 386 | pcre2_code *str_re_new(const unsigned char *re_str); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~ msa_view.c:361:38: warning: initialization of ‘pcre2_compile_context_8 *’ {aka ‘struct pcre2_real_compile_context_8 *’} from incompatible pointer type ‘pcre2_code_8 *’ {aka ‘struct pcre2_real_code_8 *’} [-Wincompatible-pointer-types] 361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)"); | ^~~~~~~~~~ arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now arm-linux-gnueabi-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<>/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition tree_doctor.c: In function ‘main’: tree_doctor.c:348:19: warning: the comparison will always evaluate as ‘true’ for the address of ‘name’ will never be NULL [-Waddress] 348 | if (n->name != NULL && n->name[0] != '\0' && | ^~ In file included from /<>/src/../include/phast/tree_model.h:26, from tree_doctor.c:14: /<>/src/../include/phast/trees.h:47:8: note: ‘name’ declared here 47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */ | ^~~~ arm-linux-gnueabi-gcc -L/<>/src/util/../../lib -o /<>/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src/util' mkdir -p ../doc/man/ Generating man pages... ../debian/help2man_wrapper: 1: ../bin/all_dists: Exec format error ../debian/help2man_wrapper: 1: ../bin/base_evolve: Exec format error ../debian/help2man_wrapper: 1: ../bin/chooseLines: Exec format error ../debian/help2man_wrapper: 1: ../bin/clean_genes: Exec format error ../debian/help2man_wrapper: 1: ../bin/consEntropy: Exec format error ../debian/help2man_wrapper: 1: ../bin/convert_coords: Exec format error ../debian/help2man_wrapper: 1: ../bin/display_rate_matrix: Exec format error ../debian/help2man_wrapper: 1: ../bin/draw_tree: Exec format error ../debian/help2man_wrapper: 1: ../bin/eval_predictions: Exec format error ../debian/help2man_wrapper: 1: ../bin/exoniphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_train: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_tweak: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelHistory: Exec format error ../debian/help2man_wrapper: 1: ../bin/maf_parse: Exec format error ../debian/help2man_wrapper: 1: ../bin/makeHKY: Exec format error ../debian/help2man_wrapper: 1: ../bin/modFreqs: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_diff: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_split: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/phast: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastBias: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastCons: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastMotif: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastOdds: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloBoot: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloP: Exec format error ../debian/help2man_wrapper: 1: ../bin/refeature: Exec format error ../debian/help2man_wrapper: 1: ../bin/stringiphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/treeGen: Exec format error ../debian/help2man_wrapper: 1: ../bin/tree_doctor: Exec format error Done. make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/phast/ -a make -j1 install DESTDIR=/<>/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' (cd src; make install DESTDIR=/<>/debian/phast ) make[2]: Entering directory '/<>/src' mkdir -p /<>/debian/phast/usr/bin/ mkdir -p /<>/debian/phast/usr/share/phast/data/ mkdir -p /<>/debian/phast/usr/share/man/man1/ cp ../bin/* /<>/debian/phast/usr/bin/ cp -R ../data/* /<>/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /<>/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \; make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-4_armel.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-4_armel.deb'. dpkg-genbuildinfo --build=any -O../phast_1.6+dfsg-4_armel.buildinfo dpkg-genchanges --build=any -O../phast_1.6+dfsg-4_armel.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 2023-12-23T18:19:34Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.6+dfsg-4_armel.changes: ------------------------------- Format: 1.8 Date: Wed, 29 Nov 2023 10:25:18 +0100 Source: phast Binary: phast phast-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 1.6+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phast - phylogenetic analysis with space/time models Closes: 1056681 Changes: phast (1.6+dfsg-4) unstable; urgency=medium . [ Andreas Tille ] * s/libatlas-base-dev/liblapacke-dev/ in Build-Depends to use LAPACKE instead of clapack * Provide alternative Build-Depends to liblapack-dev and libblas-dev * Standards-Version: 4.6.2 (routine-update) * Upstream email removed from d/copyright since its bouncing . [ Sébastien Villemot ] * Complete migration away from ATLAS Closes: #1056681 Checksums-Sha1: 31fe2155591dcc0fb044f92b8f26bb0836682de6 25269072 phast-dbgsym_1.6+dfsg-4_armel.deb daf41dc4c90a4f7401bd5333a99eaee27518bee6 5692 phast_1.6+dfsg-4_armel.buildinfo f3c207126d5e22c318dcab79e96a8b92f23211ab 2656648 phast_1.6+dfsg-4_armel.deb Checksums-Sha256: 6d06984fbd020b0d3061ce699aca70bdb1332fa2f42a5bc3c230ebd85fe42e7c 25269072 phast-dbgsym_1.6+dfsg-4_armel.deb 511f8c397d19914b5d152281c2b37913202685144a71d88153fb0d7f4da5019a 5692 phast_1.6+dfsg-4_armel.buildinfo ae90136c4d613f14b9c47f0f1d2d47c4c46d9091add88dfb710edbb8b24eb220 2656648 phast_1.6+dfsg-4_armel.deb Files: e9ca674b33ff4710429b8ba55aedc518 25269072 debug optional phast-dbgsym_1.6+dfsg-4_armel.deb 19dbca378489b81a7883c1a3b5b55a3a 5692 science optional phast_1.6+dfsg-4_armel.buildinfo 369288e4606a28a4b9db98c87523a3a2 2656648 science optional phast_1.6+dfsg-4_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast phast-dbgsym Architecture: armel Version: 1.6+dfsg-4 Checksums-Md5: e9ca674b33ff4710429b8ba55aedc518 25269072 phast-dbgsym_1.6+dfsg-4_armel.deb 369288e4606a28a4b9db98c87523a3a2 2656648 phast_1.6+dfsg-4_armel.deb Checksums-Sha1: 31fe2155591dcc0fb044f92b8f26bb0836682de6 25269072 phast-dbgsym_1.6+dfsg-4_armel.deb f3c207126d5e22c318dcab79e96a8b92f23211ab 2656648 phast_1.6+dfsg-4_armel.deb Checksums-Sha256: 6d06984fbd020b0d3061ce699aca70bdb1332fa2f42a5bc3c230ebd85fe42e7c 25269072 phast-dbgsym_1.6+dfsg-4_armel.deb ae90136c4d613f14b9c47f0f1d2d47c4c46d9091add88dfb710edbb8b24eb220 2656648 phast_1.6+dfsg-4_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 23 Dec 2023 18:19:33 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.3), bash (= 5.2.21-2), binutils (= 2.41.50.20231214-1), binutils-common (= 2.41.50.20231214-1), binutils-x86-64-linux-gnu (= 2.41.50.20231214-1), bsdextrautils (= 2.39.3-2), bsdutils (= 1:2.39.3-2), build-essential (= 12.10), bzip2 (= 1.0.8-5+b1), coreutils (= 9.4-2+b1), cpp (= 4:13.2.0-2), cpp-11 (= 11.4.0-7), cpp-13 (= 13.2.0-9), dash (= 0.5.12-6), debconf (= 1.5.82), debhelper (= 13.11.9), debianutils (= 5.14), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.2), dpkg-dev (= 1.22.2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-2), g++-13 (= 13.2.0-9), gcc (= 4:13.2.0-2), gcc-11 (= 11.4.0-7), gcc-11-base (= 11.4.0-7), gcc-13 (= 13.2.0-9), gcc-13-base (= 13.2.0-9), gettext (= 0.21-14), gettext-base (= 0.21-14), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1), help2man (= 1.49.3), hostname (= 3.23+nmu1), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.4.0-7), libasan8 (= 13.2.0-9), libatomic1 (= 13.2.0-9), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libbinutils (= 2.41.50.20231214-1), libblas-dev (= 3.11.0-2), libblas3 (= 3.11.0-2), libblkid1 (= 2.39.3-2), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.37-13), libc-dev-bin (= 2.37-13), libc6 (= 2.37-13), libc6-dev (= 2.37-13), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4), libcc1-0 (= 13.2.0-9), libcom-err2 (= 1.47.0-2+b1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41.50.20231214-1), libctf0 (= 2.41.50.20231214-1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271), libdebhelper-perl (= 13.11.9), libdpkg-perl (= 1.22.2), libelf1 (= 0.190-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-11-dev (= 11.4.0-7), libgcc-13-dev (= 13.2.0-9), libgcc-s1 (= 13.2.0-9), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 13.2.0-9), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 13.2.0-9), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41.50.20231214-1), libgssapi-krb5-2 (= 1.20.1-5), libhwasan0 (= 13.2.0-9), libicu72 (= 72.1-4), libisl23 (= 0.26-3), libitm1 (= 13.2.0-9), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblapack-dev (= 3.11.0-2), liblapack3 (= 3.11.0-2), liblocale-gettext-perl (= 1.07-6), liblsan0 (= 13.2.0-9), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.3-2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-9.1), libpam-modules-bin (= 1.5.2-9.1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1), libpcre2-16-0 (= 10.42-4), libpcre2-32-0 (= 10.42-4), libpcre2-8-0 (= 10.42-4), libpcre2-dev (= 10.42-4), libpcre2-posix3 (= 10.42-4), libperl5.36 (= 5.36.0-10), libpipeline1 (= 1.5.7-1), libquadmath0 (= 13.2.0-9), libseccomp2 (= 2.5.4-2+b1), libselinux1 (= 3.5-1+b1), libsframe1 (= 2.41.50.20231214-1), libsmartcols1 (= 2.39.3-2), libssl3 (= 3.1.4-2), libstdc++-13-dev (= 13.2.0-9), libstdc++6 (= 13.2.0-9), libsub-override-perl (= 0.10-1), libsystemd0 (= 255-1), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20231209-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtmglib-dev (= 3.11.0-2), libtmglib3 (= 3.11.0-2), libtool (= 2.4.7-7), libtsan0 (= 11.4.0-7), libtsan2 (= 13.2.0-9), libubsan1 (= 13.2.0-9), libuchardet0 (= 0.0.8-1), libudev1 (= 255-1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-2), libxml2 (= 2.9.14+dfsg-1.3+b1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.8-1), login (= 1:4.13+dfsg1-3), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231126-1), ncurses-base (= 6.4+20231209-1), ncurses-bin (= 6.4+20231209-1), patch (= 2.7.6-7), perl (= 5.36.0-10), perl-base (= 5.36.0-10), perl-modules-5.36 (= 5.36.0-10), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-5), tar (= 1.34+dfsg-1.4), usrmerge (= 38), util-linux (= 2.39.3-2), xz-utils (= 5.4.5-0.1), zlib1g (= 1:1.3.dfsg-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1701249918" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast-dbgsym_1.6+dfsg-4_armel.deb --------------------------------- new Debian package, version 2.0. size 25269072 bytes: control archive=2084 bytes. 1682 bytes, 12 lines control 3581 bytes, 34 lines md5sums Package: phast-dbgsym Source: phast Version: 1.6+dfsg-4 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 26954 Depends: phast (= 1.6+dfsg-4) Section: debug Priority: optional Description: debug symbols for phast Build-Ids: 0dc97384f9090ba763527215bd77649bb1f8c9eb 0efc83fa9bc65aad0a6a9601baa46425f452f501 18d7e4b8d4d9c4ea543cbb47ad6c734b312da5b2 2a5dce117a6afb96d32aeb92f6b1ab99b4f0c0a7 31cb28e18a9cb0d720635a86a0d9bdc63785ecab 36f3a250b3abc775ff6906c63c81f13f8f1be579 3e0bcbf244558a79687b6d3c182357e5886588af 42daee7cc02bd332fbc9ecc2a104f9b117402459 43e8efcc8d778825ea9cbff27bd09b429caec9eb 4553c1b44cc52f6e2ffddeef13735f978a04ef8c 486784a3e93639e149839770cb60f55e054c82da 4be57608f08e9c693467b3dbeb0bc964c9631da4 4df33e14b62075a49c9ae0f95966d42998b2d194 57f612d11345a12bba0c6a0c07da99abf97eedf2 64f794ab26de9c092733694125592ef396d86ee3 65713b3d6b0459e407386f57e73a46d0a3b0122b 6caa37c77e7e221c6c7f9c5f73de9b28de4368a2 747904187735b6a66297cd4dec15689802651ce2 76a3c1d53376fd9747b90eacc843cce89a78ab85 8633308bb468c17a5e379b6d8510c6fdf6cc62bd 8e3dbc6481be97a9b97231ed56ca01e0308566c4 91e61bd688647d3ed802eae469c163b1e370a6ab 950c946497ee0e5cc22a719c6ecd4af0d2ff9836 9f7138fa0656ab30f77ebd065c90d2aa01f6adad bf931fea36dd41f702dca1baa921158e70a397c4 c04b4653a4da9cf9c7089c2affeb3a1d9990c519 c1595285c624d341dd10f803b812c7ef6fdd053e c4dba33739f4193f4b5a1cb458da2e1cef10dbaa d975cb27df0f84f94a1a30299accce1c61d12eec df5952fe607b04420f735ee1d69bb861c35cf652 e4b2cf8b917a8dca686e61a10f8445e88d1d3b94 f543544f8689fe3bcb05dafc9d577da6c1b463d6 fe60c4f7566ee0b32f2cedfe1c320129133c93fa drwxr-xr-x root/root 0 2023-11-29 09:25 ./ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/lib/ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-11-29 09:25 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archive=5528 bytes. 1112 bytes, 22 lines control 14785 bytes, 195 lines md5sums Package: phast Version: 1.6+dfsg-4 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 23032 Depends: libc6 (>= 2.34), liblapack3 | liblapack.so.3, libpcre2-8-0 (>= 10.22) Section: science Priority: optional Homepage: http://compgen.cshl.edu/phast/ Description: phylogenetic analysis with space/time models PHAST is a software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. . 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8438 2023-11-29 09:25 ./usr/share/man/man1/phyloFit.1.gz -rw-r--r-- root/root 5007 2023-11-29 09:25 ./usr/share/man/man1/phyloP.1.gz -rw-r--r-- root/root 2790 2023-11-29 09:25 ./usr/share/man/man1/prequel.1.gz -rw-r--r-- root/root 1533 2023-11-29 09:25 ./usr/share/man/man1/refeature.1.gz -rw-r--r-- root/root 349 2023-11-29 09:25 ./usr/share/man/man1/stringiphy.1.gz -rw-r--r-- root/root 702 2023-11-29 09:25 ./usr/share/man/man1/treeGen.1.gz -rw-r--r-- root/root 2372 2023-11-29 09:25 ./usr/share/man/man1/tree_doctor.1.gz drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/share/phast/ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/share/phast/data/ drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/ -rw-r--r-- root/root 244 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/default-no-cns.cm -rw-r--r-- root/root 271 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/default.cm drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/ -rw-r--r-- root/root 629 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/cftr25_hybrid.nh -rw-r--r-- root/root 680372 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/default-indels-no-cns.hmm -rw-r--r-- root/root 732444 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/default-indels.hmm -rw-r--r-- root/root 14434 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/default-no-cns.hmm -rw-r--r-- root/root 15378 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/default.hmm -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-1.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-2.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-3.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-4.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.3'splice-5.mod 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./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-2.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.cds5'ss-3.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-1.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-2.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-3.mod -rw-r--r-- root/root 392 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.prestart-4.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.start-1.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.start-2.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.start-3.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.stop-1.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.stop-2.mod -rw-r--r-- root/root 363 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/hky.stop-3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc4.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.gc5.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod -rw-r--r-- root/root 62237 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod -rw-r--r-- root/root 62237 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.cns.mod -rw-r--r-- root/root 49950 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod -rw-r--r-- root/root 49950 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod -rw-r--r-- root/root 49950 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod -rw-r--r-- root/root 49950 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod -rw-r--r-- root/root 49950 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc5.mod -rw-r--r-- root/root 49949 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod -rw-r--r-- root/root 529 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models -rw-r--r-- root/root 549 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-gc1 -rw-r--r-- root/root 549 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-gc2 -rw-r--r-- root/root 549 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-gc3 -rw-r--r-- root/root 549 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-gc4 -rw-r--r-- root/root 549 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-gc5 -rw-r--r-- root/root 523 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns -rw-r--r-- root/root 539 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns-gc1 -rw-r--r-- root/root 539 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns-gc2 -rw-r--r-- root/root 539 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns-gc3 -rw-r--r-- root/root 539 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns-gc4 -rw-r--r-- root/root 539 2023-11-29 09:25 ./usr/share/phast/data/exoniphy/models-no-cns-gc5 drwxr-xr-x root/root 0 2023-11-29 09:25 ./usr/share/phast/data/phastCons/ -rw-r--r-- root/root 103302 2023-11-29 09:25 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm -rw-r--r-- root/root 584 2023-11-29 09:25 ./usr/share/phast/data/phastCons/simple-coding.hmm lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1391 B] Get:5 copy:/<>/apt_archive ./ Packages [1442 B] Fetched 3448 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:armel t1utils unzip 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 13.8 MB of archives. After this operation, 51.5 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.1.4-2 [1426 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.44.2-1 [882 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.15.0-1 [2906 kB] Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:29 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:30 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.60-1 [219 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:33 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:35 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:36 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:37 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:38 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:39 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:40 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:41 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.37-1 [131 kB] Get:42 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:43 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:46 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:49 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:50 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:56 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:57 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:60 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:61 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:62 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:64 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:65 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:72 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:73 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:74 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.084-1 [216 kB] Get:75 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:76 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:77 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:78 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.72-1 [187 kB] Get:79 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:80 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:81 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:82 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:83 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-6 [37.8 kB] Get:88 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:89 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:91 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:92 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:93 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:95 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:96 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:97 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:98 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1 [12.5 kB] Get:100 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:101 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:102 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:103 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:104 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1 [43.0 kB] Get:105 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1 [99.5 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1 [102 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:109 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.39-1 [60.3 kB] Get:110 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1 [28.8 kB] Get:111 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:113 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:114 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:115 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:116 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:117 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:118 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:119 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:120 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:121 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-6 [63.1 kB] Get:122 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:123 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:124 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:125 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:126 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.8 MB in 0s (82.5 MB/s) Selecting previously unselected package netbase. (Reading database ... 22304 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.1.4-2_amd64.deb ... Unpacking openssl (3.1.4-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../005-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package libreadline8:amd64. 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Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b1_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b1_amd64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:amd64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b1_amd64.deb ... Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../026-liburi-perl_5.21-1_all.deb ... Unpacking liburi-perl (5.21-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../027-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) ... Selecting previously unselected package libcgi-pm-perl. 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Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../034-libparams-util-perl_1.102-2+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../035-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../036-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../037-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../038-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../039-libcpanel-json-xs-perl_4.37-1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.37-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../040-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../041-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../042-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../043-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libdata-dpath-perl. Preparing to unpack .../044-libdata-dpath-perl_0.59-1_all.deb ... Unpacking libdata-dpath-perl (0.59-1) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../045-libdata-messagepack-perl_1.02-1+b1_amd64.deb ... Unpacking libdata-messagepack-perl (1.02-1+b1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../046-libnet-domain-tld-perl_1.75-3_all.deb ... Unpacking libnet-domain-tld-perl (1.75-3) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../047-libdata-validate-domain-perl_0.10-1.1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1.1) ... Selecting previously unselected package libnet-ipv6addr-perl. Preparing to unpack .../048-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... Selecting previously unselected package libnet-netmask-perl. Preparing to unpack .../049-libnet-netmask-perl_2.0002-2_all.deb ... Unpacking libnet-netmask-perl (2.0002-2) ... 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Setting up plzip (1.10-6) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:amd64 (3.44.2-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.39-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1) ... Setting up libsyntax-keyword-try-perl (0.29-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.1.4-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+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 libreadline8:amd64 (8.2-3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up gpgconf (2.2.40-1.1) ... Setting up libio-socket-ssl-perl (2.084-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.60-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.37-13) ... Processing triggers for man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 189004 Build-Time: 77 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 12 Job: phast_1.6+dfsg-4 Lintian: pass Machine Architecture: amd64 Package: phast Package-Time: 100 Source-Version: 1.6+dfsg-4 Space: 189004 Status: successful Version: 1.6+dfsg-4 -------------------------------------------------------------------------------- Finished at 2023-12-23T18:19:34Z Build needed 00:01:40, 189004k disk space