sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on gcc131.bak.milne.osuosl.org +==============================================================================+ | phast 1.5+dfsg-1 (arm64) Wed, 07 Aug 2019 03:07:32 +0000 | +==============================================================================+ Package: phast Version: 1.5+dfsg-1 Source Version: 1.5+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-bab9c331-eb10-4d4c-86c8-b4cac10fc3a4' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [149 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-06-0817.30.pdiff [22.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-06-1429.56.pdiff [15.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-06-2030.57.pdiff [30.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-07-0217.21.pdiff [12.4 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-06-0817.30.pdiff [8472 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-06-1429.56.pdiff [15.0 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-06-2030.57.pdiff [49.5 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main Sources 2019-08-07-0217.21.pdiff [12.4 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-07-0217.21.pdiff [16.4 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2019-08-07-0217.21.pdiff [16.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8197 kB] Fetched 8572 kB in 2s (4358 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: coreutils libpcre2-8-0 libpcre3 linux-libc-dev tar zlib1g 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5361 kB of archives. After this operation, 182 kB of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 coreutils amd64 8.30-3+b1 [2708 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 tar amd64 1.30+dfsg-6+b1 [780 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libpcre2-8-0 amd64 10.32-5+b1 [213 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libpcre3 amd64 2:8.39-12+b1 [341 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+b1 [91.0 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev amd64 5.2.6-1 [1227 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5361 kB in 0s (48.7 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | 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 1866 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main phast 1.5+dfsg-1 (dsc) [1988 B] Get:2 http://debian.oregonstate.edu/debian unstable/main phast 1.5+dfsg-1 (tar) [1811 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main phast 1.5+dfsg-1 (diff) [53.1 kB] Fetched 1866 kB in 0s (41.1 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/phast-abq3uO/phast-1.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-abq3uO' with '<>' +------------------------------------------------------------------------------+ | Install crossbuild-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64 Filtered Build-Depends: build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64 dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-2Ul5Yu/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Sources [362 B] Get:5 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Packages [451 B] Fetched 1770 B in 0s (77.7 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: binutils-aarch64-linux-gnu cpp-8-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 dpkg-cross file g++-8-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-8-aarch64-linux-gnu gcc-8-aarch64-linux-gnu-base gcc-8-cross-base gcc-9-cross-base gcc-aarch64-linux-gnu libasan5-arm64-cross libatomic1-arm64-cross libc6-arm64-cross libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-arm64-cross libgcc1-arm64-cross libgomp1-arm64-cross libicu63 libio-string-perl libitm1-arm64-cross liblocale-gettext-perl liblsan0-arm64-cross libmagic-mgc libmagic1 libstdc++-8-dev-arm64-cross libstdc++6-arm64-cross libtsan0-arm64-cross libubsan1-arm64-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-arm64-cross sensible-utils ucf Suggested packages: binutils-doc gcc-8-locales cpp-doc binutils-multiarch gcc-8-doc libstdc++6-8-dbg-arm64-cross libgcc1-dbg-arm64-cross libgomp1-dbg-arm64-cross libitm1-dbg-arm64-cross libatomic1-dbg-arm64-cross libasan5-dbg-arm64-cross liblsan0-dbg-arm64-cross libtsan0-dbg-arm64-cross libubsan1-dbg-arm64-cross libmpx2-dbg-arm64-cross libquadmath0-dbg-arm64-cross manpages-dev autoconf automake libtool flex bison gdb-aarch64-linux-gnu gcc-doc libyaml-shell-perl Recommended packages: libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl The following NEW packages will be installed: binutils-aarch64-linux-gnu cpp-8-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 dpkg-cross file g++-8-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-8-aarch64-linux-gnu gcc-8-aarch64-linux-gnu-base gcc-8-cross-base gcc-9-cross-base gcc-aarch64-linux-gnu libasan5-arm64-cross libatomic1-arm64-cross libc6-arm64-cross libc6-dev-arm64-cross libconfig-auto-perl libconfig-inifiles-perl libdebian-dpkgcross-perl libfile-homedir-perl libfile-which-perl libgcc-8-dev-arm64-cross libgcc1-arm64-cross libgomp1-arm64-cross libicu63 libio-string-perl libitm1-arm64-cross liblocale-gettext-perl liblsan0-arm64-cross libmagic-mgc libmagic1 libstdc++-8-dev-arm64-cross libstdc++6-arm64-cross libtsan0-arm64-cross libubsan1-arm64-cross libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-arm64-cross sbuild-build-depends-core-dummy:arm64 sensible-utils ucf 0 upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 42.3 MB of archives. After this operation, 162 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [872 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.37-5 [253 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.37-5 [119 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.37-5 [67.1 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.32.51.20190727-1 [2977 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-aarch64-linux-gnu-base amd64 8.3.0-19cross1 [192 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-8-aarch64-linux-gnu amd64 8.3.0-19cross1 [6244 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:8.3.0-1 [16.5 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-cross-base all 8.3.0-19cross1 [187 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.1.0-8cross1 [185 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.28-10cross3 [1312 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc1-arm64-cross all 1:9.1.0-8cross1 [34.1 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 9.1.0-8cross1 [76.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 9.1.0-8cross1 [24.2 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 9.1.0-8cross1 [8644 B] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-arm64-cross all 9.1.0-8cross1 [347 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 9.1.0-8cross1 [121 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 9.1.0-8cross1 [267 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 9.1.0-8cross1 [416 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 9.1.0-8cross1 [117 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-8-dev-arm64-cross all 8.3.0-19cross1 [828 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-8-aarch64-linux-gnu amd64 8.3.0-19cross1 [6687 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:8.3.0-1 [1456 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 4.19.37-5cross3 [1252 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.28-10cross3 [2322 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-8-dev-arm64-cross all 8.3.0-19cross1 [1490 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 g++-8-aarch64-linux-gnu amd64 8.3.0-19cross1 [6819 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:8.3.0-1 [1176 B] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000001-1 [51.9 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1 [344 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.29-1 [67.4 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.6 [6572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.3 MB in 1s (58.9 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 11988 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.37-5_amd64.deb ... Unpacking libmagic-mgc (1:5.37-5) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.37-5_amd64.deb ... Unpacking libmagic1:amd64 (1:5.37-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.37-5_amd64.deb ... Unpacking file (1:5.37-5) ... Selecting previously unselected package ucf. Preparing to unpack .../05-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package binutils-aarch64-linux-gnu. Preparing to unpack .../06-binutils-aarch64-linux-gnu_2.32.51.20190727-1_amd64.deb ... Unpacking binutils-aarch64-linux-gnu (2.32.51.20190727-1) ... Selecting previously unselected package gcc-8-aarch64-linux-gnu-base:amd64. Preparing to unpack .../07-gcc-8-aarch64-linux-gnu-base_8.3.0-19cross1_amd64.deb ... Unpacking gcc-8-aarch64-linux-gnu-base:amd64 (8.3.0-19cross1) ... Selecting previously unselected package cpp-8-aarch64-linux-gnu. Preparing to unpack .../08-cpp-8-aarch64-linux-gnu_8.3.0-19cross1_amd64.deb ... Unpacking cpp-8-aarch64-linux-gnu (8.3.0-19cross1) ... Selecting previously unselected package cpp-aarch64-linux-gnu. Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a8.3.0-1_amd64.deb ... Unpacking cpp-aarch64-linux-gnu (4:8.3.0-1) ... Selecting previously unselected package cross-config. Preparing to unpack .../10-cross-config_2.6.15-3_all.deb ... Unpacking cross-config (2.6.15-3) ... 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Preparing to unpack .../16-libitm1-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libitm1-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libatomic1-arm64-cross. Preparing to unpack .../17-libatomic1-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libatomic1-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libasan5-arm64-cross. Preparing to unpack .../18-libasan5-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libasan5-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package liblsan0-arm64-cross. Preparing to unpack .../19-liblsan0-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking liblsan0-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libtsan0-arm64-cross. Preparing to unpack .../20-libtsan0-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libtsan0-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libstdc++6-arm64-cross. Preparing to unpack .../21-libstdc++6-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libstdc++6-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libubsan1-arm64-cross. Preparing to unpack .../22-libubsan1-arm64-cross_9.1.0-8cross1_all.deb ... Unpacking libubsan1-arm64-cross (9.1.0-8cross1) ... Selecting previously unselected package libgcc-8-dev-arm64-cross. Preparing to unpack .../23-libgcc-8-dev-arm64-cross_8.3.0-19cross1_all.deb ... Unpacking libgcc-8-dev-arm64-cross (8.3.0-19cross1) ... Selecting previously unselected package gcc-8-aarch64-linux-gnu. Preparing to unpack .../24-gcc-8-aarch64-linux-gnu_8.3.0-19cross1_amd64.deb ... Unpacking gcc-8-aarch64-linux-gnu (8.3.0-19cross1) ... Selecting previously unselected package gcc-aarch64-linux-gnu. Preparing to unpack .../25-gcc-aarch64-linux-gnu_4%3a8.3.0-1_amd64.deb ... Unpacking gcc-aarch64-linux-gnu (4:8.3.0-1) ... Selecting previously unselected package linux-libc-dev-arm64-cross. Preparing to unpack .../26-linux-libc-dev-arm64-cross_4.19.37-5cross3_all.deb ... Unpacking linux-libc-dev-arm64-cross (4.19.37-5cross3) ... Selecting previously unselected package libc6-dev-arm64-cross. Preparing to unpack .../27-libc6-dev-arm64-cross_2.28-10cross3_all.deb ... Unpacking libc6-dev-arm64-cross (2.28-10cross3) ... Selecting previously unselected package libstdc++-8-dev-arm64-cross. Preparing to unpack .../28-libstdc++-8-dev-arm64-cross_8.3.0-19cross1_all.deb ... Unpacking libstdc++-8-dev-arm64-cross (8.3.0-19cross1) ... Selecting previously unselected package g++-8-aarch64-linux-gnu. Preparing to unpack .../29-g++-8-aarch64-linux-gnu_8.3.0-19cross1_amd64.deb ... Unpacking g++-8-aarch64-linux-gnu (8.3.0-19cross1) ... Selecting previously unselected package g++-aarch64-linux-gnu. Preparing to unpack .../30-g++-aarch64-linux-gnu_4%3a8.3.0-1_amd64.deb ... Unpacking g++-aarch64-linux-gnu (4:8.3.0-1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../31-libconfig-inifiles-perl_3.000001-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000001-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../32-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../33-libicu63_63.2-2_amd64.deb ... Unpacking libicu63:amd64 (63.2-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../34-libxml2_2.9.4+dfsg1-7+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../35-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../36-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../37-libxml-sax-perl_1.02+dfsg-1_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-1) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../38-libxml-libxml-perl_2.0134+dfsg-1_amd64.deb ... Unpacking libxml-libxml-perl (2.0134+dfsg-1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../39-libxml-simple-perl_2.25-1_all.deb ... Unpacking libxml-simple-perl (2.25-1) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../40-libyaml-perl_1.29-1_all.deb ... Unpacking libyaml-perl (1.29-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../41-libconfig-auto-perl_0.44-1_all.deb ... Unpacking libconfig-auto-perl (0.44-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../42-libfile-which-perl_1.23-1_all.deb ... Unpacking libfile-which-perl (1.23-1) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../43-libfile-homedir-perl_1.004-1_all.deb ... Unpacking libfile-homedir-perl (1.004-1) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../44-libdebian-dpkgcross-perl_2.6.15-3_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.15-3) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../45-dpkg-cross_2.6.15-3_all.deb ... Unpacking dpkg-cross (2.6.15-3) ... Selecting previously unselected package crossbuild-essential-arm64. Preparing to unpack .../46-crossbuild-essential-arm64_12.6_all.deb ... Unpacking crossbuild-essential-arm64 (12.6) ... Selecting previously unselected package sbuild-build-depends-core-dummy:arm64. Preparing to unpack .../47-sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy:arm64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000001-1) ... Setting up libfile-which-perl (1.23-1) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up gcc-8-cross-base (8.3.0-19cross1) ... Setting up libmagic1:amd64 (1:5.37-5) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up binutils-aarch64-linux-gnu (2.32.51.20190727-1) ... Setting up file (1:5.37-5) ... Setting up libyaml-perl (1.29-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up gcc-8-aarch64-linux-gnu-base:amd64 (8.3.0-19cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up cross-config (2.6.15-3) ... Setting up libc6-arm64-cross (2.28-10cross3) ... Setting up cpp-8-aarch64-linux-gnu (8.3.0-19cross1) ... Setting up gcc-9-cross-base (9.1.0-8cross1) ... Setting up linux-libc-dev-arm64-cross (4.19.37-5cross3) ... Setting up sensible-utils (0.0.12) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+b3) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libatomic1-arm64-cross (9.1.0-8cross1) ... Setting up libgcc1-arm64-cross (1:9.1.0-8cross1) ... Setting up liblsan0-arm64-cross (9.1.0-8cross1) ... Setting up libgomp1-arm64-cross (9.1.0-8cross1) ... Setting up libtsan0-arm64-cross (9.1.0-8cross1) ... Setting up libc6-dev-arm64-cross (2.28-10cross3) ... Setting up libasan5-arm64-cross (9.1.0-8cross1) ... Setting up libstdc++6-arm64-cross (9.1.0-8cross1) ... Setting up cpp-aarch64-linux-gnu (4:8.3.0-1) ... Setting up libitm1-arm64-cross (9.1.0-8cross1) ... Setting up ucf (3.0038+nmu1) ... Setting up libubsan1-arm64-cross (9.1.0-8cross1) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... 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 libgcc-8-dev-arm64-cross (8.3.0-19cross1) ... Setting up libxml-libxml-perl (2.0134+dfsg-1) ... 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-8-aarch64-linux-gnu (8.3.0-19cross1) ... Setting up libstdc++-8-dev-arm64-cross (8.3.0-19cross1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up gcc-aarch64-linux-gnu (4:8.3.0-1) ... Setting up g++-8-aarch64-linux-gnu (8.3.0-19cross1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up g++-aarch64-linux-gnu (4:8.3.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-arm64 (12.6) ... Setting up sbuild-build-depends-core-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) Setup apt archive ----------------- dpkg-deb: building package 'sbuild-build-depends-essential-dummy' in '/<>/resolver-2Ul5Yu/apt_archive/sbuild-build-depends-essential-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Sources [484 B] Get:5 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Packages [570 B] Fetched 2017 B in 0s (111 kB/s) Reading package lists... Reading package lists... Install essential build dependencies (apt-based resolver) --------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-essential-dummy:arm64 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 840 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ sbuild-build-depends-essential-dummy 0.invalid.0 [840 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 840 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-essential-dummy:arm64. (Reading database ... 15274 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-essential-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-essential-dummy:arm64 (0.invalid.0) ... Setting up sbuild-build-depends-essential-dummy:arm64 (0.invalid.0) ... +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man Filtered Build-Depends: libc-dev, libstdc++-dev, debhelper (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<>/resolver-2Ul5Yu/apt_archive/sbuild-build-depends-phast-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-phast-dummy dpkg-scanpackages: info: Wrote 3 entries to output Packages file. Ign:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Sources [663 B] Get:5 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Packages [742 B] Fetched 2368 B in 0s (129 kB/s) Reading package lists... Reading package lists... Install phast build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:arm64 gcc-9-base:arm64 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:arm64 libatomic1:arm64 libblas-dev:arm64 libblas3:arm64 libbsd0 libc6:arm64 libc6-dev:arm64 libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:arm64 libgcc1:arm64 libgfortran5:arm64 libglib2.0-0 libgomp1:arm64 libitm1:arm64 liblapack-dev:arm64 liblapack3:arm64 liblsan0:arm64 libncurses6 libpcre16-3:arm64 libpcre3:arm64 libpcre3-dev:arm64 libpcre32-3:arm64 libpcrecpp0v5:arm64 libpipeline1 libsigsegv2 libstdc++-8-dev:arm64 libstdc++6:arm64 libsub-override-perl libtmglib-dev:arm64 libtmglib3:arm64 libtool libtsan0:arm64 libubsan1:arm64 libuchardet0 linux-libc-dev:arm64 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 manpages-dev:arm64 libstdc++-8-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz gcc-8-base:arm64 gcc-9-base:arm64 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:arm64 libatomic1:arm64 libblas-dev:arm64 libblas3:arm64 libbsd0 libc6:arm64 libc6-dev:arm64 libcroco3 libelf1 libfile-stripnondeterminism-perl libgcc-8-dev:arm64 libgcc1:arm64 libgfortran5:arm64 libglib2.0-0 libgomp1:arm64 libitm1:arm64 liblapack-dev:arm64 liblapack3:arm64 liblsan0:arm64 libncurses6 libpcre16-3:arm64 libpcre3:arm64 libpcre3-dev:arm64 libpcre32-3:arm64 libpcrecpp0v5:arm64 libpipeline1 libsigsegv2 libstdc++-8-dev:arm64 libstdc++6:arm64 libsub-override-perl libtmglib-dev:arm64 libtmglib3:arm64 libtool libtsan0:arm64 libubsan1:arm64 libuchardet0 linux-libc-dev:arm64 m4 man-db po-debconf sbuild-build-depends-phast-dummy:arm64 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 25.3 MB of archives. After this operation, 116 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [900 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.8.6.1-1 [1295 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.1.0-10 [190 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-2 [203 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11 [341 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-10 [547 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.4.0-1 [21.9 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.4.0-1 [14.0 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.12.20190723-1 [80.6 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.60.6-1 [1294 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libncurses6 amd64 6.1+20190713-2 [102 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.3 [1029 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-8-base arm64 8.3.0-19 [192 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.47.10 [180 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc1 arm64 1:9.1.0-10 [34.1 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.28-10 [2521 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.1.0-10 [354 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 9.1.0-10 [8828 B] Get:37 http://debian.oregonstate.edu/debian unstable/main arm64 libgfortran5 arm64 9.1.0-10 [322 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main arm64 libblas3 arm64 3.8.0-2 [100 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main arm64 libblas-dev arm64 3.8.0-2 [105 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.2.6-1 [1206 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.28-10 [2324 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 9.1.0-10 [78.4 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 9.1.0-10 [24.7 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 9.1.0-10 [122 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 9.1.0-10 [274 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 9.1.0-10 [454 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 9.1.0-10 [117 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-8-dev arm64 8.3.0-19 [835 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main arm64 liblapack3 arm64 3.8.0-2 [1489 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main arm64 liblapack-dev arm64 3.8.0-2 [1524 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre16-3 arm64 2:8.39-12+b1 [236 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre3 arm64 2:8.39-12+b1 [317 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre32-3 arm64 2:8.39-12+b1 [230 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main arm64 libpcrecpp0v5 arm64 2:8.39-12+b1 [152 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre3-dev arm64 2:8.39-12+b1 [579 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-8-dev arm64 8.3.0-19 [1491 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main arm64 libtmglib3 arm64 3.8.0-2 [93.6 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main arm64 libtmglib-dev arm64 3.8.0-2 [94.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.3 MB in 0s (54.3 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15274 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.6.1-1_amd64.deb ... Unpacking man-db (2.8.6.1-1) ... Selecting previously unselected package gcc-9-base:arm64. 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Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21) ... Setting up man-db (2.8.6.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libc6:arm64 (2.28-10) ... Setting up libc6-dev:arm64 (2.28-10) ... Setting up libitm1:arm64 (9.1.0-10) ... Setting up libpcre16-3:arm64 (2:8.39-12+b1) ... Setting up libgcc1:arm64 (1:9.1.0-10) ... Setting up libgomp1:arm64 (9.1.0-10) ... Setting up dh-autoreconf (19) ... Setting up libasan5:arm64 (9.1.0-10) ... Setting up libpcre3:arm64 (2:8.39-12+b1) ... Setting up libpcre32-3:arm64 (2:8.39-12+b1) ... Setting up libatomic1:arm64 (9.1.0-10) ... Setting up libgfortran5:arm64 (9.1.0-10) ... Setting up dh-strip-nondeterminism (1.4.0-1) ... Setting up libstdc++6:arm64 (9.1.0-10) ... Setting up liblsan0:arm64 (9.1.0-10) ... Setting up libtsan0:arm64 (9.1.0-10) ... Setting up libpcrecpp0v5:arm64 (2:8.39-12+b1) ... Setting up libpcre3-dev:arm64 (2:8.39-12+b1) ... Setting up debhelper (12.3) ... Setting up libblas3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libubsan1:arm64 (9.1.0-10) ... Setting up libblas-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up liblapack3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libtmglib3:arm64 (3.8.0-2) ... Setting up liblapack-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgcc-8-dev:arm64 (8.3.0-19) ... Setting up libtmglib-dev:arm64 (3.8.0-2) ... Setting up libstdc++-8-dev:arm64 (8.3.0-19) ... Setting up sbuild-build-depends-phast-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.28-10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.32.51.20190727-1 dpkg-dev_1.19.7 g++-8_8.3.0-19 gcc-8_8.3.0-19 libc6-dev_2.28-10 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-arm64-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-arm64-cross_9.1.0-8cross1 linux-libc-dev_5.2.6-1 Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.46 bash_5.0-4 binutils_2.32.51.20190727-1 binutils-aarch64-linux-gnu_2.32.51.20190727-1 binutils-common_2.32.51.20190727-1 binutils-x86-64-linux-gnu_2.32.51.20190727-1 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.6 bzip2_1.0.6-9.2 coreutils_8.30-3+b1 cpp_4:8.3.0-1 cpp-8_8.3.0-19 cpp-8-aarch64-linux-gnu_8.3.0-19cross1 cpp-aarch64-linux-gnu_4:8.3.0-1 cross-config_2.6.15-3 crossbuild-essential-arm64_12.6 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.3 debian-archive-keyring_2019.1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.4.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.12.20190723-1 e2fsprogs_1.45.3-3 fakeroot_1.23-1 fdisk_2.34-0.1 file_1:5.37-5 findutils_4.6.0+git+20190510-2 g++_4:8.3.0-1 g++-8_8.3.0-19 g++-8-aarch64-linux-gnu_8.3.0-19cross1 g++-aarch64-linux-gnu_4:8.3.0-1 gcc_4:8.3.0-1 gcc-8_8.3.0-19 gcc-8-aarch64-linux-gnu_8.3.0-19cross1 gcc-8-aarch64-linux-gnu-base_8.3.0-19cross1 gcc-8-base_8.3.0-19 gcc-8-cross-base_8.3.0-19cross1 gcc-9-base_9.1.0-10 gcc-9-cross-base_9.1.0-8cross1 gcc-aarch64-linux-gnu_4:8.3.0-1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpgv_2.2.17-3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 help2man_1.47.10 hostname_3.21 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_9.1.0-10 libasan5-arm64-cross_9.1.0-8cross1 libatomic1_9.1.0-10 libatomic1-arm64-cross_9.1.0-8cross1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190727-1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.34-0.1 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.2 libc-bin_2.28-10 libc-dev-bin_2.28-10 libc6_2.28-10 libc6-arm64-cross_2.28-10cross3 libc6-dev_2.28-10 libc6-dev-arm64-cross_2.28-10cross3 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-10 libcom-err2_1.45.3-3 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000001-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.3-3 libfakeroot_1.23-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.4.0-1 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-19 libgcc-8-dev-arm64-cross_8.3.0-19cross1 libgcc1_1:9.1.0-10 libgcc1-arm64-cross_1:9.1.0-8cross1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4+b1 libgdbm6_1.18.1-4+b1 libgfortran5_9.1.0-10 libglib2.0-0_2.60.6-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-3 libgomp1_9.1.0-10 libgomp1-arm64-cross_9.1.0-8cross1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn2-0_2.2.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libitm1_9.1.0-10 libitm1-arm64-cross_9.1.0-8cross1 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 liblocale-gettext-perl_1.07-3+b4 liblsan0_9.1.0-10 liblsan0-arm64-cross_9.1.0-8cross1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.3.0-19 libncurses6_6.1+20190713-2 libncursesw6_6.1+20190713-2 libnettle6_3.4.1-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre16-3_2:8.39-12+b1 libpcre2-8-0_10.32-5+b1 libpcre3_2:8.39-12+b1 libpcre3-dev_2:8.39-12+b1 libpcre32-3_2:8.39-12+b1 libpcrecpp0v5_2:8.39-12+b1 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libquadmath0_9.1.0-10 libseccomp2_2.4.1-2 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.3-3 libstdc++-8-dev_8.3.0-19 libstdc++-8-dev-arm64-cross_8.3.0-19cross1 libstdc++6_9.1.0-10 libstdc++6-arm64-cross_9.1.0-8cross1 libsub-override-perl_0.09-2 libsystemd0_241-7 libtasn1-6_4.14-2 libtinfo6_6.1+20190713-2 libtmglib-dev_3.8.0-2 libtmglib3_3.8.0-2 libtool_2.4.6-10 libtsan0_9.1.0-10 libtsan0-arm64-cross_9.1.0-8cross1 libubsan1_9.1.0-10 libubsan1-arm64-cross_9.1.0-8cross1 libuchardet0_0.0.6-3 libudev1_241-7 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml-libxml-perl_2.0134+dfsg-1 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.4+dfsg1-7+b3 libyaml-perl_1.29-1 libzstd1_1.3.8+dfsg-3 linux-libc-dev_5.2.6-1 linux-libc-dev-arm64-cross_4.19.37-5cross3 login_1:4.7-2 logsave_1.45.3-3 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17+b3 mount_2.34-0.1 ncurses-base_6.1+20190713-2 ncurses-bin_6.1+20190713-2 passwd_1:4.7-2 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 po-debconf_1.0.21 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-essential-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.95-4 tar_1.30+dfsg-6+b1 tzdata_2019b-1 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 19 07:15:09 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./phast_1.5+dfsg-1.dsc dpkg-source: info: extracting phast in /<>/phast-1.5+dfsg dpkg-source: info: unpacking phast_1.5+dfsg.orig.tar.xz dpkg-source: info: unpacking phast_1.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying clapack.patch dpkg-source: info: applying do_not_install_to_opt.patch dpkg-source: info: applying use_debian_packaged_libpcre.patch dpkg-source: info: applying use_debian_packaged_help2man.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_test_makefile.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.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-bab9c331-eb10-4d4c-86c8-b4cac10fc3a4 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu 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 arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/phast-1.5+dfsg' dh_auto_clean cd src && make clean make[2]: Entering directory '/<>/phast-1.5+dfsg/src' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/phast-1.5+dfsg/src/lib/$dir && make clean ; done make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/base' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/msa' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/feature' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/hmm' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/phylo' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/phylo_hmm' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/motif' rm -f *.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/motif' rm -f /<>/phast-1.5+dfsg/src/lib/../../lib/* make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/dless' rm -f *.o dless.help dlessP.help /<>/phast-1.5+dfsg/src/dless/../../bin/dless /<>/phast-1.5+dfsg/src/dless/../../bin/dlessP make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/exoniphy' rm -f *.o *.help /<>/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastCons' rm -f *.o /<>/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.help make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastOdds' rm -f *.o *.help /<>/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastMotif' rm -f *.o /<>/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloFit' rm -f *.o /<>/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloBoot' rm -f *.o *.help /<>/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloP' rm -f *.o /<>/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.help make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/prequel' rm -f *.o /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain /<>/phast-1.5+dfsg/src/prequel/../../bin/prequel pbsTrain.help pbsDecode.help pbsEncode.help prequel.help pbsScoreMatrix.help make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/util' rm -f *.o *.help /<>/phast-1.5+dfsg/src/util/../../bin/hmm_train /<>/phast-1.5+dfsg/src/util/../../bin/chooseLines /<>/phast-1.5+dfsg/src/util/../../bin/modFreqs /<>/phast-1.5+dfsg/src/util/../../bin/indelHistory /<>/phast-1.5+dfsg/src/util/../../bin/clean_genes /<>/phast-1.5+dfsg/src/util/../../bin/treeGen /<>/phast-1.5+dfsg/src/util/../../bin/base_evolve /<>/phast-1.5+dfsg/src/util/../../bin/phast /<>/phast-1.5+dfsg/src/util/../../bin/tree_doctor /<>/phast-1.5+dfsg/src/util/../../bin/msa_diff /<>/phast-1.5+dfsg/src/util/../../bin/indelFit /<>/phast-1.5+dfsg/src/util/../../bin/hmm_tweak /<>/phast-1.5+dfsg/src/util/../../bin/all_dists /<>/phast-1.5+dfsg/src/util/../../bin/stringiphy /<>/phast-1.5+dfsg/src/util/../../bin/convert_coords /<>/phast-1.5+dfsg/src/util/../../bin/hmm_view /<>/phast-1.5+dfsg/src/util/../../bin/consEntropy /<>/phast-1.5+dfsg/src/util/../../bin/maf_parse /<>/phast-1.5+dfsg/src/util/../../bin/msa_split /<>/phast-1.5+dfsg/src/util/../../bin/eval_predictions /<>/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix /<>/phast-1.5+dfsg/src/util/../../bin/draw_tree /<>/phast-1.5+dfsg/src/util/../../bin/makeHKY /<>/phast-1.5+dfsg/src/util/../../bin/msa_view /<>/phast-1.5+dfsg/src/util/../../bin/phastBias /<>/phast-1.5+dfsg/src/util/../../bin/refeature make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/util' rm -rf ../bin ../lib ../doc make[2]: Leaving directory '/<>/phast-1.5+dfsg/src' make[1]: Leaving directory '/<>/phast-1.5+dfsg' dh_clean debian/rules build-arch dh build-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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc make[1]: Entering directory '/<>/phast-1.5+dfsg' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR= CLAPACKPATH=/usr/lib ) make[2]: Entering directory '/<>/phast-1.5+dfsg/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<>/phast-1.5+dfsg/src/$dir && make ; done make[3]: Entering directory '/<>/phast-1.5+dfsg/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<>/phast-1.5+dfsg/src/lib/$dir && make ; done make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/base' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_matrix.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c memory_handler.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c eigen.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c lists.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_vector.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_vector.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c numerical_opt.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c markov_matrix.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c vector.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c stringsplus.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c list_of_lists.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c hashtable.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c matrix.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_matrix.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar: creating /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o ar rs /<>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o eigen.o lists.o prob_vector.o complex_vector.o numerical_opt.o misc.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/base' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/msa' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o 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 sufficient_stats.c: In function 'ss_from_msas': sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, ^~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf.c -o 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 maf.c: In function 'maf_read_cats_subset': maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable] int i, start_idx, length, max_tuples, block_no, ^~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf_block.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c local_alignment.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c msa.c -o 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 msa.c: In function 'msa_read_fasta': msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] int maxlen, i, nseqs, j, do_toupper, line_no; ^~~~~~~ aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c multi_msa.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o ar rs /<>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/msa' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/feature' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c bed.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c wig.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c genepred.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c category_map.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c gff.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /<>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /<>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /<>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o ar rs /<>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/feature' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/hmm' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c hmm.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c em.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.o ar rs /<>/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a hmm.o em.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/phylo' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c dgamma.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_model.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_history.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_fit.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_column.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_mods.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_feature.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_likelihoods.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_mod.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c trees.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_distrib.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c bgc_hmm.c -o 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 bgc_hmm.c: In function 'bgcHmm': bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~ ~~~~~~~~~~~ bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~ bgc_hmm.c:241:7: note: 'sprintf' output 3 or more bytes (assuming 10002) into a destination of size 10000 sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:29: warning: ') ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] sprintf(warning_str, "%s)\n", warning_str); ^~~ bgc_hmm.c:242:5: note: 'sprintf' output between 3 and 10002 bytes into a destination of size 10000 sprintf(warning_str, "%s)\n", warning_str); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o tree_model.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o phast_cons.o indel_mod.o phylo_p.o phylo_p_print.o trees.o subst_distrib.o fit_em.o bgc_hmm.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/phylo' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/phylo_hmm' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phylo_hmm.c -o 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 aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c gap_patterns.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/phylo_hmm' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/motif' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c tfbs.c -o 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 tfbs.c: In function 'ms_read': tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable] int i, nseqs, j, do_toupper, line_no; ^~~~~~~ aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c motif.c -o 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 ar rs /<>/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o ar rs /<>/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/motif' make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/lib' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c bd_phylo_hmm.c -o bd_phylo_hmm.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/dless/../../lib -o /<>/phast-1.5+dfsg/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/dless/../../lib -o /<>/phast-1.5+dfsg/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/dless' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/exoniphy/../../lib -o /<>/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/exoniphy' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phastCons/../../lib -o /<>/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastCons' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phastOdds/../../lib -o /<>/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastMotif' aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition phastMotif.c: In function 'main': phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable] int i, j, separate_backgd = 0, ^~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phastMotif/../../lib -o /<>/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastMotif' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phyloFit/../../lib -o /<>/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloFit' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phyloBoot/../../lib -o /<>/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloBoot' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/phyloP/../../lib -o /<>/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phyloP' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/prequel' ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh prequel.help_src > prequel.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c simplex_grid.c -o simplex_grid.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbs_code.c -o pbs_code.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/prequel/../../lib -o /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/prequel/../../lib -o /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/prequel/../../lib -o /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/prequel/../../lib -o /<>/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/prequel/../../lib -o /<>/phast-1.5+dfsg/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/prequel' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/util' ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh treeGen.help_src > treeGen.help ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh consEntropy.help_src > consEntropy.help aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition display_rate_matrix.c: In function 'do_context_dependent_ti_tv': display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable] char tuple_i[mod->order+2], tuple_j[mod->order+2]; ^~~~~~~ aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now aarch64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<>/phast-1.5+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o : warning: "PHAST_HOME" redefined : note: this is the location of the previous definition aarch64-linux-gnu-gcc -L/<>/phast-1.5+dfsg/src/util/../../lib -o /<>/phast-1.5+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... ../debian/help2man_wrapper: 1: ../bin/all_dists: Exec format error ../debian/help2man_wrapper: 1: ../bin/base_evolve: Exec format error ../debian/help2man_wrapper: 1: ../bin/chooseLines: Exec format error ../debian/help2man_wrapper: 1: ../bin/clean_genes: Exec format error ../debian/help2man_wrapper: 1: ../bin/consEntropy: Exec format error ../debian/help2man_wrapper: 1: ../bin/convert_coords: Exec format error ../debian/help2man_wrapper: 1: ../bin/display_rate_matrix: Exec format error ../debian/help2man_wrapper: 1: ../bin/dless: Exec format error ../debian/help2man_wrapper: 1: ../bin/dlessP: Exec format error ../debian/help2man_wrapper: 1: ../bin/draw_tree: Exec format error ../debian/help2man_wrapper: 1: ../bin/eval_predictions: Exec format error ../debian/help2man_wrapper: 1: ../bin/exoniphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_train: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_tweak: Exec format error ../debian/help2man_wrapper: 1: ../bin/hmm_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/indelHistory: Exec format error ../debian/help2man_wrapper: 1: ../bin/maf_parse: Exec format error ../debian/help2man_wrapper: 1: ../bin/makeHKY: Exec format error ../debian/help2man_wrapper: 1: ../bin/modFreqs: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_diff: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_split: Exec format error ../debian/help2man_wrapper: 1: ../bin/msa_view: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsDecode: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsEncode: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsScoreMatrix: Exec format error ../debian/help2man_wrapper: 1: ../bin/pbsTrain: Exec format error ../debian/help2man_wrapper: 1: ../bin/phast: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastBias: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastCons: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastMotif: Exec format error ../debian/help2man_wrapper: 1: ../bin/phastOdds: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloBoot: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloFit: Exec format error ../debian/help2man_wrapper: 1: ../bin/phyloP: Exec format error ../debian/help2man_wrapper: 1: ../bin/prequel: Exec format error ../debian/help2man_wrapper: 1: ../bin/refeature: Exec format error ../debian/help2man_wrapper: 1: ../bin/stringiphy: Exec format error ../debian/help2man_wrapper: 1: ../bin/treeGen: Exec format error ../debian/help2man_wrapper: 1: ../bin/tree_doctor: Exec format error Done. make[2]: Leaving directory '/<>/phast-1.5+dfsg/src' make[1]: Leaving directory '/<>/phast-1.5+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/phast-1.5\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/phast-1.5+dfsg' (cd src; make install DESTDIR=/<>/phast-1.5+dfsg/debian/phast ) make[2]: Entering directory '/<>/phast-1.5+dfsg/src' mkdir -p /<>/phast-1.5+dfsg/debian/phast/usr/bin/ mkdir -p /<>/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ mkdir -p /<>/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ cp ../bin/* /<>/phast-1.5+dfsg/debian/phast/usr/bin/ cp -R ../data/* /<>/phast-1.5+dfsg/debian/phast/usr/share/phast/data/ cp -R ../doc/man/* /<>/phast-1.5+dfsg/debian/phast/usr/share/man/man1/ make[2]: Leaving directory '/<>/phast-1.5+dfsg/src' make[1]: Leaving directory '/<>/phast-1.5+dfsg' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/convert_coords debian/phast/usr/bin/prequel debian/phast/usr/bin/phast debian/phast/usr/bin/modFreqs debian/phast/usr/bin/indelHistory debian/phast/usr/bin/exoniphy debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/consEntropy debian/phast/usr/bin/msa_diff debian/phast/usr/bin/makeHKY debian/phast/usr/bin/dless debian/phast/usr/bin/chooseLines debian/phast/usr/bin/refeature debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/phastMotif debian/phast/usr/bin/phastCons debian/phast/usr/bin/maf_parse debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/phyloFit debian/phast/usr/bin/indelFit debian/phast/usr/bin/msa_view debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastOdds debian/phast/usr/bin/all_dists debian/phast/usr/bin/clean_genes debian/phast/usr/bin/base_evolve debian/phast/usr/bin/treeGen debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/phyloP debian/phast/usr/bin/msa_split debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/dlessP debian/phast/usr/bin/hmm_view debian/phast/usr/bin/draw_tree debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phastBias debian/phast/usr/bin/hmm_tweak were not linked against libtmglib.so.3 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/convert_coords debian/phast/usr/bin/prequel debian/phast/usr/bin/phast debian/phast/usr/bin/modFreqs debian/phast/usr/bin/indelHistory debian/phast/usr/bin/exoniphy debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/consEntropy debian/phast/usr/bin/msa_diff debian/phast/usr/bin/makeHKY debian/phast/usr/bin/dless debian/phast/usr/bin/chooseLines debian/phast/usr/bin/refeature debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/phastMotif debian/phast/usr/bin/phastCons debian/phast/usr/bin/maf_parse debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/phyloFit debian/phast/usr/bin/indelFit debian/phast/usr/bin/msa_view debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phastOdds debian/phast/usr/bin/all_dists debian/phast/usr/bin/clean_genes debian/phast/usr/bin/base_evolve debian/phast/usr/bin/treeGen debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/phyloP debian/phast/usr/bin/msa_split debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/dlessP debian/phast/usr/bin/hmm_view debian/phast/usr/bin/draw_tree debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phastBias debian/phast/usr/bin/hmm_tweak were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phast' in '../phast_1.5+dfsg-1_arm64.deb'. dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.5+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phast_1.5+dfsg-1_arm64.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 2019-08-07T03:10:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/resolver-2Ul5Yu/apt_archive/sbuild-build-depends-lintian-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-essential-dummy sbuild-build-depends-lintian-dummy sbuild-build-depends-phast-dummy dpkg-scanpackages: info: Wrote 4 entries to output Packages file. Ign:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Sources [782 B] Get:5 copy:/<>/resolver-2Ul5Yu/apt_archive ./ Packages [854 B] Fetched 2599 B in 0s (139 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libcgi-fast-perl libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libclass-xsaccessor-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libauthen-sasl-perl libunicode-utf8-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-op-check-perl libcapture-tiny-perl libcgi-pm-perl libclass-accessor-perl libclass-method-modifiers-perl libclone-perl libdevel-callchecker-perl libdevel-globaldestruction-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-pty-perl libio-socket-ssl-perl libipc-run-perl libipc-system-simple-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-runtime-perl libmoo-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl liburi-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:arm64 t1utils 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 8535 kB of archives. After this operation, 23.8 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2Ul5Yu/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-2 [72.4 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-2 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 5.6 [19.4 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.62-1+b1 [33.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.17-3 [524 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.29.0-1 [645 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.17-3 [881 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b1 [71.2 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b1 [11.4 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libcgi-pm-perl all 4.44-1 [223 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.21-1+b3 [13.6 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-accessor-perl all 0.51-1 [23.2 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libclone-perl amd64 0.41-1+b1 [14.6 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1 [15.7 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libdigest-hmac-perl all 1.03+dfsg-2 [10.6 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1c-1 [1535 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ssleay-perl amd64 1.88-1 [320 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 libio-socket-ssl-perl all 2.066-1 [210 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libmailtools-perl all 2.21-1 [95.5 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-ip-perl all 1.26-2 [29.0 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-dns-perl all 1.20-1 [367 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-1 [33.3 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libemail-valid-perl all 1.202-1 [23.0 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libexporter-tiny-perl all 1.002001-1 [36.9 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-system-simple-perl all 1.25-4 [26.5 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-basedir-perl all 0.08-1 [17.7 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libfuture-perl all 0.41-1 [79.0 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b1 [25.5 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libstruct-dumb-perl all 0.09-1 [11.1 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-perl all 0.74-1 [268 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 liblinux-epoll-perl amd64 0.016-1+b1 [17.0 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libio-async-loop-epoll-perl all 0.20-1 [11.9 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b5 [33.7 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libipc-run-perl all 20180523.0-1 [101 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-compare-perl all 0.53-1 [68.9 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b4 [64.2 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.000006-1 [19.4 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006003-1 [19.7 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.003004-2 [57.4 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.108-1 [53.3 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.004004-1 [266 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.79+repack-2 [34.0 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-3 [62.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.17.0 [1273 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8535 kB in 0s (28.5 MB/s) Selecting previously unselected package readline-common. (Reading database ... 18279 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-2_all.deb ... Unpacking readline-common (8.0-2) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-2_amd64.deb ... Unpacking libreadline8:amd64 (8.0-2) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_5.6_all.deb ... Unpacking netbase (5.6) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.62-1+b1_amd64.deb ... Unpacking diffstat (1.62-1+b1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.17-3_amd64.deb ... Unpacking gpgconf (2.2.17-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../06-libsqlite3-0_3.29.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.29.0-1) ... Selecting previously unselected package gpg. Preparing to unpack .../07-gpg_2.2.17-3_amd64.deb ... Unpacking gpg (2.2.17-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../08-libapt-pkg-perl_0.1.36+b1_amd64.deb ... Unpacking libapt-pkg-perl (0.1.36+b1) ... Selecting previously unselected package libb-hooks-op-check-perl. Preparing to unpack .../09-libb-hooks-op-check-perl_0.22-1+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl (0.22-1+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../10-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../11-libhtml-tagset-perl_3.20-3_all.deb ... Unpacking libhtml-tagset-perl (3.20-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../12-liburi-perl_1.76-1_all.deb ... Unpacking liburi-perl (1.76-1) ... Selecting previously unselected package libhtml-parser-perl. Preparing to unpack .../13-libhtml-parser-perl_3.72-3+b3_amd64.deb ... Unpacking libhtml-parser-perl (3.72-3+b3) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../14-libcgi-pm-perl_4.44-1_all.deb ... Unpacking libcgi-pm-perl (4.44-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../15-libsub-name-perl_0.21-1+b3_amd64.deb ... Unpacking libsub-name-perl (0.21-1+b3) ... Selecting previously unselected package libclass-accessor-perl. Preparing to unpack .../16-libclass-accessor-perl_0.51-1_all.deb ... Unpacking libclass-accessor-perl (0.51-1) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../17-libclass-method-modifiers-perl_2.12-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.12-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../18-libclone-perl_0.41-1+b1_amd64.deb ... Unpacking libclone-perl (0.41-1+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../19-libdynaloader-functions-perl_0.003-1_all.deb ... Unpacking libdynaloader-functions-perl (0.003-1) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../20-libdevel-callchecker-perl_0.008-1_amd64.deb ... Unpacking libdevel-callchecker-perl (0.008-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../21-libsub-exporter-progressive-perl_0.001013-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../22-libdevel-globaldestruction-perl_0.14-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.14-1) ... 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I: Lintian run was successful. +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ phast_1.5+dfsg-1_arm64.changes: ------------------------------- Format: 1.8 Date: Fri, 19 Oct 2018 09:10:34 +0200 Source: phast Binary: phast phast-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 1.5+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: phast - phylogenetic analysis with space/time models Changes: phast (1.5+dfsg-1) unstable; urgency=medium . * New upstream version * Fix homepage * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Run part or the test suite Checksums-Sha1: 0b88225579dec849545619d417cb03880981310d 32379316 phast-dbgsym_1.5+dfsg-1_arm64.deb a81a9a8c016076a847058294e0b1263f333ce2d4 4946 phast_1.5+dfsg-1_arm64.buildinfo 6276bb85775b32b727b1f5eb0706ab99dd458211 1585524 phast_1.5+dfsg-1_arm64.deb Checksums-Sha256: 58b7bdcc6992ca48373dc9f816d6e42a4e951bf7676e482a649a57c5027b0818 32379316 phast-dbgsym_1.5+dfsg-1_arm64.deb 09a223f351b329b194de47e6de31888d2088f70edbd852e8d906f946030f8644 4946 phast_1.5+dfsg-1_arm64.buildinfo b6ffadec6b9e57bac0c0307222876666f058c1e99dc02f8c20996d8d5f873ab1 1585524 phast_1.5+dfsg-1_arm64.deb Files: d5579019936a1038ff45cde7d6636f43 32379316 debug optional phast-dbgsym_1.5+dfsg-1_arm64.deb b13edfa57cd56dfc42b039b15922066c 4946 science optional phast_1.5+dfsg-1_arm64.buildinfo c47e0d4a8fde161314796549839eb219 1585524 science optional phast_1.5+dfsg-1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: phast Binary: phast Architecture: arm64 Version: 1.5+dfsg-1 Checksums-Md5: d5579019936a1038ff45cde7d6636f43 32379316 phast-dbgsym_1.5+dfsg-1_arm64.deb c47e0d4a8fde161314796549839eb219 1585524 phast_1.5+dfsg-1_arm64.deb Checksums-Sha1: 0b88225579dec849545619d417cb03880981310d 32379316 phast-dbgsym_1.5+dfsg-1_arm64.deb 6276bb85775b32b727b1f5eb0706ab99dd458211 1585524 phast_1.5+dfsg-1_arm64.deb Checksums-Sha256: 58b7bdcc6992ca48373dc9f816d6e42a4e951bf7676e482a649a57c5027b0818 32379316 phast-dbgsym_1.5+dfsg-1_arm64.deb b6ffadec6b9e57bac0c0307222876666f058c1e99dc02f8c20996d8d5f873ab1 1585524 phast_1.5+dfsg-1_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 07 Aug 2019 03:10:15 +0000 Build-Path: /<>/phast-1.5+dfsg Installed-Build-Depends: autoconf (= 2.69-11), automake (= 1:1.16.1-4), autopoint (= 0.19.8.1-9), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.46), bash (= 5.0-4), binutils (= 2.32.51.20190727-1), binutils-common (= 2.32.51.20190727-1), binutils-x86-64-linux-gnu (= 2.32.51.20190727-1), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.34-0.1), build-essential (= 12.6), bzip2 (= 1.0.6-9.2), coreutils (= 8.30-3+b1), cpp (= 4:8.3.0-1), cpp-8 (= 8.3.0-19), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.3), debianutils (= 4.8.6.3), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.4.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.12.20190723-1), fdisk (= 2.34-0.1), file (= 1:5.37-5), findutils (= 4.6.0+git+20190510-2), g++ (= 4:8.3.0-1), g++-8 (= 8.3.0-19), gcc (= 4:8.3.0-1), gcc-8 (= 8.3.0-19), gcc-8-base (= 8.3.0-19), gcc-9-base (= 9.1.0-10), gettext (= 0.19.8.1-9), gettext-base (= 0.19.8.1-9), grep (= 3.3-1), groff-base (= 1.22.4-3), gzip (= 1.9-3), help2man (= 1.47.10), hostname (= 3.21), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-4), libarchive-zip-perl (= 1.64-1), libasan5 (= 9.1.0-10), libatomic1 (= 9.1.0-10), libattr1 (= 1:2.4.48-4), libaudit-common (= 1:2.8.5-2), libaudit1 (= 1:2.8.5-2), libbinutils (= 2.32.51.20190727-1), libblas-dev (= 3.8.0-2), libblas3 (= 3.8.0-2), libblkid1 (= 2.34-0.1), libbsd0 (= 0.9.1-2), libbz2-1.0 (= 1.0.6-9.2), libc-bin (= 2.28-10), libc-dev-bin (= 2.28-10), libc6 (= 2.28-10), libc6-dev (= 2.28-10), libcap-ng0 (= 0.7.9-2), libcc1-0 (= 9.1.0-10), libcroco3 (= 0.6.12-3), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.249), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libfdisk1 (= 2.34-0.1), libffi6 (= 3.2.1-9), libfile-stripnondeterminism-perl (= 1.4.0-1), libgcc-8-dev (= 8.3.0-19), libgcc1 (= 1:9.1.0-10), libgcrypt20 (= 1.8.4-5), libgdbm-compat4 (= 1.18.1-4+b1), libgdbm6 (= 1.18.1-4+b1), libgfortran5 (= 9.1.0-10), libglib2.0-0 (= 2.60.6-1), libgmp10 (= 2:6.1.2+dfsg-4), libgomp1 (= 9.1.0-10), libgpg-error0 (= 1.36-7), libicu63 (= 63.2-2), libisl19 (= 0.20-2), libitm1 (= 9.1.0-10), liblapack-dev (= 3.8.0-2), liblapack3 (= 3.8.0-2), liblocale-gettext-perl (= 1.07-3+b4), liblsan0 (= 9.1.0-10), liblz4-1 (= 1.8.3-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.37-5), libmagic1 (= 1:5.37-5), libmount1 (= 2.34-0.1), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libmpx2 (= 8.3.0-19), libncurses6 (= 6.1+20190713-2), libncursesw6 (= 6.1+20190713-2), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre16-3 (= 2:8.39-12+b1), libpcre2-8-0 (= 10.32-5+b1), libpcre3 (= 2:8.39-12+b1), libpcre3-dev (= 2:8.39-12+b1), libpcre32-3 (= 2:8.39-12+b1), libpcrecpp0v5 (= 2:8.39-12+b1), libperl5.28 (= 5.28.1-6), libpipeline1 (= 1.5.1-2), libquadmath0 (= 9.1.0-10), libseccomp2 (= 2.4.1-2), libselinux1 (= 2.9-2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1), libstdc++-8-dev (= 8.3.0-19), libstdc++6 (= 9.1.0-10), libsub-override-perl (= 0.09-2), libsystemd0 (= 241-7), libtinfo6 (= 6.1+20190713-2), libtmglib-dev (= 3.8.0-2), libtmglib3 (= 3.8.0-2), libtool (= 2.4.6-10), libtsan0 (= 9.1.0-10), libubsan1 (= 9.1.0-10), libuchardet0 (= 0.0.6-3), libudev1 (= 241-7), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1), libxml2 (= 2.9.4+dfsg1-7+b3), linux-libc-dev (= 5.2.6-1), login (= 1:4.7-2), m4 (= 1.4.18-2), make (= 4.2.1-1.2), man-db (= 2.8.6.1-1), mawk (= 1.3.3-17+b3), ncurses-base (= 6.1+20190713-2), ncurses-bin (= 6.1+20190713-2), patch (= 2.7.6-6), perl (= 5.28.1-6), perl-base (= 5.28.1-6), perl-modules-5.28 (= 5.28.1-6), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12), sysvinit-utils (= 2.95-4), tar (= 1.30+dfsg-6+b1), util-linux (= 2.34-0.1), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-1+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1539933034" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ phast-dbgsym_1.5+dfsg-1_arm64.deb --------------------------------- new Debian package, version 2.0. size 32379316 bytes: control archive=2352 bytes. 1969 bytes, 12 lines control 4240 bytes, 40 lines md5sums Package: phast-dbgsym Source: phast Version: 1.5+dfsg-1 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 35176 Depends: phast (= 1.5+dfsg-1) Section: debug Priority: optional Description: debug symbols for phast Build-Ids: 07a848d037086550b4272baa3a22f35e1aab3ed7 08a1b5164a9421f2e94aac262338943a879c6123 12d69d54d928dbeba0bdb1967b3d775ae65053d5 174005b67000e1afb704068e7782e03f1f8fe29f 206b70c7f5168e9467a2f3326e7f5b46b7476395 22feba8ee610609e3f3f061e0ed9c9f9cfc47e44 258a3262032d29a40e12d4824432bd0f67d49f0a 2d8f93c512475053e3e2555144183a4f00eae093 34bd3311ead47842050cea72aa8493302331a483 41a41723fbbd63701bea01a3ed57ce4fe8bd9b60 42c691a03f56dfb487946a777330e5227971c53a 42dba13a8104b239d577ec5d304fe1aa2489b33b 444f65181c2a4e5402d79f5ec3ec75d0fe979de3 4719441c49ecda53021a229edda527e8afb1281f 5599e553a603c3add9809d843238df891b6b755b 59bf3cbce3564105bcbee4e54da68590fdb633d0 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-------------------------- new Debian package, version 2.0. size 1585524 bytes: control archive=4744 bytes. 1134 bytes, 22 lines control 12208 bytes, 165 lines md5sums Package: phast Version: 1.5+dfsg-1 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 25237 Depends: libblas3 | libblas.so.3, libc6 (>= 2.23), liblapack3 | liblapack.so.3, libpcre3, libtmglib3 Section: science Priority: optional Homepage: http://compgen.cshl.edu/phast/ Description: phylogenetic analysis with space/time models PHAST is a software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. . PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison). drwxr-xr-x root/root 0 2018-10-19 07:10 ./ drwxr-xr-x root/root 0 2018-10-19 07:10 ./usr/ drwxr-xr-x root/root 0 2018-10-19 07:10 ./usr/bin/ -rwxr-xr-x root/root 555176 2018-10-19 07:10 ./usr/bin/all_dists -rwxr-xr-x root/root 556952 2018-10-19 07:10 ./usr/bin/base_evolve -rwxr-xr-x root/root 559144 2018-10-19 07:10 ./usr/bin/chooseLines -rwxr-xr-x root/root 582504 2018-10-19 07:10 ./usr/bin/clean_genes -rwxr-xr-x root/root 556880 2018-10-19 07:10 ./usr/bin/consEntropy -rwxr-xr-x root/root 559144 2018-10-19 07:10 ./usr/bin/convert_coords -rwxr-xr-x root/root 563240 2018-10-19 07:10 ./usr/bin/display_rate_matrix -rwxr-xr-x root/root 654096 2018-10-19 07:10 ./usr/bin/dless -rwxr-xr-x root/root 696120 2018-10-19 07:10 ./usr/bin/dlessP -rwxr-xr-x root/root 10168 2018-10-19 07:10 ./usr/bin/draw_tree -rwxr-xr-x root/root 563240 2018-10-19 07:10 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Package: phast Package-Time: 164 Source-Version: 1.5+dfsg-1 Space: 275304 Status: successful Version: 1.5+dfsg-1 -------------------------------------------------------------------------------- Finished at 2019-08-07T03:10:16Z Build needed 00:02:44, 275304k disk space