https://launchpad.net/ubuntu/+archive/test-rebuild-20190906-lto/+build/17698940 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-068 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:12:37 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_177 python-lpbuildd_177 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 17 Sep 19:20:51 ntpdate[1929]: adjust time server 10.211.37.1 offset -0.011184 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 --image-type chroot /home/buildd/filecache-default/b148568f42c06950756bf7fea120011aafea366b Creating target for build PACKAGEBUILD-17698940 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 Starting target for build PACKAGEBUILD-17698940 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan main' 'deb http://ftpmaster.internal/ubuntu eoan main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-17698940 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 Adding trusted keys to build-PACKAGEBUILD-17698940 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 Updating target for build PACKAGEBUILD-17698940 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan InRelease [15.4 kB] Get:2 http://ftpmaster.internal/ubuntu eoan InRelease [255 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan InRelease [20.8 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main arm64 Packages [2820 B] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu eoan/main Translation-en [4848 B] Get:6 http://ftpmaster.internal/ubuntu eoan/main arm64 Packages [936 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main arm64 Packages [1688 B] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main Translation-en [1760 B] Get:9 http://ftpmaster.internal/ubuntu eoan/main Translation-en [504 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/restricted arm64 Packages [1064 B] Get:11 http://ftpmaster.internal/ubuntu eoan/restricted Translation-en [4836 B] Get:12 http://ftpmaster.internal/ubuntu eoan/universe arm64 Packages [8679 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/universe Translation-en [5224 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/multiverse arm64 Packages [121 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/multiverse Translation-en [111 kB] Fetched 15.9 MB in 8s (2113 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: logsave The following packages will be upgraded: binutils binutils-aarch64-linux-gnu binutils-common build-essential coreutils cpp cpp-9 dpkg dpkg-dev e2fsprogs g++ g++-9 gcc gcc-9 gcc-9-base libapparmor1 libasan5 libatomic1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-9-dev libgcc1 libgnutls30 libgomp1 libip4tc2 libisl21 libitm1 liblsan0 libp11-kit0 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libtsan0 libubsan1 linux-libc-dev login passwd tzdata 47 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 50.3 MB of archives. After this operation, 837 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu eoan/main arm64 coreutils arm64 8.30-3ubuntu2 [1174 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main arm64 dpkg arm64 1.19.7ubuntu77 [2206 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main arm64 login arm64 1:4.5-1.1ubuntu4 [261 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main arm64 libc6-dev arm64 2.30-0ubuntu1 [2091 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main arm64 dpkg-dev all 1.19.7ubuntu77 [1793 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main arm64 libc-dev-bin arm64 2.30-0ubuntu1 [64.2 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main arm64 linux-libc-dev arm64 5.3.0-10.11 [1042 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu eoan/main arm64 libdpkg-perl all 1.19.7ubuntu77 [1434 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main arm64 libcc1-0 arm64 9.2.1-8ubuntu1 [46.5 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main arm64 binutils-aarch64-linux-gnu arm64 2.32.51.20190905-0ubuntu1 [2022 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main arm64 libbinutils arm64 2.32.51.20190905-0ubuntu1 [471 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main arm64 binutils-common arm64 2.32.51.20190905-0ubuntu1 [203 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main arm64 binutils arm64 2.32.51.20190905-0ubuntu1 [3392 B] Get:14 http://ftpmaster.internal/ubuntu eoan/main arm64 gcc-9-base arm64 9.2.1-8ubuntu1 [19.2 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main arm64 libgcc1 arm64 1:9.2.1-8ubuntu1 [34.1 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main arm64 libgomp1 arm64 9.2.1-8ubuntu1 [80.5 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main arm64 libitm1 arm64 9.2.1-8ubuntu1 [25.0 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main arm64 libatomic1 arm64 9.2.1-8ubuntu1 [9172 B] Get:19 http://ftpmaster.internal/ubuntu eoan/main arm64 libasan5 arm64 9.2.1-8ubuntu1 [365 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main arm64 liblsan0 arm64 9.2.1-8ubuntu1 [126 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main arm64 libtsan0 arm64 9.2.1-8ubuntu1 [283 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main arm64 libubsan1 arm64 9.2.1-8ubuntu1 [121 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main arm64 g++-9 arm64 9.2.1-8ubuntu1 [9437 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main arm64 libstdc++-9-dev arm64 9.2.1-8ubuntu1 [1673 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main arm64 libgcc-9-dev arm64 9.2.1-8ubuntu1 [914 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main arm64 gcc-9 arm64 9.2.1-8ubuntu1 [9062 kB] Get:27 http://ftpmaster.internal/ubuntu eoan/main arm64 cpp-9 arm64 9.2.1-8ubuntu1 [8312 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main arm64 libstdc++6 arm64 9.2.1-8ubuntu1 [467 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main arm64 libisl21 arm64 0.21-2 [521 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main arm64 libc6 arm64 2.30-0ubuntu1 [2271 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main arm64 libc-bin arm64 2.30-0ubuntu1 [476 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main arm64 libext2fs2 arm64 1.45.3-4ubuntu1 [174 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main arm64 e2fsprogs arm64 1.45.3-4ubuntu1 [502 kB] Get:34 http://ftpmaster.internal/ubuntu eoan/main arm64 logsave arm64 1.45.3-4ubuntu1 [9584 B] Get:35 http://ftpmaster.internal/ubuntu eoan/main arm64 passwd arm64 1:4.5-1.1ubuntu4 [791 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main arm64 libp11-kit0 arm64 0.23.17-2 [177 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main arm64 libgnutls30 arm64 3.6.9-4build1 [721 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main arm64 libcom-err2 arm64 1.45.3-4ubuntu1 [8712 B] Get:39 http://ftpmaster.internal/ubuntu eoan/main arm64 libss2 arm64 1.45.3-4ubuntu1 [10.7 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main arm64 libapparmor1 arm64 2.13.3-5ubuntu1 [34.3 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main arm64 libdevmapper1.02.1 arm64 2:1.02.155-2ubuntu6 [110 kB] Get:42 http://ftpmaster.internal/ubuntu eoan/main arm64 libsqlite3-0 arm64 3.29.0-2 [494 kB] Get:43 http://ftpmaster.internal/ubuntu eoan/main arm64 tzdata all 2019c-1 [188 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main arm64 g++ arm64 4:9.2.1-3.1ubuntu1 [1596 B] Get:45 http://ftpmaster.internal/ubuntu eoan/main arm64 gcc arm64 4:9.2.1-3.1ubuntu1 [5228 B] Get:46 http://ftpmaster.internal/ubuntu eoan/main arm64 cpp arm64 4:9.2.1-3.1ubuntu1 [27.6 kB] Get:47 http://ftpmaster.internal/ubuntu eoan/main arm64 build-essential arm64 12.7ubuntu1 [4644 B] Get:48 http://ftpmaster.internal/ubuntu eoan/main arm64 libip4tc2 arm64 1.8.3-2ubuntu4 [20.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.3 MB in 1s (38.5 MB/s) (Reading database ... 12720 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_arm64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu1) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 12720 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.7ubuntu77_arm64.deb ... Unpacking dpkg (1.19.7ubuntu77) over (1.19.7ubuntu1) ... Setting up dpkg (1.19.7ubuntu77) ... (Reading database ... 12721 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1ubuntu4_arm64.deb ... Unpacking login (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up login (1:4.5-1.1ubuntu4) ... (Reading database ... 12721 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu1_arm64.deb ... Unpacking libc6-dev:arm64 (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu1_arm64.deb ... Unpacking libc-dev-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Preparing to unpack .../2-linux-libc-dev_5.3.0-10.11_arm64.deb ... Unpacking linux-libc-dev:arm64 (5.3.0-10.11) over (5.2.0-15.16) ... Preparing to unpack .../3-libcc1-0_9.2.1-8ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../4-binutils-aarch64-linux-gnu_2.32.51.20190905-0ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../5-libbinutils_2.32.51.20190905-0ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../6-binutils-common_2.32.51.20190905-0ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../7-binutils_2.32.51.20190905-0ubuntu1_arm64.deb ... Unpacking binutils (2.32.51.20190905-0ubuntu1) over (2.32.51.20190821-1ubuntu1) ... Preparing to unpack .../8-gcc-9-base_9.2.1-8ubuntu1_arm64.deb ... Unpacking gcc-9-base:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Setting up gcc-9-base:arm64 (9.2.1-8ubuntu1) ... (Reading database ... 12729 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a9.2.1-8ubuntu1_arm64.deb ... Unpacking libgcc1:arm64 (1:9.2.1-8ubuntu1) over (1:9.2.1-6ubuntu1) ... Setting up libgcc1:arm64 (1:9.2.1-8ubuntu1) ... (Reading database ... 12729 files and directories currently installed.) Preparing to unpack .../00-libgomp1_9.2.1-8ubuntu1_arm64.deb ... Unpacking libgomp1:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../01-libitm1_9.2.1-8ubuntu1_arm64.deb ... Unpacking libitm1:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../02-libatomic1_9.2.1-8ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../03-libasan5_9.2.1-8ubuntu1_arm64.deb ... Unpacking libasan5:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../04-liblsan0_9.2.1-8ubuntu1_arm64.deb ... Unpacking liblsan0:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../05-libtsan0_9.2.1-8ubuntu1_arm64.deb ... Unpacking libtsan0:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../06-libubsan1_9.2.1-8ubuntu1_arm64.deb ... Unpacking libubsan1:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../07-g++-9_9.2.1-8ubuntu1_arm64.deb ... Unpacking g++-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../08-libstdc++-9-dev_9.2.1-8ubuntu1_arm64.deb ... Unpacking libstdc++-9-dev:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../09-libgcc-9-dev_9.2.1-8ubuntu1_arm64.deb ... Unpacking libgcc-9-dev:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../10-gcc-9_9.2.1-8ubuntu1_arm64.deb ... Unpacking gcc-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../11-cpp-9_9.2.1-8ubuntu1_arm64.deb ... Unpacking cpp-9 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Preparing to unpack .../12-libstdc++6_9.2.1-8ubuntu1_arm64.deb ... Unpacking libstdc++6:arm64 (9.2.1-8ubuntu1) over (9.2.1-6ubuntu1) ... Setting up libstdc++6:arm64 (9.2.1-8ubuntu1) ... (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../libisl21_0.21-2_arm64.deb ... Unpacking libisl21:arm64 (0.21-2) over (0.21-1) ... Preparing to unpack .../libc6_2.30-0ubuntu1_arm64.deb ... Unpacking libc6:arm64 (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Setting up libc6:arm64 (2.30-0ubuntu1) ... (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../libc-bin_2.30-0ubuntu1_arm64.deb ... Unpacking libc-bin (2.30-0ubuntu1) over (2.29-0ubuntu3) ... Setting up libc-bin (2.30-0ubuntu1) ... (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.45.3-4ubuntu1_arm64.deb ... Unpacking libext2fs2:arm64 (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Setting up libext2fs2:arm64 (1.45.3-4ubuntu1) ... (Reading database ... 12732 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.45.3-4ubuntu1_arm64.deb ... Unpacking e2fsprogs (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Selecting previously unselected package logsave. Preparing to unpack .../logsave_1.45.3-4ubuntu1_arm64.deb ... Unpacking logsave (1.45.3-4ubuntu1) ... Preparing to unpack .../passwd_1%3a4.5-1.1ubuntu4_arm64.deb ... Unpacking passwd (1:4.5-1.1ubuntu4) over (1:4.5-1.1ubuntu3) ... Setting up passwd (1:4.5-1.1ubuntu4) ... (Reading database ... 12735 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.17-2_arm64.deb ... Unpacking libp11-kit0:arm64 (0.23.17-2) over (0.23.16.1-2) ... Setting up libp11-kit0:arm64 (0.23.17-2) ... (Reading database ... 12735 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.9-4build1_arm64.deb ... Unpacking libgnutls30:arm64 (3.6.9-4build1) over (3.6.9-4) ... Setting up libgnutls30:arm64 (3.6.9-4build1) ... (Reading database ... 12735 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.45.3-4ubuntu1_arm64.deb ... Unpacking libcom-err2:arm64 (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../01-libss2_1.45.3-4ubuntu1_arm64.deb ... Unpacking libss2:arm64 (1.45.3-4ubuntu1) over (1.45.2-1ubuntu1) ... Preparing to unpack .../02-libapparmor1_2.13.3-5ubuntu1_arm64.deb ... Unpacking libapparmor1:arm64 (2.13.3-5ubuntu1) over (2.13.2-9ubuntu7) ... Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.155-2ubuntu6_arm64.deb ... Unpacking libdevmapper1.02.1:arm64 (2:1.02.155-2ubuntu6) over (2:1.02.155-2ubuntu5) ... Preparing to unpack .../04-libsqlite3-0_3.29.0-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.29.0-2) over (3.29.0-1) ... Preparing to unpack .../05-tzdata_2019c-1_all.deb ... Unpacking tzdata (2019c-1) over (2019b-2) ... Preparing to unpack .../06-g++_4%3a9.2.1-3.1ubuntu1_arm64.deb ... Unpacking g++ (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../07-gcc_4%3a9.2.1-3.1ubuntu1_arm64.deb ... Unpacking gcc (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../08-cpp_4%3a9.2.1-3.1ubuntu1_arm64.deb ... Unpacking cpp (4:9.2.1-3.1ubuntu1) over (4:9.2.1-2ubuntu2) ... Preparing to unpack .../09-dpkg-dev_1.19.7ubuntu77_all.deb ... Unpacking dpkg-dev (1.19.7ubuntu77) over (1.19.7ubuntu1) ... Preparing to unpack .../10-libdpkg-perl_1.19.7ubuntu77_all.deb ... Unpacking libdpkg-perl (1.19.7ubuntu77) over (1.19.7ubuntu1) ... Preparing to unpack .../11-build-essential_12.7ubuntu1_arm64.deb ... Unpacking build-essential (12.7ubuntu1) over (12.6ubuntu2) ... Preparing to unpack .../12-libip4tc2_1.8.3-2ubuntu4_arm64.deb ... Unpacking libip4tc2:arm64 (1.8.3-2ubuntu4) over (1.8.3-2ubuntu2) ... Setting up libip4tc2:arm64 (1.8.3-2ubuntu4) ... Setting up libisl21:arm64 (0.21-2) ... Setting up libapparmor1:arm64 (2.13.3-5ubuntu1) ... Setting up libsqlite3-0:arm64 (3.29.0-2) ... Setting up binutils-common:arm64 (2.32.51.20190905-0ubuntu1) ... Setting up linux-libc-dev:arm64 (5.3.0-10.11) ... Setting up libcom-err2:arm64 (1.45.3-4ubuntu1) ... Setting up libgomp1:arm64 (9.2.1-8ubuntu1) ... Setting up tzdata (2019c-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Sep 17 19:21:27 UTC 2019. Universal Time is now: Tue Sep 17 19:21:27 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasan5:arm64 (9.2.1-8ubuntu1) ... Setting up libatomic1:arm64 (9.2.1-8ubuntu1) ... Setting up libss2:arm64 (1.45.3-4ubuntu1) ... Setting up libdpkg-perl (1.19.7ubuntu77) ... Setting up logsave (1.45.3-4ubuntu1) ... Setting up libubsan1:arm64 (9.2.1-8ubuntu1) ... Setting up libdevmapper1.02.1:arm64 (2:1.02.155-2ubuntu6) ... Setting up cpp-9 (9.2.1-8ubuntu1) ... Setting up libbinutils:arm64 (2.32.51.20190905-0ubuntu1) ... Setting up libc-dev-bin (2.30-0ubuntu1) ... Setting up libcc1-0:arm64 (9.2.1-8ubuntu1) ... Setting up liblsan0:arm64 (9.2.1-8ubuntu1) ... Setting up libitm1:arm64 (9.2.1-8ubuntu1) ... Setting up libtsan0:arm64 (9.2.1-8ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.32.51.20190905-0ubuntu1) ... Setting up e2fsprogs (1.45.3-4ubuntu1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/e2scrub.conf ... Setting up binutils (2.32.51.20190905-0ubuntu1) ... Setting up dpkg-dev (1.19.7ubuntu77) ... Setting up libgcc-9-dev:arm64 (9.2.1-8ubuntu1) ... Setting up cpp (4:9.2.1-3.1ubuntu1) ... Setting up libc6-dev:arm64 (2.30-0ubuntu1) ... Setting up gcc-9 (9.2.1-8ubuntu1) ... Setting up libstdc++-9-dev:arm64 (9.2.1-8ubuntu1) ... Setting up gcc (4:9.2.1-3.1ubuntu1) ... Setting up g++-9 (9.2.1-8ubuntu1) ... Setting up g++ (4:9.2.1-3.1ubuntu1) ... Setting up build-essential (12.7ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17698940 arm64 eoan -c chroot:build-PACKAGEBUILD-17698940 --arch=arm64 --dist=eoan --nolog phast_1.5+dfsg-1.dsc Initiating build PACKAGEBUILD-17698940 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-161-generic #189-Ubuntu SMP Tue Aug 27 08:12:37 UTC 2019 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-068.buildd +==============================================================================+ | phast 1.5+dfsg-1 (arm64) 17 Sep 2019 19:21 | +==============================================================================+ Package: phast Version: 1.5+dfsg-1 Source Version: 1.5+dfsg-1 Distribution: eoan Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/phast-j6Jj3g/phast-1.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/phast-j6Jj3g' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17698940/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- phast_1.5+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-jP77ec/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-jP77ec/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jP77ec/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jP77ec/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jP77ec/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-jP77ec/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (119 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 NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-jP77ec/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12744 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man Filtered Build-Depends: debhelper (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<>/resolver-YTNtVu/apt_archive/sbuild-build-depends-phast-dummy.deb'. Ign:1 copy:/<>/resolver-YTNtVu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-YTNtVu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-YTNtVu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-YTNtVu/apt_archive ./ Sources [241 B] Get:5 copy:/<>/resolver-YTNtVu/apt_archive ./ Packages [559 B] Fetched 2919 B in 0s (126 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 file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu63 liblapack-dev liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 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 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs 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 file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libcroco3 libelf1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu63 liblapack-dev liblapack3 liblocale-gettext-perl libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-phast-dummy 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 21.1 MB of archives. After this operation, 87.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-YTNtVu/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [888 B] Get:2 http://ftpmaster.internal/ubuntu eoan/main arm64 liblocale-gettext-perl arm64 1.07-3build3 [16.3 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main arm64 bsdmainutils arm64 11.1.2ubuntu2 [175 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main arm64 groff-base arm64 1.22.4-3 [813 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main arm64 libpipeline1 arm64 1.5.1-2 [24.4 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main arm64 man-db arm64 2.8.7-3 [1096 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main arm64 libmagic-mgc arm64 1:5.37-5 [209 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main arm64 libmagic1 arm64 1:5.37-5 [70.9 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main arm64 file arm64 1:5.37-5 [23.2 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main arm64 libelf1 arm64 0.176-1.1 [43.6 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main arm64 libglib2.0-0 arm64 2.62.0-1 [1178 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main arm64 libicu63 arm64 63.2-2 [8146 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main arm64 libxml2 arm64 2.9.4+dfsg1-7ubuntu3 [562 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main arm64 gettext-base arm64 0.19.8.1-9 [48.0 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main arm64 m4 arm64 1.4.18-2 [194 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main arm64 autoconf all 2.69-11 [322 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main arm64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main arm64 autopoint all 0.19.8.1-9 [412 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main arm64 libtool all 2.4.6-11 [194 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main arm64 dh-autoreconf all 19 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main arm64 libarchive-zip-perl all 1.65-1 [83.6 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu eoan/main arm64 libfile-stripnondeterminism-perl all 1.6.0-1 [16.2 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main arm64 dh-strip-nondeterminism all 1.6.0-1 [5208 B] Get:29 http://ftpmaster.internal/ubuntu eoan/main arm64 dwz arm64 0.13-1 [73.4 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:31 http://ftpmaster.internal/ubuntu eoan/main arm64 gettext arm64 0.19.8.1-9 [853 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main arm64 po-debconf all 1.0.21 [233 kB] Get:34 http://ftpmaster.internal/ubuntu eoan/main arm64 debhelper all 12.4ubuntu1 [910 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/universe arm64 help2man arm64 1.47.11 [172 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main arm64 libblas3 arm64 3.8.0-2 [89.8 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main arm64 libblas-dev arm64 3.8.0-2 [92.2 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main arm64 libgfortran5 arm64 9.2.1-8ubuntu1 [333 kB] Get:39 http://ftpmaster.internal/ubuntu eoan/main arm64 liblapack3 arm64 3.8.0-2 [1478 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main arm64 liblapack-dev arm64 3.8.0-2 [1512 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main arm64 libpcre16-3 arm64 2:8.39-12 [126 kB] Get:42 http://ftpmaster.internal/ubuntu eoan/main arm64 libpcre32-3 arm64 2:8.39-12 [119 kB] Get:43 http://ftpmaster.internal/ubuntu eoan/main arm64 libpcrecpp0v5 arm64 2:8.39-12 [14.8 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main arm64 libpcre3-dev arm64 2:8.39-12 [468 kB] Get:45 http://ftpmaster.internal/ubuntu eoan/main arm64 libtmglib3 arm64 3.8.0-2 [80.6 kB] Get:46 http://ftpmaster.internal/ubuntu eoan/main arm64 libtmglib-dev arm64 3.8.0-2 [82.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.1 MB in 1s (28.4 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12744 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3build3_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-3build3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../01-libbsd0_0.10.0-1_arm64.deb ... Unpacking libbsd0:arm64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu2_arm64.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../03-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../04-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../05-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../06-man-db_2.8.7-3_arm64.deb ... Unpacking man-db (2.8.7-3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.37-5_arm64.deb ... Unpacking libmagic-mgc (1:5.37-5) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.37-5_arm64.deb ... Unpacking libmagic1:arm64 (1:5.37-5) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.37-5_arm64.deb ... Unpacking file (1:5.37-5) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../10-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../11-libglib2.0-0_2.62.0-1_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.62.0-1) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../12-libicu63_63.2-2_arm64.deb ... Unpacking libicu63:arm64 (63.2-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../13-libxml2_2.9.4+dfsg1-7ubuntu3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7ubuntu3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../14-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../15-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../16-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../17-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../18-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../19-automake_1%3a1.16.1-4ubuntu3_all.deb ... Unpacking automake (1:1.16.1-4ubuntu3) ... Selecting previously unselected package autopoint. Preparing to unpack .../20-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../21-libtool_2.4.6-11_all.deb ... Unpacking libtool (2.4.6-11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../22-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../23-libarchive-zip-perl_1.65-1_all.deb ... Unpacking libarchive-zip-perl (1.65-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../24-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../25-libfile-stripnondeterminism-perl_1.6.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.6.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../26-dh-strip-nondeterminism_1.6.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.6.0-1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.13-1_arm64.deb ... Unpacking dwz (0.13-1) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../28-libcroco3_0.6.13-1_arm64.deb ... Unpacking libcroco3:arm64 (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.4ubuntu1_all.deb ... Unpacking debhelper (12.4ubuntu1) ... Selecting previously unselected package help2man. Preparing to unpack .../33-help2man_1.47.11_arm64.deb ... Unpacking help2man (1.47.11) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../34-libblas3_3.8.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.8.0-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../35-libblas-dev_3.8.0-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.8.0-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../36-libgfortran5_9.2.1-8ubuntu1_arm64.deb ... Unpacking libgfortran5:arm64 (9.2.1-8ubuntu1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../37-liblapack3_3.8.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.8.0-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../38-liblapack-dev_3.8.0-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.8.0-2) ... Selecting previously unselected package libpcre16-3:arm64. Preparing to unpack .../39-libpcre16-3_2%3a8.39-12_arm64.deb ... Unpacking libpcre16-3:arm64 (2:8.39-12) ... Selecting previously unselected package libpcre32-3:arm64. Preparing to unpack .../40-libpcre32-3_2%3a8.39-12_arm64.deb ... Unpacking libpcre32-3:arm64 (2:8.39-12) ... Selecting previously unselected package libpcrecpp0v5:arm64. Preparing to unpack .../41-libpcrecpp0v5_2%3a8.39-12_arm64.deb ... Unpacking libpcrecpp0v5:arm64 (2:8.39-12) ... Selecting previously unselected package libpcre3-dev:arm64. Preparing to unpack .../42-libpcre3-dev_2%3a8.39-12_arm64.deb ... Unpacking libpcre3-dev:arm64 (2:8.39-12) ... Selecting previously unselected package libtmglib3:arm64. Preparing to unpack .../43-libtmglib3_3.8.0-2_arm64.deb ... Unpacking libtmglib3:arm64 (3.8.0-2) ... Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../44-libtmglib-dev_3.8.0-2_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.8.0-2) ... Selecting previously unselected package sbuild-build-depends-phast-dummy. Preparing to unpack .../45-sbuild-build-depends-phast-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-phast-dummy (0.invalid.0) ... Setting up libpcrecpp0v5:arm64 (2:8.39-12) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up libpcre16-3:arm64 (2:8.39-12) ... Setting up libmagic-mgc (1:5.37-5) ... Setting up libarchive-zip-perl (1.65-1) ... Setting up libglib2.0-0:arm64 (2.62.0-1) ... No schema files found: doing nothing. Setting up libmagic1:arm64 (1:5.37-5) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.37-5) ... Setting up libicu63:arm64 (63.2-2) ... Setting up autotools-dev (20180224.1) ... 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 libsigsegv2:arm64 (2.12-2) ... Setting up libpcre32-3:arm64 (2:8.39-12) ... Setting up autopoint (0.19.8.1-9) ... Setting up libgfortran5:arm64 (9.2.1-8ubuntu1) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:arm64 (0.10.0-1) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7ubuntu3) ... Setting up liblocale-gettext-perl (1.07-3build3) ... 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 libfile-stripnondeterminism-perl (1.6.0-1) ... 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 libtool (2.4.6-11) ... Setting up libpcre3-dev:arm64 (2:8.39-12) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.11) ... Setting up libtmglib3:arm64 (3.8.0-2) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode 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 libcroco3:arm64 (0.6.13-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.13-1) ... Setting up groff-base (1.22.4-3) ... Setting up libtmglib-dev:arm64 (3.8.0-2) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.7-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.4ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.6.0-1) ... Setting up sbuild-build-depends-phast-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-161-generic arm64 (aarch64) Toolchain package versions: binutils_2.32.51.20190905-0ubuntu1 dpkg-dev_1.19.7ubuntu77 g++-9_9.2.1-8ubuntu1 gcc-9_9.2.1-8ubuntu1 libc6-dev_2.30-0ubuntu1 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 linux-libc-dev_5.3.0-10.11 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.3 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2ubuntu6 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.32.51.20190905-0ubuntu1 binutils-aarch64-linux-gnu_2.32.51.20190905-0ubuntu1 binutils-common_2.32.51.20190905-0ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu2 build-essential_12.7ubuntu1 bzip2_1.0.6-9.2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.4ubuntu1 debianutils_4.8.6.3 dh-autoreconf_19 dh-strip-nondeterminism_1.6.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu77 dpkg-dev_1.19.7ubuntu77 dwz_0.13-1 e2fsprogs_1.45.3-4ubuntu1 fakeroot_1.23-1 fdisk_2.34-0.1ubuntu2 file_1:5.37-5 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-8ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-8ubuntu1 gcc-9-base_9.2.1-8ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.12-1ubuntu3 gpg-agent_2.2.12-1ubuntu3 gpgconf_2.2.12-1ubuntu3 gpgv_2.2.12-1ubuntu3 grep_3.3-1 groff-base_1.22.4-3 gzip_1.10-0ubuntu3 help2man_1.47.11 hostname_3.22 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapparmor1_2.13.3-5ubuntu1 libapt-pkg5.90_1.9.3 libarchive-zip-perl_1.65-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-8ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-8ubuntu1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.5-2ubuntu1 libaudit1_1:2.8.5-2ubuntu1 libbinutils_2.32.51.20190905-0ubuntu1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.34-0.1ubuntu2 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.2 libc-bin_2.30-0ubuntu1 libc-dev-bin_2.30-0ubuntu1 libc6_2.30-0ubuntu1 libc6-dev_2.30-0ubuntu1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_9.2.1-8ubuntu1 libcom-err2_1.45.3-4ubuntu1 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.0-3ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.249ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu6 libdpkg-perl_1.19.7ubuntu77 libelf1_0.176-1.1 libext2fs2_1.45.3-4ubuntu1 libfakeroot_1.23-1 libfdisk1_2.34-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.0-1 libgcc-9-dev_9.2.1-8ubuntu1 libgcc1_1:9.2.1-8ubuntu1 libgcrypt20_1.8.4-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-8ubuntu1 libglib2.0-0_2.62.0-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4build1 libgomp1_9.2.1-8ubuntu1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libicu63_63.2-2 libidn11_1.33-2.2ubuntu2 libidn2-0_2.2.0-1 libip4tc2_1.8.3-2ubuntu4 libisl21_0.21-2 libitm1_9.2.1-8ubuntu1 libjson-c4_0.13.1+dfsg-4 libkmod2_26-1ubuntu1 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 liblocale-gettext-perl_1.07-3build3 liblockfile-bin_1.15-1 liblockfile1_1.15-1 liblsan0_9.2.1-8ubuntu1 liblz4-1_1.9.1-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.34-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1ubuntu1 libncursesw6_6.1+20190803-1ubuntu1 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.17-2 libpam-modules_1.3.1-5ubuntu1 libpam-modules-bin_1.3.1-5ubuntu1 libpam-runtime_1.3.1-5ubuntu1 libpam0g_1.3.1-5ubuntu1 libpcre16-3_2:8.39-12 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libpcre3-dev_2:8.39-12 libpcre32-3_2:8.39-12 libpcrecpp0v5_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libreadline8_8.0-3 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu2 libsqlite3-0_3.29.0-2 libss2_1.45.3-4ubuntu1 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-8ubuntu1 libstdc++6_9.2.1-8ubuntu1 libsub-override-perl_0.09-2 libsystemd0_241-7ubuntu1 libtasn1-6_4.14-2 libtinfo6_6.1+20190803-1ubuntu1 libtmglib-dev_3.8.0-2 libtmglib3_3.8.0-2 libtool_2.4.6-11 libtsan0_9.2.1-8ubuntu1 libubsan1_9.2.1-8ubuntu1 libuchardet0_0.0.6-3 libudev1_241-7ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu2 libxml2_2.9.4+dfsg1-7ubuntu3 libzstd1_1.4.3+dfsg-1 linux-libc-dev_5.3.0-10.11 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu1 lsb-base_11.0.1ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu2 ncurses-base_6.1+20190803-1ubuntu1 ncurses-bin_6.1+20190803-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_241-7ubuntu1 systemd-sysv_241-7ubuntu1 sysvinit-utils_2.95-5ubuntu2 tar_1.30+dfsg-6 tzdata_2019c-1 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- 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 disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17698940 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17698940 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17698940 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package phast dpkg-buildpackage: info: source version 1.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable 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/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/all_dists /<>/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/consEntropy /<>/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/phast /<>/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/hmm_tweak /<>/phast-1.5+dfsg/src/util/../../bin/eval_predictions /<>/phast-1.5+dfsg/src/util/../../bin/chooseLines /<>/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 -j4 "INSTALL=install --strip-program=true" 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' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. 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' gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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' gcc -g -O2 -flto=auto -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] 140 | else | ^~~~ sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ gcc -g -O2 -flto=auto -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] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ gcc -g -O2 -flto=auto -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' gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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' gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 ar rs /<>/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o make[4]: Leaving directory '/<>/phast-1.5+dfsg/src/lib/hmm' make[4]: Entering directory '/<>/phast-1.5+dfsg/src/lib/phylo' gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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] 241 | 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] 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~~~~~~~~~ ~~~~~~~~~~~ ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o bgc_hmm.o ar rs /<>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_model.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o tree_likelihoods.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.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' gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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' gcc -g -O2 -flto=auto -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] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘ih_read_compact’ at indel_history.c:317:14, inlined from ‘ih_new_from_file’ at indel_history.c:368:30, inlined from ‘main’ at dless.c:146:12: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘main’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_partition_nodes’ at trees.c:1318:3, inlined from ‘ih_expand’ at indel_history.c:82:5, inlined from ‘ih_new_from_file’ at indel_history.c:369:22, inlined from ‘main’ at dless.c:146:12: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘main’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_preorder’ at trees.c:563:5: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_preorder’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘tm_new_from_file.constprop’ at tree_model.c:438:14: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/phastOdds' make[3]: Entering directory '/<>/phast-1.5+dfsg/src/phastMotif' gcc -g -O2 -flto=auto -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] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_preorder’ at trees.c:563:5: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_preorder’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ 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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ 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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_preorder’ at trees.c:563:5: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_preorder’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ 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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -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 makeHKY.help_src > makeHKY.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh indelFit.help_src > indelFit.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 consEntropy.help_src > consEntropy.help gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_preorder’ at trees.c:563:5: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_preorder’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘tm_new_from_file.constprop’ at tree_model.c:438:14: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tm_new_from_file.constprop’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_preorder’ at trees.c:563:5: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_preorder’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘tr_new_from_string’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘tr_new_from_file’ at trees.c:55:12, inlined from ‘main’ at hmm_view.c:63:14: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘main’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘tr_new_from_file’ at trees.c:55:12, inlined from ‘main’ at hmm_tweak.c:117:14: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘main’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now In function ‘srealloc’, inlined from ‘lst_push’ at /<>/phast-1.5+dfsg/src/../include/lists.h:497:26, inlined from ‘lst_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/lists.h:534:4, inlined from ‘stk_push_ptr’ at /<>/phast-1.5+dfsg/src/../include/stacks.h:110:42, inlined from ‘tr_set_nnodes’ at trees.c:165:3, inlined from ‘tr_new_from_string’ at trees.c:149:3, inlined from ‘tr_new_from_file’ at trees.c:55:12, inlined from ‘main’ at makeHKY.c:60:14: misc.c:461:18: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] misc.c: In function ‘main’: /usr/include/stdlib.h:550:14: note: in a call to allocation function ‘realloc’ declared here 550 | extern void *realloc (void *__ptr, size_t __size) | ^ gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now gcc -g -O2 -flto=auto -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 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,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/phast-1.5+dfsg/src/util' mkdir -p ../doc/man/ Generating man pages... USAGE: convert_coords -m -f [-s ] [-d ] [-p] [-n] [-i PHYLIP|FASTA|MPM] DESCRIPTION: Converts coordinates of features in a GFF file according to a multiple alignment. Will map from the coordinate system of any sequence to any other sequence; can also map to or from the coordinate system of the entire alignment. In addition, supports translation of coordinates by specified offset. OPTIONS: -m (required) Name of file in which alignment is defined. -f (required) Name of file in which features are defined (GFF). -s Index of frame of reference for feature coordinates, as defined in the GFF file. Use an integer 1-N (if N seqs) or 0 to indicate the coordinate system of the alignment as a whole. Default behavior is to match features with alignment sequences by name (feature by feature). -d Index of destination frame of reference. Default is 0 (whole MSA). -p Positive coordinate offset. This value will be added to all coordinates. Useful when the alignment (or sequence) for which the coordinates are specified is a sub-alignment of yours. -n Negative coordinate offset. This value will be subtracted from all coordinates. Useful when your alignment is a sub-alignment of the alignment (or sequence) for which the coordinates are specified. -i FASTA|PHYLIP|MPM|SS Alignment format. Default is to guess format from file contents PROGRAM: draw_tree DESCRIPTION: Produces a simple postscript rendering of a tree. USAGE: draw_tree [-dbvs] | OPTIONS: (Required) File name of tree (expected to be in Newick format, unless filename ends with '.mod', in which case expected to be a tree model file). -d Print "diagonal" branches, instead of "right-angle" or "square" ones (produces a "cladogram", as opposed to a "phenogram"). This option implies -s. -b Suppress branch lengths. -v Vertical layout. -s Don't draw branches to scale. Done. make[2]: Leaving directory '/<>/phast-1.5+dfsg/src' make[1]: Leaving directory '/<>/phast-1.5+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/phast-1.5+dfsg' cd test && PATH=/<>/phast-1.5+dfsg/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view make[2]: Entering directory '/<>/phast-1.5+dfsg/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa E: Caught signal ‘Terminated’: terminating immediately make: *** [debian/rules:8: build-arch] Terminated make[1]: *** wait: No child processes. Stop. make[1]: *** Waiting for unfinished jobs.... make[1]: *** wait: No child processes. Stop. make[2]: *** [Makefile:9: msa_view] Terminated Build killed with signal TERM after 150 minutes of inactivity -------------------------------------------------------------------------------- Build finished at 20190917-2154 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 44252 Build-Time: 9153 Distribution: eoan Fail-Stage: build Host Architecture: arm64 Install-Time: 19 Job: phast_1.5+dfsg-1.dsc Machine Architecture: arm64 Package: phast Package-Time: 9175 Source-Version: 1.5+dfsg-1 Space: 44252 Status: attempted Version: 1.5+dfsg-1 -------------------------------------------------------------------------------- Finished at 20190917-2154 Build needed 02:32:55, 44252k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=eoan --arch=arm64 PACKAGEBUILD-17698940 Scanning for processes to kill in build PACKAGEBUILD-17698940