RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux auburn 3.13.0-65-generic #105-Ubuntu SMP Mon Sep 21 19:10:52 UTC 2015 aarch64 Buildd toolchain package versions: launchpad-buildd_134 python-lpbuildd_134 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 dpkg-dev_1.17.5ubuntu5.4 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 18 Dec 02:10:46 ntpdate[19507]: adjust time server 10.211.37.1 offset -0.025461 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8454928', '/home/buildd/filecache-default/e4334328d0a439a5c9a1262cdf1f64d583863c1f'] Unpacking chroot for build PACKAGEBUILD-8454928 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8454928'] Mounting chroot for build PACKAGEBUILD-8454928 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8454928', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8454928 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8454928', 'arm64'] Updating debian chroot for build PACKAGEBUILD-8454928 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main arm64 Packages [1411 kB] Get:6 http://ftpmaster.internal xenial/universe arm64 Packages [6851 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [847 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4744 kB] Get:9 http://ftpmaster.internal xenial-security/main arm64 Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe arm64 Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main arm64 Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe arm64 Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main arm64 Packages [91.6 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe arm64 Packages [570 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [61.4 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [349 kB] Fetched 15.5 MB in 16s (948 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'apt-get autoremove' to remove them. The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libisl15 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: advancecomp apt apt-transport-https base-files binutils bsdutils cpp cpp-5 debconf diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmount1 libmpfr4 libncurses5 libncursesw5 libpng12-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 103 upgraded, 5 newly installed, 1 to remove and 0 not upgraded. Need to get 109 MB of archives. After this operation, 306 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files arm64 9.4ubuntu3 [68.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils arm64 1:2.27.1-1ubuntu3 [49.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils arm64 1:3.3-2 [144 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg arm64 1.18.3ubuntu1 [2038 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev arm64 2.21-0ubuntu5 [1677 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin arm64 2.21-0ubuntu5 [58.8 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev arm64 4.3.0-5.16 [793 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 arm64 1:2.24-12 [12.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin arm64 2.21-0ubuntu5 [1035 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 arm64 5.3.1-3ubuntu3 [45.7 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libitm1 arm64 5.3.1-3ubuntu3 [23.9 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 arm64 5.3.1-3ubuntu3 [6380 B] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 arm64 5.3.1-3ubuntu3 [232 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base arm64 5.3.1-3ubuntu3 [16.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 arm64 1:5.3.1-3ubuntu3 [30.8 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 arm64 5.3.1-3ubuntu3 [88.4 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 arm64 0.15-3 [393 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 arm64 5.3.1-3ubuntu3 [23.3 MB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 arm64 5.3.1-3ubuntu3 [27.2 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main binutils arm64 2.25.90.20151211-0ubuntu2 [2456 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 arm64 5.3.1-3ubuntu3 [25.0 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 arm64 5.3.1-3ubuntu3 [23.6 MB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev arm64 5.3.1-3ubuntu3 [495 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev arm64 5.3.1-3ubuntu3 [1371 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 arm64 5.3.1-3ubuntu3 [362 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 arm64 2:6.1.0+dfsg-2 [202 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 arm64 3.1.3-2 [172 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libc6 arm64 2.21-0ubuntu5 [4077 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs arm64 1.42.13-1ubuntu1 [169 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs arm64 1.42.13-1ubuntu1 [744 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main findutils arm64 4.4.2-10 [258 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep arm64 2.22-1 [135 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main hostname arm64 3.16ubuntu2 [11.2 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main init arm64 1.24ubuntu2 [3964 B] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 arm64 2.27.1-1ubuntu3 [52.2 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 arm64 2.27.1-1ubuntu3 [14.0 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 arm64 2.27.1-1ubuntu3 [87.5 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 arm64 2.27.1-1ubuntu3 [113 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils arm64 2.88dsf-59.2ubuntu3 [25.1 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main initscripts arm64 2.88dsf-59.2ubuntu3 [24.7 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main util-linux arm64 2.27.1-1ubuntu3 [785 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 arm64 228-2ubuntu2 [47.1 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main udev arm64 228-2ubuntu2 [927 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 arm64 228-2ubuntu2 [162 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main systemd arm64 228-2ubuntu2 [2881 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 arm64 2.4-3 [46.4 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 arm64 6.0+20151024-2ubuntu1 [66.5 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 arm64 6.0+20151024-2ubuntu1 [75.3 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 arm64 6.0+20151024-2ubuntu1 [92.8 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 arm64 2:3.3.10-4ubuntu1 [28.7 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main procps arm64 2:3.3.10-4ubuntu1 [208 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapparmor1 arm64 2.10-0ubuntu9 [26.2 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 arm64 1:2.4.4-4ubuntu1 [33.4 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 arm64 2.27.1-1ubuntu3 [93.7 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 arm64 2.2.3-2ubuntu3 [31.3 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin arm64 1:2.24-12 [20.0 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main mount arm64 2.27.1-1ubuntu3 [115 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin arm64 6.0+20151024-2ubuntu1 [130 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-modules-5.22 all 5.22.1-1 [2648 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libperl5.22 arm64 5.22.1-1 [2763 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl arm64 5.22.1-1 [237 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-base arm64 5.22.1-1 [1139 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main tar arm64 1.28-2.1 [184 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 arm64 1.1.5 [623 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main apt arm64 1.1.5 [939 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main gpgv arm64 1.4.19-6ubuntu1 [138 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main gnupg arm64 1.4.19-6ubuntu1 [565 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv arm64 228-2ubuntu2 [15.1 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 arm64 1.42.13-1ubuntu1 [65.1 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 arm64 0.198ubuntu1 [6202 B] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 arm64 2:1.02.110-1ubuntu2 [115 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 arm64 1.21-1 [29.7 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 arm64 1.6.4-3 [270 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 arm64 2.4-2 [150 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:81 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 arm64 2.4-3 [65.2 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libss2 arm64 1.42.13-1ubuntu1 [68.6 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support arm64 2.21-0ubuntu5 [7180 B] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 arm64 3.2.1-4 [16.3 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 arm64 4.7-2 [37.7 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 arm64 3.3.18-1ubuntu1 [415 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 arm64 1.2.54-1 [106 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 arm64 3.9.2-1 [332 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 arm64 1.0.2e-1ubuntu1 [694 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup arm64 2:1.02.110-1ubuntu2 [50.9 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 arm64 1.13.2+dfsg-4 [96.7 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 arm64 1.13.2+dfsg-4 [228 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 arm64 1.13.2+dfsg-4 [27.4 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 arm64 1.13.2+dfsg-4 [73.2 kB] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 arm64 1.5.9-8ubuntu1 [9424 B] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 arm64 1.32-3ubuntu1 [42.3 kB] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls arm64 7.45.0-1ubuntu1 [151 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https arm64 1.1.5 [23.7 kB] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 arm64 1.10.6-1ubuntu1 [136 kB] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main openssl arm64 1.0.2e-1ubuntu1 [470 kB] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp arm64 1.20-1 [145 kB] Get:102 http://ftpmaster.internal/ubuntu/ xenial/main cpp arm64 4:5.2.1-16ubuntu2 [27.6 kB] Get:103 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:104 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:105 http://ftpmaster.internal/ubuntu/ xenial/main gcc arm64 4:5.2.1-16ubuntu2 [5230 B] Get:106 http://ftpmaster.internal/ubuntu/ xenial/main g++ arm64 4:5.2.1-16ubuntu2 [1496 B] Get:107 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:108 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 109 MB in 40s (2730 kB/s) (Reading database ... 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Setting up libstdc++6:arm64 (5.3.1-3ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11557 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.1.0+dfsg-2_arm64.deb ... Unpacking libgmp10:arm64 (2:6.1.0+dfsg-2) over (2:6.0.0+dfsg-7) ... Preparing to unpack .../libmpfr4_3.1.3-2_arm64.deb ... Unpacking libmpfr4:arm64 (3.1.3-2) over (3.1.3-1) ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up e2fslibs:arm64 (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11557 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.13-1ubuntu1_arm64.deb ... Unpacking e2fsprogs (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Setting up e2fsprogs (1.42.13-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11558 files and directories currently installed.) Preparing to unpack .../findutils_4.4.2-10_arm64.deb ... Unpacking findutils (4.4.2-10) over (4.4.2-9build1) ... Setting up findutils (4.4.2-10) ... (Reading database ... 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11567 files and directories currently installed.) Preparing to unpack .../systemd_228-2ubuntu2_arm64.deb ... Unpacking systemd (228-2ubuntu2) over (225-1ubuntu9) ... Setting up systemd (228-2ubuntu2) ... Installing new version of config file /etc/pam.d/systemd-user ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11568 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_arm64.deb ... Unpacking libselinux1:arm64 (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:arm64 (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11568 files and directories currently installed.) Preparing to unpack .../libtinfo5_6.0+20151024-2ubuntu1_arm64.deb ... Unpacking libtinfo5:arm64 (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libtinfo5:arm64 (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11568 files and directories currently installed.) Preparing to unpack .../libncurses5_6.0+20151024-2ubuntu1_arm64.deb ... Unpacking libncurses5:arm64 (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:arm64 (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Unpacking libapparmor1:arm64 (2.10-0ubuntu9) over (2.10-0ubuntu6) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapparmor1:arm64 (2.10-0ubuntu9) ... Processing triggers for systemd (228-2ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11577 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.4-4ubuntu1_all.deb ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11577 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_arm64.deb ... Unpacking libmount1:arm64 (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:arm64 (2.27.1-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Setting up linux-libc-dev:arm64 (4.3.0-5.16) ... Setting up libc6-dev:arm64 (2.21-0ubuntu5) ... Setting up libgomp1:arm64 (5.3.1-3ubuntu3) ... Setting up libitm1:arm64 (5.3.1-3ubuntu3) ... Setting up libatomic1:arm64 (5.3.1-3ubuntu3) ... Setting up libasan2:arm64 (5.3.1-3ubuntu3) ... Setting up libubsan0:arm64 (5.3.1-3ubuntu3) ... Setting up libgmp10:arm64 (2:6.1.0+dfsg-2) ... Setting up libisl15:arm64 (0.15-3) ... Setting up libmpfr4:arm64 (3.1.3-2) ... Setting up cpp-5 (5.3.1-3ubuntu3) ... Setting up libcc1-0:arm64 (5.3.1-3ubuntu3) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgcc-5-dev:arm64 (5.3.1-3ubuntu3) ... Setting up gcc-5 (5.3.1-3ubuntu3) ... Setting up libstdc++-5-dev:arm64 (5.3.1-3ubuntu3) ... Setting up g++-5 (5.3.1-3ubuntu3) ... Setting up libprocps4:arm64 (2:3.3.10-4ubuntu1) ... Setting up procps (2:3.3.10-4ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up udev (228-2ubuntu2) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up perl-modules-5.22 (5.22.1-1) ... Setting up libperl5.22:arm64 (5.22.1-1) ... Setting up perl (5.22.1-1) ... Setting up apt (1.1.5) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libffi6:arm64 (3.2.1-4) ... Setting up libtasn1-6:arm64 (4.7-2) ... Setting up libgnutls-deb0-28:arm64 (3.3.18-1ubuntu1) ... Setting up libpng12-0:arm64 (1.2.54-1) ... Setting up libsqlite3-0:arm64 (3.9.2-1) ... Setting up libssl1.0.0:arm64 (1.0.2e-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libkrb5support0:arm64 (1.13.2+dfsg-4) ... Setting up libk5crypto3:arm64 (1.13.2+dfsg-4) ... Setting up libkeyutils1:arm64 (1.5.9-8ubuntu1) ... Setting up libkrb5-3:arm64 (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:arm64 (1.13.2+dfsg-4) ... Setting up libidn11:arm64 (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.5) ... Setting up libdbus-1-3:arm64 (1.10.6-1ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... Setting up pkgbinarymangler (125) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8454928', 'arm64', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=arm64', '--dist=xenial-proposed', '--purge=never', '--nolog', 'fastml_3.1-2.dsc'] Initiating build PACKAGEBUILD-8454928 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.13.0-65-generic #105-Ubuntu SMP Mon Sep 21 19:10:52 UTC 2015 aarch64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on auburn.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ fastml 3.1-2 (arm64) 18 Dec 2015 02:15 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: fastml Version: 3.1-2 Source Version: 3.1-2 Distribution: xenial-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/fastml-IgREKa/fastml-3.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/fastml-IgREKa' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8454928/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── fastml_3.1-2.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 '/«BUILDDIR»/resolver-vw7KbP/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Packages [527 B] Ign:4 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Packages [527 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. 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 0 B/770 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-vw7KbP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12174 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9) Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9) dpkg-deb: building package 'sbuild-build-depends-fastml-dummy' in '/«BUILDDIR»/resolver-plHvYz/apt_archive/sbuild-build-depends-fastml-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Sources [421 B] Get:5 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Packages [687 B] Ign:4 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Sources [421 B] Get:5 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Packages [687 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install fastml build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu55 libmagic1 libpipeline1 libtimedate-perl libunistring0 libxml2 man-db po-debconf sbuild-build-depends-fastml-dummy 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 13.9 MB/13.9 MB of archives. After this operation, 56.0 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-fastml-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-plHvYz/apt_archive ./ sbuild-build-depends-fastml-dummy 0.invalid.0 [928 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main arm64 groff-base arm64 1.22.3-4 [1119 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main arm64 bsdmainutils arm64 9.0.6ubuntu1 [171 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main arm64 libpipeline1 arm64 1.4.1-1 [21.9 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main arm64 man-db arm64 2.7.5-1 [832 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main arm64 libunistring0 arm64 0.9.3-5.2ubuntu1 [251 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main arm64 libmagic1 arm64 1:5.25-2ubuntu1 [209 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main arm64 file arm64 1:5.25-2ubuntu1 [21.2 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main arm64 libasprintf0v5 arm64 0.19.6-1ubuntu1 [6934 B] Get:10 http://ftpmaster.internal/ubuntu xenial/main arm64 gettext-base arm64 0.19.6-1ubuntu1 [45.9 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main arm64 libglib2.0-0 arm64 2.47.3-3 [922 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main arm64 libicu55 arm64 55.1-6ubuntu1 [7505 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main arm64 libxml2 arm64 2.9.2+zdfsg1-4ubuntu2 [564 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main arm64 libcroco3 arm64 0.6.10-1 [66.8 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main arm64 gettext arm64 0.19.6-1ubuntu1 [1004 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main arm64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main arm64 po-debconf all 1.0.18 [234 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main arm64 libarchive-zip-perl all 1.53-1 [87.0 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main arm64 libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main arm64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main arm64 dh-strip-nondeterminism all 0.014-1 [5596 B] Get:22 http://ftpmaster.internal/ubuntu xenial/main arm64 debhelper all 9.20151126ubuntu1 [741 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.9 MB in 3s (3620 kB/s) Selecting previously unselected package groff-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12174 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-4_arm64.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_arm64.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../libpipeline1_1.4.1-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_arm64.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libunistring0:arm64. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_arm64.deb ... Unpacking libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_arm64.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package libasprintf0v5:arm64. Preparing to unpack .../libasprintf0v5_0.19.6-1ubuntu1_arm64.deb ... Unpacking libasprintf0v5:arm64 (0.19.6-1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.6-1ubuntu1_arm64.deb ... Unpacking gettext-base (0.19.6-1ubuntu1) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../libglib2.0-0_2.47.3-3_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.47.3-3) ... Selecting previously unselected package libicu55:arm64. Preparing to unpack .../libicu55_55.1-6ubuntu1_arm64.deb ... Unpacking libicu55:arm64 (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu2_arm64.deb ... Unpacking libxml2:arm64 (2.9.2+zdfsg1-4ubuntu2) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../libcroco3_0.6.10-1_arm64.deb ... Unpacking libcroco3:arm64 (0.6.10-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.6-1ubuntu1_arm64.deb ... Unpacking gettext (0.19.6-1ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.18_all.deb ... Unpacking po-debconf (1.0.18) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ... Unpacking libarchive-zip-perl (1.53-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.014-1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ... Unpacking dh-strip-nondeterminism (0.014-1) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20151126ubuntu1_all.deb ... Unpacking debhelper (9.20151126ubuntu1) ... Selecting previously unselected package sbuild-build-depends-fastml-dummy. Preparing to unpack .../sbuild-build-depends-fastml-dummy.deb ... Unpacking sbuild-build-depends-fastml-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up groff-base (1.22.3-4) ... Setting up bsdmainutils (9.0.6ubuntu1) ... 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 libpipeline1:arm64 (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libunistring0:arm64 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:arm64 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:arm64 (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:arm64 (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:arm64 (55.1-6ubuntu1) ... Setting up libxml2:arm64 (2.9.2+zdfsg1-4ubuntu2) ... Setting up libcroco3:arm64 (0.6.10-1) ... Setting up gettext (0.19.6-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.53-1) ... Setting up libfile-stripnondeterminism-perl (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up dh-strip-nondeterminism (0.014-1) ... Setting up debhelper (9.20151126ubuntu1) ... Setting up sbuild-build-depends-fastml-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.13.0-65-generic arm64 (aarch64) Toolchain package versions: binutils_2.25.90.20151211-0ubuntu2 dpkg-dev_1.18.3ubuntu1 g++-5_5.3.1-3ubuntu3 gcc-5_5.3.1-3ubuntu3 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-3ubuntu3 libstdc++6_5.3.1-3ubuntu3 linux-libc-dev_4.3.0-5.16 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.5 apt-transport-https_1.1.5 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.90.20151211-0ubuntu2 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.3.1-3ubuntu3 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1ubuntu2 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 g++_4:5.2.1-16ubuntu2 g++-5_5.3.1-3ubuntu3 gcc_4:5.2.1-16ubuntu2 gcc-5_5.3.1-3ubuntu3 gcc-5-base_5.3.1-3ubuntu3 gettext_0.19.6-1ubuntu1 gettext-base_0.19.6-1ubuntu1 gnupg_1.4.19-6ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu9 libapt-pkg4.16_1.0.10.2ubuntu1 libapt-pkg5.0_1.1.5 libarchive-zip-perl_1.53-1 libasan2_5.3.1-3ubuntu3 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.6-1ubuntu1 libatomic1_5.3.1-3ubuntu3 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu5 libc-dev-bin_2.21-0ubuntu5 libc6_2.21-0ubuntu5 libc6-dev_2.21-0ubuntu5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-3ubuntu3 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.10-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu1 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu2 libdpkg-perl_1.18.3ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.3.1-3ubuntu3 libgcc1_1:5.3.1-3ubuntu3 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.3-3 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.3.1-3ubuntu3 libgpg-error0_1.21-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libisl15_0.15-3 libitm1_5.3.1-3ubuntu3 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu2 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4ubuntu27 libnih1_1.0.3-4ubuntu27 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libperl5.22_5.22.1-1 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libprocps4_2:3.3.10-4ubuntu1 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2e-1ubuntu1 libstdc++-5-dev_5.3.1-3ubuntu3 libstdc++6_5.3.1-3ubuntu3 libsystemd0_228-2ubuntu2 libtasn1-6_4.7-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2ubuntu1 libubsan0_5.3.1-3ubuntu3 libudev1_228-2ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4ubuntu2 linux-libc-dev_4.3.0-5.16 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu5 ncurses-base_6.0+20151024-2ubuntu1 ncurses-bin_6.0+20151024-2ubuntu1 openssl_1.0.2e-1ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.22.1-1 perl-base_5.22.1-1 perl-modules-5.22_5.22.1-1 pkg-create-dbgsym_0.70 pkgbinarymangler_125 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu1 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastml-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-2ubuntu2 systemd-sysv_228-2ubuntu2 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-2ubuntu2 util-linux_2.27.1-1ubuntu3 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Thu Dec 17 12:18:59 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./fastml_3.1-2.dsc dpkg-source: info: extracting fastml in fastml-3.1 dpkg-source: info: unpacking fastml_3.1.orig.tar.gz dpkg-source: info: unpacking fastml_3.1-2.debian.tar.xz dpkg-source: info: applying gcc_5.patch dpkg-source: info: applying fix_makefile4test.patch dpkg-source: info: applying fix_intall_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch dpkg-source: info: applying skip_failing_tests.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=8 HOME=/home/buildd LANG=C LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package fastml dpkg-buildpackage: source version 3.1-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build fastml-3.1 dpkg-buildpackage: host architecture arm64 fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_clean make -j1 clean make[2]: Entering directory '/«PKGBUILDDIR»' cd libs;make clean make[3]: Entering directory '/«PKGBUILDDIR»/libs' cd phylogeny && make clean make[4]: Entering directory '/«PKGBUILDDIR»/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/«PKGBUILDDIR»/libs/phylogeny' make[3]: Leaving directory '/«PKGBUILDDIR»/libs' cd programs;make clean make[3]: Entering directory '/«PKGBUILDDIR»/programs' cd fastml && make clean make[4]: Entering directory '/«PKGBUILDDIR»/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/«PKGBUILDDIR»/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/«PKGBUILDDIR»/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/«PKGBUILDDIR»/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/«PKGBUILDDIR»/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/«PKGBUILDDIR»/programs/indelCoder' make[3]: Leaving directory '/«PKGBUILDDIR»/programs' make[2]: Leaving directory '/«PKGBUILDDIR»' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/«PKGBUILDDIR»' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_auto_configure -a dh_auto_build -a make -j1 make[1]: Entering directory '/«PKGBUILDDIR»' cd libs;make all make[2]: Entering directory '/«PKGBUILDDIR»/libs' cd phylogeny && make all make[3]: Entering directory '/«PKGBUILDDIR»/libs/phylogeny' making depend g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o AddLog.o AddLog.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiProp.o NNiProp.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiSep.o NNiSep.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Nni.o Nni.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o aaJC.o aaJC.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTrees.o allTrees.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o alphabet.o alphabet.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o amino.o amino.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlpha.o bestAlpha.cpp bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': bestAlpha.cpp:371:10: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] MDOUBLE oldA=0; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ bestAlphaManyTrees.cpp:184:13: warning: variable 'bx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ bestAlphaManyTrees.cpp:184:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bootstrap.o bootstrap.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM.o bblEM.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o clustalFormat.o clustalFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codon.o codon.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonJC.o codonJC.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeCounts.o computeCounts.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePijComponent.o computePijComponent.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlg.o computeUpAlg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from computeSubstitutionCounts.cpp:1:0: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::__cxx11::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:12: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] ^ computeSubstitutionCounts.h:53:6: warning: 'int computeSubstitutionCounts::_simulationsIterNum' [-Wreorder] int _simulationsIterNum; ^ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): ^ In file included from computeSubstitutionCounts.cpp:1:0: computeSubstitutionCounts.h:54:10: warning: 'computeSubstitutionCounts::_probCutOffSum' will be initialized after [-Wreorder] MDOUBLE _probCutOffSum; ^ computeSubstitutionCounts.h:52:7: warning: 'bool computeSubstitutionCounts::_isSilent' [-Wreorder] bool _isSilent; ^ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distribution.o distribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o findRateOfGene.o findRateOfGene.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3:0: fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)': fromCountTableComponentToDistancePropEB.h:29:12: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] const int _nodeID; ^ fromCountTableComponentToDistancePropEB.h:28:27: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistribution.o gammaDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaUtilities.o gammaUtilities.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o goldmanYangModel.o goldmanYangModel.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): ^ goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o hky.o hky.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateWithDependence.o simulateWithDependence.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o KH_calculation.o KH_calculation.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist.o likeDist.cpp likeDist.cpp: In instantiation of 'double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]': likeDist.cpp:274:18: required from here likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] MDOUBLE oldIntervalSize = currentIntervalSize; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logFile.o logFile.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o maseFormat.o maseFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o molphyFormat.o molphyFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nexusFormat.o nexusFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nj.o nj.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o njConstrain.o njConstrain.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucJC.o nucJC.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucleotide.o nucleotide.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] //* for (i=1;isize() == 4) && (other._alphabet->size()%4 == 0)) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequenceContainer.o sequenceContainer.cpp sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^ sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositionsAllSeqs()': sequenceContainer.cpp:199:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^ sequenceContainer.cpp: In member function 'int sequenceContainer::getNumOfOccurancesPerPos(int, char)': sequenceContainer.cpp:452:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^ sequenceContainer.cpp: In member function 'std::vector > sequenceContainer::getSeqNamesThatMatchPos(int, char)': sequenceContainer.cpp:467:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateTree.o simulateTree.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o someUtil.o someUtil.cpp someUtil.cpp: In function 'void createDir(const string&, const string&)': someUtil.cpp:516:33: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(sysCall.c_str()); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o split.o split.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitMap.o splitMap.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitTreeUtil.o splitTreeUtil.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o talRandom.o talRandom.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tree.o tree.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeIt.o treeIt.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniDistribution.o uniDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniformDistribution.o uniformDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GLaguer.o GLaguer.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from distanceBasedSeqs2Tree.cpp:12:0: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logRep.o logRep.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indel.o indel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indelModel.o indelModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o matrixUtils.o matrixUtils.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaUtilities.o betaUtilities.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistribution.o betaDistribution.cpp In file included from betaDistribution.cpp:3:0: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:18: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] vector _boundary; ^ betaDistribution.h:47:10: warning: 'double betaDistribution::_alpha' [-Wreorder] MDOUBLE _alpha; ^ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] betaDistribution::betaDistribution(const betaDistribution& other) : ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o samplingSequences.o samplingSequences.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o normalDist.o normalDist.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tamura92.o tamura92.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeJumps.o computeJumps.cpp In file included from computeJumps.cpp:1:0: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:11: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] MDOUBLE _Lambda2; ^ computeJumps.h:57:11: warning: 'double computeJumps::gFunc::_r' [-Wreorder] MDOUBLE _r; ^ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqeuncesFilter.o seqeuncesFilter.cpp seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] const alphabet* pAlph = sc.getAlphabet(); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mixtureDistribution.o mixtureDistribution.cpp mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:210:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^ mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::ratesProb(int) const': mixtureDistribution.cpp:228:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:12: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] MDOUBLE Exp_Rk, Exp_LogRk, sum; ^ suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': suffStatGammaMixture.cpp:224:11: warning: unused variable 'first' [-Wunused-variable] MDOUBLE first = _MkVec[comp] * log(P_k); ^ suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable] MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); ^ suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable] MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); ^ suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable] MDOUBLE fourth = -_AkVec[comp]*beta_k; ^ suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable] MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); ^ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] MDOUBLE res2 = 0.0; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp In file included from GamMixtureOptimizer.cpp:3:0: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); ^ optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp In file included from optGammaMixtureEM.cpp:1:0: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); ^ optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gainLossAlphabet.o gainLossAlphabet.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o wYangModel.o wYangModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonUtils.o codonUtils.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gtrModel.o gtrModel.cpp In file included from gtrModel.cpp:1:0: gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': gtrModel.h:54:10: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] MDOUBLE _g2t; ^ gtrModel.h:47:10: warning: 'Vdouble gtrModel::_freq' [-Wreorder] Vdouble _freq; ^ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] gtrModel::gtrModel(const Vdouble& freq, ^ gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ gtrModel.cpp: In member function 'double gtrModel::get_a2g() const': gtrModel.cpp:153:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ gtrModel.cpp: In member function 'double gtrModel::get_a2t() const': gtrModel.cpp:167:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ gtrModel.cpp: In member function 'double gtrModel::get_c2g() const': gtrModel.cpp:181:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ gtrModel.cpp: In member function 'double gtrModel::get_c2t() const': gtrModel.cpp:195:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ gtrModel.cpp: In member function 'double gtrModel::get_g2t() const': gtrModel.cpp:209:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from bestGtrModelParams.cpp:3:0: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o integerAlphabet.o integerAlphabet.cpp ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o ar: creating libEvolTree.a a - AddLog.o a - NNiProp.o a - NNiSep.o a - Nni.o a - aaJC.o a - allTrees.o a - allTreesSeparateModel.o a - alphabet.o a - amino.o a - bestAlpha.o a - bestAlphaManyTrees.o a - bestHKYparam.o a - bootstrap.o a - bblEM.o a - bblEMfixRoot.o a - bblEMProprtional.o a - bblEMProportionalEB.o a - bblLSProportionalEB.o a - bblEMSeperate.o a - chebyshevAccelerator.o a - clustalFormat.o a - codon.o a - codonJC.o a - computeCounts.o a - computeDownAlg.o a - computeMarginalAlg.o a - computePijComponent.o a - computeUpAlg.o a - computeUpAlgFactors.o a - computeSubstitutionCounts.o a - computePosteriorExpectationOfSubstitutions.o a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o a - ConversionUtils.o a - countTableComponent.o a - datMatrixHolder.o a - distanceTable.o a - distribution.o a - errorMsg.o a - evaluateCharacterFreq.o a - fastStartTree.o a - fastaFormat.o a - findRateOfGene.o a - fromCountTableComponentToDistance.o a - fromCountTableComponentToDistancefixRoot.o a - fromCountTableComponentToDistanceProp.o a - fromCountTableComponentToDistancePropEB.o a - fromQtoPt.o a - generalGammaDistributionFixedCategories.o a - gammaDistribution.o a - gammaUtilities.o a - generalGammaDistribution.o a - getRandomWeights.o a - goldmanYangModel.o a - granthamChemicalDistances.o a - hky.o a - simulateWithDependence.o a - KH_calculation.o a - likeDist.o a - likeDistfixRoot.o a - likeDistProp.o a - likeDistPropEB.o a - likelihoodComputation.o a - likelihoodComputationFactors.o a - logFile.o a - maseFormat.o a - molphyFormat.o a - nexusFormat.o a - nj.o a - njConstrain.o a - nucJC.o a - nucleotide.o a - numRec.o a - Parameters.o a - phylipFormat.o a - pijAccelerator.o a - readDatMatrix.o a - readTree.o a - recognizeFormat.o a - replacementModel.o a - searchStatus.o a - seqContainerTreeMap.o a - sequence.o a - sequenceContainer.o a - simulateTree.o a - siteSpecificRate.o a - someUtil.o a - split.o a - splitMap.o a - splitTreeUtil.o a - stochasticProcess.o a - suffStatComponent.o a - talRandom.o a - tree.o a - treeIt.o a - treeUtil.o a - uniDistribution.o a - uniformDistribution.o a - cmdline2EvolObjs.o a - generalGammaDistributionLaguerre.o a - gammaDistributionLaguerre.o a - GLaguer.o a - givenRatesMLDistance.o a - distanceBasedSeqs2Tree.o a - posteriorDistance.o a - pairwiseGammaDistance.o a - doubleRep.o a - logRep.o a - indel.o a - indelModel.o a - mulAlphabet.o a - replacementModelSSRV.o a - stochasticProcessSSRV.o a - bestAlphaAndNu.o a - C_evalParamUSSRV.o a - matrixUtils.o a - betaOmegaDistribution.o a - betaUtilities.o a - betaDistribution.o a - geneticCodeHolder.o a - samplingSequences.o a - bblEM2USSRV.o a - bestParamUSSRV.o a - likeDist2USSRV.o a - ussrvModel.o a - likelihoodComputation2USSRV.o a - fromCountTableComponentToDistance2USSRV.o a - normalDist.o a - tamura92.o a - bestTamura92param.o a - phylipSequentialFormat.o a - simulateCodonsJumps.o a - simulateJumpsAbstract.o a - ssrvDistanceSeqs2Tree.o a - multipleStochasticProcess.o a - distributionPlusInvariant.o a - extremeValDistribution.o a - gammaDistributionFixedCategories.o a - generalGammaDistributionPlusInvariant.o a - gammaDistributionPlusInvariant.o a - distributionPlusCategory.o a - simulateJumps.o a - computeJumps.o a - seqeuncesFilter.o a - optGammaMixtureLS.o a - mixtureDistribution.o a - suffStatGammaMixture.o a - GamMixtureOptimizer.o a - optGammaMixtureEM.o a - gainLossAlphabet.o a - wYangModel.o a - codonUtils.o a - likelihoodComputation2Codon.o a - likeDist2Codon.o a - unObservableData.o a - likelihoodComputationGL.o a - threeStateModel.o a - threeStateAlphabet.o a - oneTwoMoreModel.o a - betaDistributionFixedCategories.o a - betaDistributionFixedCategoriesWithOmegaUniform.o a - bblEM2codon.o a - bestAlphaAndK.o a - fromCountTableComponentToDistance2Codon.o a - gtrModel.o a - bestGtrModelParams.o a - simulateRateShiftJumps.o a - integerAlphabet.o ranlib libEvolTree.a make[3]: Leaving directory '/«PKGBUILDDIR»/libs/phylogeny' make[2]: Leaving directory '/«PKGBUILDDIR»/libs' cd programs;make all make[2]: Entering directory '/«PKGBUILDDIR»/programs' cd fastml && make all make[3]: Entering directory '/«PKGBUILDDIR»/programs/fastml' making depend g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o fastml.o fastml.cpp In file included from bbAlg.h:8:0, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^ In file included from mainbb.h:4:0, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbAlg.o bbAlg.cpp In file included from bbAlg.h:8:0, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^ In file included from bbAlg.cpp:1:0: bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, bbAlg::boundMethod, const string&, double, const distribution*)': bbAlg.h:61:16: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbAlg.h:60:20: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^ In file included from bbAlg.cpp:1:0: bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^ bbAlg.h:29:14: warning: 'const tree& bbAlg::_et' [-Wreorder] const tree& _et; ^ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^ In file included from bbNodeOrderAlg.h:5:0, from bbAlg.h:5, from bbAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp In file included from bbEvaluateSpecificAV.cpp:1:0: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:27: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] const sequenceContainer& _sc; ^ bbEvaluateSpecificAV.h:31:23: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] const computePijGam& _bbcpij; ^ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, ^ bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] MDOUBLE rate = _sp.rates(categor); // the r. ^ In file included from bbEvaluateSpecificAV.h:4:0, from bbEvaluateSpecificAV.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp In file included from bbfindBestAVDynProg.h:5:0, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from bbNodeOrderAlg.cpp:1:0: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': bbNodeOrderAlg.h:33:27: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] const sequenceContainer& _sc; ^ bbNodeOrderAlg.h:32:23: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] const computePijGam& _cpij; ^ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, ^ In file included from bbNodeOrderAlg.h:5:0, from bbNodeOrderAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bb_options.o bb_options.cpp In file included from bb_options.cpp:2:0: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:9: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] string reportFile; ^ bb_options.h:44:9: warning: 'std::__cxx11::string bb_options::outFile_seq_joint' [-Wreorder] string outFile_seq_joint; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:45:9: warning: 'bb_options::outFile_seq_marginal' will be initialized after [-Wreorder] string outFile_seq_marginal; ^ bb_options.h:42:9: warning: 'std::__cxx11::string bb_options::outFile_prob_joint' [-Wreorder] string outFile_prob_joint; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:43:9: warning: 'bb_options::outFile_prob_marginal' will be initialized after [-Wreorder] string outFile_prob_marginal; ^ bb_options.h:24:9: warning: 'std::__cxx11::string bb_options::seqfile' [-Wreorder] string seqfile; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:30:21: warning: 'bb_options::distributionName' will be initialized after [-Wreorder] distributionsNames distributionName; ^ bb_options.h:26:16: warning: 'bb_options::SeqFileFormat bb_options::seqOutputFormat' [-Wreorder] SeqFileFormat seqOutputFormat; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:41:9: warning: 'bb_options::outTreeFileAncestor' will be initialized after [-Wreorder] string outTreeFileAncestor; ^ bb_options.h:32:15: warning: 'bb_options::boundMethods bb_options::boundMethod' [-Wreorder] boundMethods boundMethod; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:47:10: warning: 'bb_options::gammaPar' will be initialized after [-Wreorder] MDOUBLE gammaPar; ^ bb_options.h:28:7: warning: 'bool bb_options::userProvideAlpha' [-Wreorder] bool userProvideAlpha; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:48:6: warning: 'bb_options::gammaCategies' will be initialized after [-Wreorder] int gammaCategies; ^ bb_options.h:36:19: warning: 'bb_options::modelNameOptions bb_options::modelName' [-Wreorder] modelNameOptions modelName; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h:39:7: warning: 'bb_options::useChebyshev' will be initialized after [-Wreorder] bool useChebyshev; ^ bb_options.h:27:9: warning: 'std::__cxx11::string bb_options::treeOutFile' [-Wreorder] string treeOutFile; ^ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^ In file included from bb_options.cpp:2:0: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbReport.o bbReport.cpp In file included from bbReport.cpp:1:0: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^ bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbReport.h:51:12: warning: 'const int BandBReport::_position' [-Wreorder] const int _position; ^ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] MDOUBLE likelihoodOfPos = 0; ^ computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o jointNoGamma.o jointNoGamma.cpp jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^ jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': jointNoGamma.cpp:108:12: warning: unused variable 'maxL' [-Wunused-variable] MDOUBLE maxL = VERYSMALL; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o mainbb.o mainbb.cpp In file included from bbAlg.h:8:0, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^ In file included from mainbb.cpp:31:0: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^ ../../libs/phylogeny/bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^ mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); ^ In file included from mainbb.h:4:0, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o sequenceDataDiff.o sequenceDataDiff.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -L../../libs/phylogeny fastml.o libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/«PKGBUILDDIR»/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/«PKGBUILDDIR»/programs/gainLoss' making depend g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptions.o gainLossOptions.cpp gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const string&)': gainLossOptions.cpp:2064:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^ gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const string&)': gainLossOptions.cpp:2111:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^ gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const string&)': gainLossOptions.cpp:2419:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss.o gainLoss.cpp In file included from gainLoss.h:35:0, from gainLoss.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from gainLoss.cpp:41:0: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ In file included from gainLoss.cpp:20:0: gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:21: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ gainLoss.h:240:16: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] distribution* _lossDist; ^ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ In file included from gainLoss.cpp:20:0: gainLoss.h:240:16: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^ gainLoss.h:239:16: warning: 'distribution* gainLoss::_gainDist' [-Wreorder] distribution* _gainDist; ^ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ In file included from gainLoss.cpp:20:0: gainLoss.h:273:12: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder] sequence* _refSeq; // the reference sequence ^ gainLoss.h:267:11: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder] Vdouble* _weightsUniqPatterns; ^ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] char missigDataChar = -2; ^ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:57: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(sp); ^ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); ^ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^ gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': gainLoss.cpp:4283:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^ gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': gainLoss.cpp:4382:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^ gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': gainLoss.cpp:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:2035:76: warning: 'currLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ^ gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': gainLoss.cpp:3980:52: warning: 'AlphaLoss' may be used uninitialized in this function [-Wmaybe-uninitialized] gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); ^ gainLoss.cpp:3980:52: warning: 'AlphaGain' may be used uninitialized in this function [-Wmaybe-uninitialized] gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': gainLoss.cpp:869:23: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted ^ gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': gainLoss.cpp:2511:22: warning: 'countsGL' may be used uninitialized in this function [-Wmaybe-uninitialized] if(countsGL) delete countsGL; ^ gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': gainLoss.cpp:1127:25: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted ^ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1195:10: warning: 'pDm' may be used uninitialized in this function [-Wmaybe-uninitialized] delete pDm; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossUtils.o gainLossUtils.cpp In file included from gainLossUtils.cpp:19:0: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if(probs) ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if(probs) ^ gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] MDOUBLE normFactor; ^ gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] MDOUBLE scale; ^ gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from optimizeGainLossModel.h:27:0, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from optimizeGainLossModel.cpp:17:0: optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModel.h:87:11: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^ optimizeGainLossModel.h:86:20: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, ^ optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from optimizeGainLossModelVV.h:27:0, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from optimizeGainLossModelVV.cpp:17:0: optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModelVV.h:82:11: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^ optimizeGainLossModelVV.h:81:20: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, ^ optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); ^ optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossModel.o gainLossModel.cpp In file included from gainLossModel.cpp:17:0: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': gainLossModel.h:108:10: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] MDOUBLE _gain; // _Q[0][1] ^ gainLossModel.h:105:10: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] Vdouble _freq; ^ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^ In file included from gainLossModel.cpp:17:0: gainLossModel.h:112:7: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] bool _isRootFreqEQstationary; ^ gainLossModel.h:111:7: warning: 'bool gainLossModel::_isReversible' [-Wreorder] bool _isReversible; ^ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^ In file included from gainLossModel.cpp:17:0: gainLossModel.h:114:7: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] bool _isHGT_with_Q; ^ gainLossModel.h:110:8: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] q2pt *_q2pt; // dont use q2p ^ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from siteSpecificGL.cpp:24:0: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from computePosteriorExpectationOfChange.cpp:25:0: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h:35:0, from gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:35:0, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from gainLossOptimizer.cpp:20:0: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:134:7: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] tree _tr; ^ gainLossOptimizer.h:109:21: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] stochasticProcess *_sp; ^ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] sequenceContainer _sc; ^ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:139:16: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^ gainLossOptimizer.h:135:20: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] sequenceContainer _sc; ^ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] sequenceContainer _sc; ^ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^ In file included from gainLossOptimizer.cpp:17:0: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': gainLossOptimizer.cpp:498:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:487:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': gainLossOptimizer.cpp:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^ gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h:35:0, from rate4siteGL.h:24, from rate4siteGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from rate4siteGL.cpp:17:0: rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, unObservableData*)': rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] tree _tr; ^ rate4siteGL.h:58:21: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] stochasticProcess *_sp; ^ rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): ^ rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': rate4siteGL.cpp:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable] int precisionHigh = 5; ^ rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] int precisionLow = 3; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h:35:0, from computeCountsGL.h:24, from computeCountsGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from computeCountsGL.cpp:17:0: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, VVdouble&, double, bool)': computeCountsGL.h:104:7: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] tree _tr; ^ computeCountsGL.h:102:21: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] stochasticProcess *_sp; ^ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^ In file included from computeCountsGL.cpp:17:0: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] MDOUBLE _distanceFromNearestOTUForRecent; ^ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^ In file included from computeCountsGL.cpp:17:0: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::__cxx11::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:16: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^ computeCountsGL.h:105:20: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] sequenceContainer _sc; ^ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^ In file included from computeCountsGL.cpp:17:0: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] MDOUBLE _distanceFromNearestOTUForRecent; ^ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCorrelations.o computeCorrelations.cpp In file included from gainLoss.h:35:0, from computeCorrelations.h:25, from computeCorrelations.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:408:8: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] int isHigherNminReducedFreqOfHighCorr = false; ^ computeCorrelations.cpp:348:7: warning: unused variable 'typeIndex' [-Wunused-variable] int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used ^ computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': computeCorrelations.cpp:559:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^ computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^ computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': computeCorrelations.cpp:676:9: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationsInRange = 1; ^ computeCorrelations.cpp:677:9: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; ^ computeCorrelations.cpp:679:9: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin ^ computeCorrelations.cpp:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] bool isNextLowerBinAllowed = true; ^ computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': computeCorrelations.cpp:894:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(!numOfSites_A == numOfSites_B){ ^ computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::__cxx11::string*)': computeCorrelations.cpp:1009:7: warning: unused variable 'isPearson' [-Wunused-variable] bool isPearson = false; ^ computeCorrelations.cpp:1025:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^ computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': computeCorrelations.cpp:1347:112: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' inside { } is ill-formed in C++11 [-Wnarrowing] float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; ^ computeCorrelations.cpp:1300:7: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] it_B it_siteB = it_siteA->second.begin(); ^ computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:505:5: warning: 'expextedFreq' may be used uninitialized in this function [-Wmaybe-uninitialized] if(freqOfHighCorr>expextedFreq && freqOfHighCorr >, distribution*, distribution*, std::__cxx11::string&, unObservableData*, double)': gainLoss4site.h:68:7: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] tree _tr; ^ gainLoss4site.h:61:38: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] vector > _spVVec; //save stochasticProcess for each category ^ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, ^ In file included from gainLoss4site.cpp:17:0: gainLoss4site.h:79:20: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; // ^ gainLoss4site.h:78:10: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] MDOUBLE _alphaConf; ^ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from gainLoss.h:35:0, from simulateChangesAlongTree.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:35:0, from simulateOnePos.cpp:32: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^ In file included from simulateOnePos.cpp:18:0: simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::__cxx11::string, std::ostream*, std::ostream*, int, std::__cxx11::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:7: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] bool _simulateNullModel; ^ simulateOnePos.h:63:6: warning: 'int simulateOnePos::_simNum' [-Wreorder] int _simNum; ^ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^ In file included from simulateOnePos.cpp:18:0: simulateOnePos.h:65:10: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] MDOUBLE _theta; ^ simulateOnePos.h:64:10: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] MDOUBLE _sumGainLoss; ^ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^ In file included from simulateOnePos.cpp:18:0: simulateOnePos.h:75:11: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] Vdouble* _freq_cpN; ^ simulateOnePos.h:69:11: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] ostream *_simulatedEvents; ^ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^ simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::__cxx11::string)': simulateOnePos.cpp:181:9: warning: unused variable 'isRevers' [-Wunused-variable] bool isRevers = false; ^ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bblLS.o bblLS.cpp In file included from bblLS.cpp:17:0: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:36:14: warning: NULL used in arithmetic [-Wpointer-arith] if (curL == NULL) ^ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:112:14: warning: NULL used in arithmetic [-Wpointer-arith] if (curL == NULL) ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from sankoffReconstructGL.cpp:17:0: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::__cxx11::string&, double, double)': sankoffReconstructGL.h:85:9: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] string _outDir; ^ sankoffReconstructGL.h:84:10: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] MDOUBLE _costMatrixGainLossRatio; ^ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^ In file included from sankoffReconstructGL.cpp:17:0: sankoffReconstructGL.h:84:10: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] MDOUBLE _costMatrixGainLossRatio; ^ sankoffReconstructGL.h:83:10: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] MDOUBLE _distanceFromRootForRecent; ^ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^ ar rv libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o ar: creating libgainLoss.a a - gainLossOptions.o a - gainLoss.o a - gainLossUtils.o a - optimizeGainLossModel.o a - optimizeGainLossModelVV.o a - ../../libs/phylogeny/likelihoodComputationGL.o a - gainLossModel.o a - siteSpecificGL.o a - computePosteriorExpectationOfChange.o a - gainLossProject.o a - gainLossOptimizer.o a - ancestralReconstructStates.o a - rate4siteGL.o a - computeCountsGL.o a - computeCorrelations.o a - gainLoss4site.o a - simulateChangesAlongTree.o a - simulateOnePos.o a - bblLS.o a - sankoffReconstructGL.o ranlib libgainLoss.a g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -L../../libs/phylogeny gainLoss.o libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss make[3]: Leaving directory '/«PKGBUILDDIR»/programs/gainLoss' cd indelCoder && make all make[3]: Entering directory '/«PKGBUILDDIR»/programs/indelCoder' making depend g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoder.o indelCoder.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; ^ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; ^ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o character.o character.cpp character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] return longestGapStIndex; ^ g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gaps.o gaps.cpp ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o a - indelCoderUtils.o a - character.o a - gaps.o ranlib libindelCoder.a g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/«PKGBUILDDIR»/programs/indelCoder' make[2]: Leaving directory '/«PKGBUILDDIR»/programs' make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_auto_test make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_test # || true make -j1 test make[2]: Entering directory '/«PKGBUILDDIR»' cd libs;make test make[3]: Entering directory '/«PKGBUILDDIR»/libs' cd phylogeny && make test make[4]: Entering directory '/«PKGBUILDDIR»/libs/phylogeny' cd tests; make -k test make[5]: Entering directory '/«PKGBUILDDIR»/libs/phylogeny/tests' g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test ./split_test > split_test.out.tmp diff split_test.out.tmp split_test.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. splitMap_test.cpp ../libEvolTree.a -lEvolTree -o splitMap_test ./splitMap_test > splitMap_test.out.tmp diff splitMap_test.out.tmp splitMap_test.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. given2seqTheDistBetweenThem-3.cpp ../libEvolTree.a -lEvolTree -o given2seqTheDistBetweenThem-3 ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. given2seqEstimateTheDistBetweenThem.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThem ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. given2seqEstimateTheDistBetweenThemGamma.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThemGamma ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep ./doubleRep > doubleRep.out.tmp diff doubleRep.out.tmp doubleRep.out.standard g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -ftemplate-depth-25 -O0 -L.. readTreeWithComments.cpp ../libEvolTree.a -lEvolTree -o readTreeWithComments ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard make[5]: Leaving directory '/«PKGBUILDDIR»/libs/phylogeny/tests' make[4]: Leaving directory '/«PKGBUILDDIR»/libs/phylogeny' make[3]: Leaving directory '/«PKGBUILDDIR»/libs' cd programs;make test make[3]: Entering directory '/«PKGBUILDDIR»/programs' cd fastml && make test make[4]: Entering directory '/«PKGBUILDDIR»/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/«PKGBUILDDIR»/programs/fastml' cd gainLoss && make test make[4]: Entering directory '/«PKGBUILDDIR»/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/«PKGBUILDDIR»/programs/gainLoss' cd indelCoder && make test make[4]: Entering directory '/«PKGBUILDDIR»/programs/indelCoder' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/«PKGBUILDDIR»/programs/indelCoder' make[3]: Leaving directory '/«PKGBUILDDIR»/programs' echo test test make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/fastml AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/«PKGBUILDDIR»' cd libs;make all make[2]: Entering directory '/«PKGBUILDDIR»/libs' cd phylogeny && make all make[3]: Entering directory '/«PKGBUILDDIR»/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/«PKGBUILDDIR»/libs/phylogeny' make[2]: Leaving directory '/«PKGBUILDDIR»/libs' cd programs;make install make[2]: Entering directory '/«PKGBUILDDIR»/programs' cd fastml && make install make[3]: Entering directory '/«PKGBUILDDIR»/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Leaving directory '/«PKGBUILDDIR»/programs/fastml' cd gainLoss && make install make[3]: Entering directory '/«PKGBUILDDIR»/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/«PKGBUILDDIR»/programs/gainLoss' cd indelCoder && make install make[3]: Entering directory '/«PKGBUILDDIR»/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/«PKGBUILDDIR»/programs/indelCoder' make[2]: Leaving directory '/«PKGBUILDDIR»/programs' make[1]: Leaving directory '/«PKGBUILDDIR»' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform arm64: fastml dh_strip debug symbol extraction: packages to act on: fastml dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastml/usr/bin/indelCoder debian/fastml/usr/bin/fastml debian/fastml/usr/bin/gainLoss were not linked against ld-linux-aarch64.so.1 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform arm64: fastml dh_gencontrol debug symbol wrapper: packages to act on: fastml dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package fastml (pkgdir debian/fastml, ddeb package dir debian/fastml-dbgsym) dh_gencontrol debug symbol wrapper: building fastml-dbgsym_3.1-2_arm64.ddeb dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.1-2_arm64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile fastml-dbgsym_3.1-2_arm64.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 125 pkgstriptranslations: processing fastml (in debian/fastml); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/fastml/DEBIAN/control, package fastml, directory debian/fastml DEBUG: wait fastml 1:fastml DEBUG: clear fastml 1:fastml DEBUG: done fastml pkgstripfiles: Running PNG optimization (using 8 cpus) for package fastml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'fastml' in '../fastml_3.1-2_arm64.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../fastml_3.1-2_arm64.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build fastml-3.1 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151218-0230 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ fastml_3.1-2_arm64.changes: ─────────────────────────── Format: 1.8 Date: Thu, 17 Dec 2015 13:10:06 +0100 Source: fastml Binary: fastml Architecture: arm64 Version: 3.1-2 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Changes: fastml (3.1-2) unstable; urgency=medium . * Turn on testing in general but exclude failed tests Checksums-Sha1: bc65cf98d1b0fc1bf0770e4375abf193e05f6d3f 10131458 fastml-dbgsym_3.1-2_arm64.ddeb ea186df312e33ccccab96a58db9b36fe3d0a129d 830864 fastml_3.1-2_arm64.deb Checksums-Sha256: 33a3db2c435c0f07bc41b8433975c076d1de73ee6d46d42f0ff12f7368037548 10131458 fastml-dbgsym_3.1-2_arm64.ddeb 44fbf51ddc687b89f7fd84c3c27069a60b7fb75eaa8e25e9d7c03b55bf8782a1 830864 fastml_3.1-2_arm64.deb Files: e3b06f5416d7fb312461e0dee064096d 10131458 science extra fastml-dbgsym_3.1-2_arm64.ddeb 93ea47837c894219b04109d2f579d52c 830864 science optional fastml_3.1-2_arm64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ fastml_3.1-2_arm64.deb ────────────────────── new debian package, version 2.0. size 830864 bytes: control archive=1195 bytes. 1511 bytes, 27 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.1-2 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3255 Depends: libc6 (>= 2.17), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://fastml.tau.ac.il/ Description: maximum likelihood ancestral amino-acid sequence reconstruction FastML is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. FastML runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters. For character reconstruction the previously described FastML algorithms are used to efficiently infer the most likely ancestral sequences for each internal node of the tree. Both joint and the marginal reconstructions are provided. For indels reconstruction the sequences are first coded according to the indel events detected within the multiple sequence alignment (MSA) and then a state-of-the-art likelihood model is used to reconstruct ancestral indels states. The results are the most probable sequences, together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. FastML is generic and is applicable for any type of molecular sequences (nucleotide, protein, or codon sequences). drwxr-xr-x root/root 0 2015-12-18 02:29 ./ drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/ drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/bin/ -rwxr-xr-x root/root 1235960 2015-12-18 02:29 ./usr/bin/fastml -rwxr-xr-x root/root 1801288 2015-12-18 02:29 ./usr/bin/gainLoss -rwxr-xr-x root/root 277408 2015-12-18 02:29 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/share/ drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/share/doc/fastml/ -rw-r--r-- root/root 218 2015-12-17 07:11 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2936 2015-12-17 07:11 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-18 02:29 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2015-12-18 02:29 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2015-12-18 02:29 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2015-12-18 02:29 ./usr/share/man/man1/indelCoder.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: arm64 Build-Space: 505012 Build-Time: 825 Distribution: xenial-proposed Host Architecture: arm64 Install-Time: 50 Job: fastml_3.1-2.dsc Machine Architecture: arm64 Package: fastml Package-Time: 876 Source-Version: 3.1-2 Space: 505012 Status: successful Version: 3.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151218-0230 Build needed 00:14:36, 505012k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8454928'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8454928/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8454928'] Unmounting chroot for build PACKAGEBUILD-8454928... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8454928'] Removing build PACKAGEBUILD-8454928