RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-010 4.3.0-0-generic #9 SMP Tue Dec 1 18:12:15 CET 2015 s390x Buildd toolchain package versions: launchpad-buildd_136 python-lpbuildd_136 sbuild_0.66.0-5ubuntu1 dpkg-dev_1.18.3ubuntu1 python-debian_0.1.27ubuntu1. Syncing the system clock with the buildd NTP service... 17 Dec 17:07:32 ntpdate[60057]: adjust time server 10.211.37.1 offset 0.000320 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8454933', '/home/buildd/filecache-default/8808aeb45a9438550e8005f67e1dc6d720c06f47'] Unpacking chroot for build PACKAGEBUILD-8454933 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8454933'] Mounting chroot for build PACKAGEBUILD-8454933 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8454933', '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-8454933 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8454933', 's390x'] Updating debian chroot for build PACKAGEBUILD-8454933 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Ign http://archive-team.internal xenial InRelease Ign http://archive-team.internal xenial Release.gpg Get:2 http://archive-team.internal xenial Release [755 B] Ign http://archive-team.internal xenial/main s390x Packages/DiffIndex Get:3 http://archive-team.internal xenial/main Translation-en [661 kB] Get:4 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:5 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:6 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:7 http://ftpmaster.internal xenial/main s390x Packages [1377 kB] Get:8 http://archive-team.internal xenial/main s390x Packages [1613 kB] Get:9 http://ftpmaster.internal xenial/universe s390x Packages [6077 kB] Get:10 http://ftpmaster.internal xenial/main Translation-en [847 kB] Get:11 http://ftpmaster.internal xenial/universe Translation-en [4745 kB] Get:12 http://ftpmaster.internal xenial-security/main s390x Packages [28 B] Get:13 http://ftpmaster.internal xenial-security/universe s390x Packages [28 B] Get:14 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:15 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/main s390x Packages [28 B] Get:17 http://ftpmaster.internal xenial-updates/universe s390x Packages [28 B] Get:18 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:19 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:20 http://ftpmaster.internal xenial-proposed/main s390x Packages [100 kB] Get:21 http://ftpmaster.internal xenial-proposed/universe s390x Packages [530 kB] Get:22 http://ftpmaster.internal xenial-proposed/main Translation-en [53.1 kB] Get:23 http://ftpmaster.internal xenial-proposed/universe Translation-en [303 kB] Fetched 16.9 MB in 5s (2902 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: libapt-pkg5.0 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: apt apt-transport-https binutils cpp-5 dmsetup g++-5 gcc-5 gcc-5-base grep libapt-pkg4.16 libatomic1 libcc1-0 libdevmapper1.02.1 libffi6 libgcc-5-dev libgcc1 libgomp1 libgpg-error0 libkeyutils1 libmpfr4 libncurses5 libncursesw5 libseccomp2 libselinux1 libsemanage-common libsemanage1 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtinfo5 libudev1 linux-libc-dev ncurses-base ncurses-bin openssl perl perl-base pkgbinarymangler procps systemd systemd-sysv udev 43 upgraded, 4 newly installed, 1 to remove and 0 not upgraded. Need to get 98.4 MB of archives. After this operation, 30.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libapt-pkg4.16 Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep s390x 2.22-1 [145 kB] Get:2 http://archive-team.internal/bootstrap/s390x-stage2/ xenial/main libapt-pkg4.16 s390x 1.0.10.2ubuntu1 [601 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 s390x 6.0+20151024-2ubuntu1 [90.2 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 s390x 6.0+20151024-2ubuntu1 [75.4 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 s390x 6.0+20151024-2ubuntu1 [108 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin s390x 6.0+20151024-2ubuntu1 [134 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-modules-5.22 all 5.22.1-1 [2648 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libperl5.22 s390x 5.22.1-1 [3219 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl s390x 5.22.1-1 [237 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial-proposed/main perl-base s390x 5.22.1-1 [1244 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 s390x 5.3.1-3ubuntu3 [38.5 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main binutils s390x 2.25.90.20151211-0ubuntu2 [1057 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base s390x 5.3.1-3ubuntu3 [16.1 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 s390x 1:5.3.1-3ubuntu3 [24.8 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 s390x 5.3.1-3ubuntu3 [53.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 s390x 5.3.1-3ubuntu3 [7976 B] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 s390x 5.3.1-3ubuntu3 [27.2 MB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev s390x 5.3.1-3ubuntu3 [1377 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev s390x 5.3.1-3ubuntu3 [218 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 s390x 5.3.1-3ubuntu3 [25.4 MB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 s390x 5.3.1-3ubuntu3 [25.1 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 s390x 5.3.1-3ubuntu3 [398 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 s390x 3.1.3-2 [187 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 s390x 1.1.5 [637 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main apt s390x 1.1.5 [947 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main udev s390x 228-2ubuntu2 [948 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 s390x 228-2ubuntu2 [53.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 s390x 2.4-3 [53.3 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 s390x 2:3.3.10-4ubuntu1 [31.7 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main procps s390x 2:3.3.10-4ubuntu1 [221 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 s390x 228-2ubuntu2 [189 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main systemd s390x 228-2ubuntu2 [3160 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv s390x 228-2ubuntu2 [15.1 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 s390x 2:1.02.110-1ubuntu2 [133 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 s390x 1.21-1 [33.7 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:38 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 s390x 2.4-3 [74.3 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 s390x 3.2.1-4 [16.3 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 s390x 1.0.2e-1ubuntu1 [794 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup s390x 2:1.02.110-1ubuntu2 [57.5 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 s390x 2.2.3-2ubuntu3 [37.7 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https s390x 1.1.5 [24.3 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 s390x 1.5.9-8ubuntu1 [9918 B] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main openssl s390x 1.0.2e-1ubuntu1 [477 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev s390x 4.3.0-5.16 [810 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 98.4 MB in 37s (2604 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11407 files and directories currently installed.) Preparing to unpack .../archives/grep_2.22-1_s390x.deb ... Unpacking grep (2.22-1) over (2.21-2) ... Setting up grep (2.22-1) ... (Reading database ... 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Setting up libtinfo5:s390x (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 ... 11407 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.0+20151024-2ubuntu1_s390x.deb ... Unpacking libncursesw5:s390x (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncursesw5:s390x (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 ... 11407 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.0+20151024-2ubuntu1_s390x.deb ... Unpacking ncurses-bin (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-bin (6.0+20151024-2ubuntu1) ... dpkg: perl-modules: dependency problems, but removing anyway as you requested: perl depends on perl-modules (>= 5.20.2-6). 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Unpacking libperl5.22:s390x (5.22.1-1) ... Preparing to unpack .../perl-base_5.22.1-1_s390x.deb ... Unpacking perl-base (5.22.1-1) over (5.20.2-6) ... Setting up perl-base (5.22.1-1) ... (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 ... 11980 files and directories currently installed.) Preparing to unpack .../libcc1-0_5.3.1-3ubuntu3_s390x.deb ... Unpacking libcc1-0:s390x (5.3.1-3ubuntu3) over (5.2.1-27ubuntu1) ... 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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 ... 11979 files and directories currently installed.) Preparing to unpack .../archives/apt_1.1.5_s390x.deb ... Unpacking apt (1.1.5) over (1.0.10.2ubuntu1) ... Selecting previously unselected package libapt-pkg5.0:s390x. Preparing to unpack .../libapt-pkg5.0_1.1.5_s390x.deb ... Unpacking libapt-pkg5.0:s390x (1.1.5) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapt-pkg5.0:s390x (1.1.5) ... 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 ... 12007 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.0+20151024-2ubuntu1_all.deb ... Unpacking ncurses-base (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-base (6.0+20151024-2ubuntu1) ... (Reading database ... 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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 ... 12006 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_s390x.deb ... Unpacking libselinux1:s390x (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:s390x (2.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Selecting previously unselected package libprocps4:s390x. (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 ... 12006 files and directories currently installed.) Preparing to unpack .../libprocps4_2%3a3.3.10-4ubuntu1_s390x.deb ... Unpacking libprocps4:s390x (2:3.3.10-4ubuntu1) ... Preparing to unpack .../procps_2%3a3.3.10-4ubuntu1_s390x.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.10-4ubuntu1) over (1:3.3.9-1ubuntu8) ... 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Unpacking systemd (228-2ubuntu2) over (228-2ubuntu1) ... Setting up systemd (228-2ubuntu2) ... 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 ... 12017 files and directories currently installed.) Preparing to unpack .../systemd-sysv_228-2ubuntu2_s390x.deb ... Unpacking systemd-sysv (228-2ubuntu2) over (228-2ubuntu1) ... Setting up systemd-sysv (228-2ubuntu2) ... (Reading database ... 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Preparing to unpack .../libseccomp2_2.2.3-2ubuntu3_s390x.deb ... Unpacking libseccomp2:s390x (2.2.3-2ubuntu3) over (2.2.3-2ubuntu1) ... Preparing to unpack .../apt-transport-https_1.1.5_s390x.deb ... Unpacking apt-transport-https (1.1.5) over (1.0.10.2ubuntu1) ... Preparing to unpack .../libkeyutils1_1.5.9-8ubuntu1_s390x.deb ... Unpacking libkeyutils1:s390x (1.5.9-8ubuntu1) over (1.5.9-5ubuntu1) ... Preparing to unpack .../openssl_1.0.2e-1ubuntu1_s390x.deb ... Unpacking openssl (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu2) ... Preparing to unpack .../linux-libc-dev_4.3.0-5.16_s390x.deb ... Unpacking linux-libc-dev:s390x (4.3.0-5.16) over (4.3.0-1.10) ... Preparing to unpack .../pkgbinarymangler_125_all.deb ... Unpacking pkgbinarymangler (125) over (123) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:s390x (6.0+20151024-2ubuntu1) ... Setting up perl-modules-5.22 (5.22.1-1) ... Setting up libperl5.22:s390x (5.22.1-1) ... Setting up perl (5.22.1-1) ... Setting up libcc1-0:s390x (5.3.1-3ubuntu3) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgomp1:s390x (5.3.1-3ubuntu3) ... Setting up libatomic1:s390x (5.3.1-3ubuntu3) ... Setting up libmpfr4:s390x (3.1.3-2) ... Setting up cpp-5 (5.3.1-3ubuntu3) ... Setting up libgcc-5-dev:s390x (5.3.1-3ubuntu3) ... Setting up gcc-5 (5.3.1-3ubuntu3) ... Setting up libstdc++-5-dev:s390x (5.3.1-3ubuntu3) ... Setting up g++-5 (5.3.1-3ubuntu3) ... 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 libprocps4:s390x (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 libffi6:s390x (3.2.1-4) ... Setting up libssl1.0.0:s390x (1.0.2e-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu2) ... Setting up libseccomp2:s390x (2.2.3-2ubuntu3) ... Setting up apt-transport-https (1.1.5) ... Setting up libkeyutils1:s390x (1.5.9-8ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up linux-libc-dev:s390x (4.3.0-5.16) ... 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-8454933', 's390x', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=xenial-proposed', '--purge=never', '--nolog', 'fastml_3.1-2.dsc'] Initiating build PACKAGEBUILD-8454933 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.3.0-0-generic #9 SMP Tue Dec 1 18:12:15 CET 2015 s390x sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on z13-010.buildd +==============================================================================+ | fastml 3.1-2 (s390x) 17 Dec 2015 17:09 | +==============================================================================+ Package: fastml Version: 3.1-2 Source Version: 3.1-2 Distribution: xenial-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/fastml-aEamcw/fastml-3.1' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-aEamcw' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8454933/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | 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 '/<>/resolver-TkXZV8/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/<>/resolver-TkXZV8/apt_archive ./ InRelease Ign:1 file:/<>/resolver-TkXZV8/apt_archive ./ InRelease Get:2 file:/<>/resolver-TkXZV8/apt_archive ./ Release [2119 B] Get:2 file:/<>/resolver-TkXZV8/apt_archive ./ Release [2119 B] Get:3 file:/<>/resolver-TkXZV8/apt_archive ./ Release.gpg Ign:3 file:/<>/resolver-TkXZV8/apt_archive ./ Release.gpg Get:4 file:/<>/resolver-TkXZV8/apt_archive ./ Sources [214 B] Get:5 file:/<>/resolver-TkXZV8/apt_archive ./ Packages [527 B] Ign:4 file:/<>/resolver-TkXZV8/apt_archive ./ Sources Get:4 file:/<>/resolver-TkXZV8/apt_archive ./ Sources [214 B] Ign:5 file:/<>/resolver-TkXZV8/apt_archive ./ Packages Get:5 file:/<>/resolver-TkXZV8/apt_archive ./ Packages [527 B] Reading package lists... W: The repository 'file:/<>/resolver-TkXZV8/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 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/772 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:/<>/resolver-TkXZV8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Get:1 file:/<>/resolver-Qj8oXy/apt_archive ./ InRelease Ign:1 file:/<>/resolver-Qj8oXy/apt_archive ./ InRelease Get:2 file:/<>/resolver-Qj8oXy/apt_archive ./ Release [2119 B] Get:2 file:/<>/resolver-Qj8oXy/apt_archive ./ Release [2119 B] Get:3 file:/<>/resolver-Qj8oXy/apt_archive ./ Release.gpg Ign:3 file:/<>/resolver-Qj8oXy/apt_archive ./ Release.gpg Get:4 file:/<>/resolver-Qj8oXy/apt_archive ./ Sources [208 B] Get:5 file:/<>/resolver-Qj8oXy/apt_archive ./ Packages [525 B] Ign:4 file:/<>/resolver-Qj8oXy/apt_archive ./ Sources Get:4 file:/<>/resolver-Qj8oXy/apt_archive ./ Sources [208 B] Ign:5 file:/<>/resolver-Qj8oXy/apt_archive ./ Packages Get:5 file:/<>/resolver-Qj8oXy/apt_archive ./ Packages [525 B] Reading package lists... W: The repository 'file:/<>/resolver-Qj8oXy/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 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 14.2 MB/14.2 MB of archives. After this operation, 58.1 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:/<>/resolver-Qj8oXy/apt_archive ./ sbuild-build-depends-fastml-dummy 0.invalid.0 [772 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main s390x groff-base s390x 1.22.3-4 [1199 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main s390x bsdmainutils s390x 9.0.6ubuntu1 [178 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main s390x libpipeline1 s390x 1.4.1-1 [24.7 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main s390x man-db s390x 2.7.5-1 [850 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main s390x libmagic1 s390x 1:5.25-2ubuntu1 [214 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main s390x file s390x 1:5.25-2ubuntu1 [21.5 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main s390x libasprintf0v5 s390x 0.19.6-1ubuntu1 [6856 B] Get:9 http://ftpmaster.internal/ubuntu xenial/main s390x gettext-base s390x 0.19.6-1ubuntu1 [48.4 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main s390x libglib2.0-0 s390x 2.47.3-3 [1041 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main s390x libicu55 s390x 55.1-6ubuntu1 [7478 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main s390x libxml2 s390x 2.9.2+zdfsg1-4ubuntu2 [641 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main s390x libcroco3 s390x 0.6.10-1 [77.1 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main s390x libunistring0 s390x 0.9.3-5.2ubuntu1 [262 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main s390x gettext s390x 0.19.6-1ubuntu1 [1047 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main s390x intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main s390x po-debconf all 1.0.18 [234 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main s390x libarchive-zip-perl all 1.53-1 [87.0 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main s390x libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main s390x libtimedate-perl all 2.3000-2 [37.5 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main s390x dh-strip-nondeterminism all 0.014-1 [5596 B] Get:22 http://ftpmaster.internal/ubuntu xenial/main s390x debhelper all 9.20151126ubuntu1 [741 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.2 MB in 7s (1915 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 ... 12019 files and directories currently installed.) Preparing to unpack .../groff-base_1.22.3-4_s390x.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_s390x.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../libpipeline1_1.4.1-1_s390x.deb ... Unpacking libpipeline1:s390x (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_s390x.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking libmagic1:s390x (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_s390x.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package libasprintf0v5:s390x. Preparing to unpack .../libasprintf0v5_0.19.6-1ubuntu1_s390x.deb ... Unpacking libasprintf0v5:s390x (0.19.6-1ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.6-1ubuntu1_s390x.deb ... Unpacking gettext-base (0.19.6-1ubuntu1) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../libglib2.0-0_2.47.3-3_s390x.deb ... Unpacking libglib2.0-0:s390x (2.47.3-3) ... Selecting previously unselected package libicu55:s390x. Preparing to unpack .../libicu55_55.1-6ubuntu1_s390x.deb ... Unpacking libicu55:s390x (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu2_s390x.deb ... Unpacking libxml2:s390x (2.9.2+zdfsg1-4ubuntu2) ... Selecting previously unselected package libcroco3:s390x. Preparing to unpack .../libcroco3_0.6.10-1_s390x.deb ... Unpacking libcroco3:s390x (0.6.10-1) ... Selecting previously unselected package libunistring0:s390x. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_s390x.deb ... Unpacking libunistring0:s390x (0.9.3-5.2ubuntu1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.6-1ubuntu1_s390x.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:s390x (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libmagic1:s390x (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:s390x (0.19.6-1ubuntu1) ... Setting up gettext-base (0.19.6-1ubuntu1) ... Setting up libglib2.0-0:s390x (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:s390x (55.1-6ubuntu1) ... Setting up libxml2:s390x (2.9.2+zdfsg1-4ubuntu2) ... Setting up libcroco3:s390x (0.6.10-1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... 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 4.3.0-0-generic s390x (s390x) 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 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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 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 libisl15_0.15-3 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 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 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=4 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=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && '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 s390x fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' cd libs;make clean make[3]: Entering directory '/<>/libs' cd phylogeny && make clean make[4]: Entering directory '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/<>/libs/phylogeny' make[3]: Leaving directory '/<>/libs' cd programs;make clean make[3]: Entering directory '/<>/programs' cd fastml && make clean make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/<>/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/<>/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/programs/indelCoder' make[3]: Leaving directory '/<>/programs' make[2]: Leaving directory '/<>' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/<>' 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 '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/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 nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&)': nj.cpp:100:41: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeJ = currentNodes[minCol]; ^ nj.cpp:107:101: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); ^ 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(); ^ In file included from seqeuncesFilter.h:6:0, from seqeuncesFilter.cpp:1: sequenceContainer.h: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const string&, std::__cxx11::string)': sequenceContainer.h:31:81: warning: 'refID' may be used uninitialized in this function [-Wmaybe-uninitialized] const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} ^ seqeuncesFilter.cpp:165:6: note: 'refID' was declared here int refID; ^ 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; ^ In file included from mixtureDistribution.h:12:0, from mixtureDistribution.cpp:1: generalGammaDistribution.h:27:65: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] virtual const MDOUBLE rates(const int i) const {return _rates[i]*_globalRate;} ^ mixtureDistribution.cpp:210:20: note: 'categoryInComponent' was declared here 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; ^ In file included from mixtureDistribution.h:12:0, from mixtureDistribution.cpp:1: generalGammaDistribution.h:28:73: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] virtual const MDOUBLE ratesProb(const int i) const {return _ratesProb[i];} ^ mixtureDistribution.cpp:228:20: note: 'categoryInComponent' was declared here 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 '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make all make[2]: Entering directory '/<>/programs' cd fastml && make all make[3]: Entering directory '/<>/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 '/<>/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/<>/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 '/<>/programs/gainLoss' cd indelCoder && make all make[3]: Entering directory '/<>/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; ^ character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:63: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][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 '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test # || true make -j1 test make[2]: Entering directory '/<>' cd libs;make test make[3]: Entering directory '/<>/libs' cd phylogeny && make test make[4]: Entering directory '/<>/libs/phylogeny' cd tests; make -k test make[5]: Entering directory '/<>/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 '/<>/libs/phylogeny/tests' make[4]: Leaving directory '/<>/libs/phylogeny' make[3]: Leaving directory '/<>/libs' cd programs;make test make[3]: Entering directory '/<>/programs' cd fastml && make test make[4]: Entering directory '/<>/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/<>/programs/fastml' cd gainLoss && make test make[4]: Entering directory '/<>/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make test make[4]: Entering directory '/<>/programs/indelCoder' if [ -d tests ] ; then cd tests && make -k ; fi make[4]: Leaving directory '/<>/programs/indelCoder' make[3]: Leaving directory '/<>/programs' echo test test make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/debian/fastml AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make install make[2]: Entering directory '/<>/programs' cd fastml && make install make[3]: Entering directory '/<>/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make install make[3]: Entering directory '/<>/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make install make[3]: Entering directory '/<>/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' 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 s390x: 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 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 s390x: 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_s390x.ddeb dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.1-2_s390x.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile fastml-dbgsym_3.1-2_s390x.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 4 cpus) for package fastml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'fastml' in '../fastml_3.1-2_s390x.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../fastml_3.1-2_s390x.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 20151217-1713 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.1-2_s390x.changes: --------------------------- Format: 1.8 Date: Thu, 17 Dec 2015 13:10:06 +0100 Source: fastml Binary: fastml Architecture: s390x 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: fe9054bc987c75b55bbf00ad0c4eb5d3d76bbde4 9559644 fastml-dbgsym_3.1-2_s390x.ddeb d4c860d64f8ef488ca6438fff45ffcbc34738399 862432 fastml_3.1-2_s390x.deb Checksums-Sha256: 2d815b3a9078ff20dbf1867cc6e1d16346e9bb68d6364a18f561cdacafd1df7c 9559644 fastml-dbgsym_3.1-2_s390x.ddeb ae2d3fca5584a007fd36a303e032140b1343aa83a91e4cb731b578de0d012c21 862432 fastml_3.1-2_s390x.deb Files: 3b83ebfff0a41ec5c718e6b36ea0ff0c 9559644 science extra fastml-dbgsym_3.1-2_s390x.ddeb b291e59d3d77aa99eb01b50dd5a3c8b0 862432 science optional fastml_3.1-2_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml_3.1-2_s390x.deb ---------------------- new debian package, version 2.0. size 862432 bytes: control archive=1196 bytes. 1510 bytes, 27 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.1-2 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3891 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1), 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 2015-12-17 17:13 ./ drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/ drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/bin/ -rwxr-xr-x root/root 1486368 2015-12-17 17:13 ./usr/bin/fastml -rwxr-xr-x root/root 2151928 2015-12-17 17:13 ./usr/bin/gainLoss -rwxr-xr-x root/root 326824 2015-12-17 17:13 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/share/ drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/share/doc/fastml/ -rw-r--r-- root/root 218 2015-12-17 12:11 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2936 2015-12-17 12:11 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-17 17:13 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2015-12-17 17:13 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2015-12-17 17:13 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2015-12-17 17:13 ./usr/share/man/man1/indelCoder.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 515248 Build-Time: 255 Distribution: xenial-proposed Host Architecture: s390x Install-Time: 23 Job: fastml_3.1-2.dsc Machine Architecture: s390x Package: fastml Package-Time: 278 Source-Version: 3.1-2 Space: 515248 Status: successful Version: 3.1-2 -------------------------------------------------------------------------------- Finished at 20151217-1713 Build needed 00:04:38, 515248k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8454933'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8454933/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8454933'] Unmounting chroot for build PACKAGEBUILD-8454933... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8454933'] Removing build PACKAGEBUILD-8454933