RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-ppc64el-008 4.4.0-104-generic #127-Ubuntu SMP Mon Dec 11 12:16:48 UTC 2017 ppc64le Buildd toolchain package versions: launchpad-buildd_157 python-lpbuildd_157 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.3 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 24 Dec 01:08:17 ntpdate[1766]: adjust time server 10.211.37.1 offset 0.005484 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 /home/buildd/filecache-default/64ab4a3b1843816d631a3747c16f42fa2d8de59d Creating target for build PACKAGEBUILD-13900887 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 Starting target for build PACKAGEBUILD-13900887 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-13900887 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 Updating target for build PACKAGEBUILD-13900887 Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [235 kB] Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el Packages [972 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [517 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/restricted Translation-en [2788 B] Get:7 http://ftpmaster.internal/ubuntu bionic/universe ppc64el Packages [8088 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4918 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/multiverse ppc64el Packages [133 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/multiverse Translation-en [109 kB] Fetched 15.1 MB in 3s (4589 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: liblsan0 libnghttp2-14 libtsan0 The following packages will be upgraded: adduser apt apt-transport-https base-files base-passwd binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils build-essential coreutils cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++-7 gcc-7 gcc-7-base gnupg gnupg-agent gpgv libapparmor1 libapt-pkg5.0 libasan4 libasn1-8-heimdal libassuan0 libatomic1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libgpg-error0 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libidn2-0 libip4tc0 libitm1 libkeyutils1 libkrb5-26-heimdal liblockfile-bin liblockfile1 libmount1 libnettle6 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libpsl5 libroken18-heimdal libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libuuid1 libwind0-heimdal linux-libc-dev lsb-base mount multiarch-support openssl optipng perl perl-base perl-modules-5.26 pinentry-curses sensible-utils systemd systemd-sysv sysvinit-utils tzdata util-linux 105 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 59.6 MB of archives. After this operation, 9367 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-files ppc64el 10ubuntu1 [55.9 kB] Get:2 http://ftpmaster.internal/ubuntu bionic/main ppc64el bsdutils ppc64el 1:2.30.2-0.1ubuntu1 [61.8 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main ppc64el coreutils ppc64el 8.26-3ubuntu4 [1251 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el debianutils ppc64el 4.8.3 [86.0 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg ppc64el 1.19.0.4ubuntu1 [1149 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6-dev ppc64el 2.26-0ubuntu2 [2458 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-dev-bin ppc64el 2.26-0ubuntu2 [65.4 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el linux-libc-dev ppc64el 4.13.0-17.20 [955 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgomp1 ppc64el 7.2.0-18ubuntu2 [69.2 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main ppc64el libitm1 ppc64el 7.2.0-18ubuntu2 [29.7 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7-base ppc64el 7.2.0-18ubuntu2 [19.0 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc1 ppc64el 1:7.2.0-18ubuntu2 [29.8 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main ppc64el libatomic1 ppc64el 7.2.0-18ubuntu2 [8532 B] Get:14 http://ftpmaster.internal/ubuntu bionic/main ppc64el libasan4 ppc64el 7.2.0-18ubuntu2 [367 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblsan0 ppc64el 7.2.0-18ubuntu2 [134 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtsan0 ppc64el 7.2.0-18ubuntu2 [287 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main ppc64el libubsan0 ppc64el 7.2.0-18ubuntu2 [136 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main ppc64el cpp-7 ppc64el 7.2.0-18ubuntu2 [6260 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcc1-0 ppc64el 7.2.0-18ubuntu2 [39.3 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main ppc64el g++-7 ppc64el 7.2.0-18ubuntu2 [7106 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main ppc64el gcc-7 ppc64el 7.2.0-18ubuntu2 [6903 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcc-7-dev ppc64el 7.2.0-18ubuntu2 [986 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++-7-dev ppc64el 7.2.0-18ubuntu2 [1524 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main ppc64el libstdc++6 ppc64el 7.2.0-18ubuntu2 [440 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main ppc64el libbinutils ppc64el 2.29.1-12ubuntu1 [457 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils ppc64el 2.29.1-12ubuntu1 [3404 B] Get:27 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils-common ppc64el 2.29.1-12ubuntu1 [190 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.29.1-12ubuntu1 [1969 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc6 ppc64el 2.26-0ubuntu2 [2619 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main ppc64el e2fslibs ppc64el 1.43.7-1 [173 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main ppc64el e2fsprogs ppc64el 1.43.7-1 [510 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main ppc64el findutils ppc64el 4.6.0+git+20170828-2 [314 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl-modules-5.26 all 5.26.1-3 [2761 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main ppc64el libperl5.26 ppc64el 5.26.1-3 [3399 kB] Get:35 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl ppc64el 5.26.1-3 [201 kB] Get:36 http://ftpmaster.internal/ubuntu bionic/main ppc64el perl-base ppc64el 5.26.1-3 [1304 kB] Get:37 http://ftpmaster.internal/ubuntu bionic/main ppc64el libuuid1 ppc64el 2.30.2-0.1ubuntu1 [15.5 kB] Get:38 http://ftpmaster.internal/ubuntu bionic/main ppc64el libblkid1 ppc64el 2.30.2-0.1ubuntu1 [128 kB] Get:39 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsmartcols1 ppc64el 2.30.2-0.1ubuntu1 [84.7 kB] Get:40 http://ftpmaster.internal/ubuntu bionic/main ppc64el libfdisk1 ppc64el 2.30.2-0.1ubuntu1 [160 kB] Get:41 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpcre3 ppc64el 2:8.39-8 [224 kB] Get:42 http://ftpmaster.internal/ubuntu bionic/main ppc64el libselinux1 ppc64el 2.7-2 [78.6 kB] Get:43 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmount1 ppc64el 2.30.2-0.1ubuntu1 [139 kB] Get:44 http://ftpmaster.internal/ubuntu bionic/main ppc64el fdisk ppc64el 2.30.2-0.1ubuntu1 [108 kB] Get:45 http://ftpmaster.internal/ubuntu bionic/main ppc64el util-linux ppc64el 2.30.2-0.1ubuntu1 [881 kB] Get:46 http://ftpmaster.internal/ubuntu bionic/main ppc64el base-passwd ppc64el 3.5.44 [50.1 kB] Get:47 http://ftpmaster.internal/ubuntu bionic/main ppc64el libc-bin ppc64el 2.26-0ubuntu2 [573 kB] Get:48 http://ftpmaster.internal/ubuntu bionic/main ppc64el sysvinit-utils ppc64el 2.88dsf-59.10ubuntu1 [20.6 kB] Get:49 http://ftpmaster.internal/ubuntu bionic/main ppc64el libudev1 ppc64el 235-3ubuntu2 [60.8 kB] Get:50 http://ftpmaster.internal/ubuntu bionic/main ppc64el libapt-pkg5.0 ppc64el 1.6~alpha5 [878 kB] Get:51 http://ftpmaster.internal/ubuntu bionic/main ppc64el debconf all 1.5.65 [124 kB] Get:52 http://ftpmaster.internal/ubuntu bionic/main ppc64el adduser all 3.116ubuntu1 [163 kB] Get:53 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgpg-error0 ppc64el 1.27-5 [42.1 kB] Get:54 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgcrypt20 ppc64el 1.8.1-4 [448 kB] Get:55 http://ftpmaster.internal/ubuntu bionic/main ppc64el gpgv ppc64el 2.1.15-1ubuntu8 [218 kB] Get:56 http://ftpmaster.internal/ubuntu bionic/main ppc64el libseccomp2 ppc64el 2.3.1-2.1ubuntu3 [47.2 kB] Get:57 http://ftpmaster.internal/ubuntu bionic/main ppc64el apt ppc64el 1.6~alpha5 [1191 kB] Get:58 http://ftpmaster.internal/ubuntu bionic/main ppc64el libapparmor1 ppc64el 2.11.0-2ubuntu18 [29.9 kB] Get:59 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap2 ppc64el 1:2.25-1.2 [13.5 kB] Get:60 http://ftpmaster.internal/ubuntu bionic/main ppc64el libidn11 ppc64el 1.33-2.1 [46.4 kB] Get:61 http://ftpmaster.internal/ubuntu bionic/main ppc64el libip4tc0 ppc64el 1.6.1-2ubuntu2 [23.6 kB] Get:62 http://ftpmaster.internal/ubuntu bionic/main ppc64el mount ppc64el 2.30.2-0.1ubuntu1 [111 kB] Get:63 http://ftpmaster.internal/ubuntu bionic/main ppc64el systemd ppc64el 235-3ubuntu2 [2962 kB] Get:64 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsystemd0 ppc64el 235-3ubuntu2 [213 kB] Get:65 http://ftpmaster.internal/ubuntu bionic/main ppc64el systemd-sysv ppc64el 235-3ubuntu2 [13.1 kB] Get:66 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcap-ng0 ppc64el 0.7.7-3.1 [11.6 kB] Get:67 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcomerr2 ppc64el 1.43.7-1 [11.6 kB] Get:68 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage-common all 2.7-2 [6916 B] Get:69 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsemanage1 ppc64el 2.7-2 [85.4 kB] Get:70 http://ftpmaster.internal/ubuntu bionic/main ppc64el libss2 ppc64el 1.43.7-1 [11.4 kB] Get:71 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnettle6 ppc64el 3.3-2 [120 kB] Get:72 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhogweed4 ppc64el 3.3-2 [134 kB] Get:73 http://ftpmaster.internal/ubuntu bionic/main ppc64el libp11-kit0 ppc64el 0.23.9-2 [167 kB] Get:74 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtasn1-6 ppc64el 4.12-3 [39.8 kB] Get:75 http://ftpmaster.internal/ubuntu bionic/main ppc64el lsb-base all 9.20170808ubuntu1 [12.5 kB] Get:76 http://ftpmaster.internal/ubuntu bionic/main ppc64el sensible-utils all 0.0.11 [14.8 kB] Get:77 http://ftpmaster.internal/ubuntu bionic/main ppc64el libassuan0 ppc64el 2.5.1-1 [33.9 kB] Get:78 http://ftpmaster.internal/ubuntu bionic/main ppc64el pinentry-curses ppc64el 1.0.0-3 [37.5 kB] Get:79 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnpth0 ppc64el 1.5-3 [7780 B] Get:80 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg ppc64el 2.1.15-1ubuntu8 [847 kB] Get:81 http://ftpmaster.internal/ubuntu bionic/main ppc64el gnupg-agent ppc64el 2.1.15-1ubuntu8 [291 kB] Get:82 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsqlite3-0 ppc64el 3.21.0-1 [464 kB] Get:83 http://ftpmaster.internal/ubuntu bionic/main ppc64el libroken18-heimdal ppc64el 7.5.0+dfsg-1 [42.2 kB] Get:84 http://ftpmaster.internal/ubuntu bionic/main ppc64el libasn1-8-heimdal ppc64el 7.5.0+dfsg-1 [140 kB] Get:85 http://ftpmaster.internal/ubuntu bionic/main ppc64el libheimbase1-heimdal ppc64el 7.5.0+dfsg-1 [30.5 kB] Get:86 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhcrypto4-heimdal ppc64el 7.5.0+dfsg-1 [100 kB] Get:87 http://ftpmaster.internal/ubuntu bionic/main ppc64el libwind0-heimdal ppc64el 7.5.0+dfsg-1 [48.0 kB] Get:88 http://ftpmaster.internal/ubuntu bionic/main ppc64el libhx509-5-heimdal ppc64el 7.5.0+dfsg-1 [108 kB] Get:89 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkrb5-26-heimdal ppc64el 7.5.0+dfsg-1 [216 kB] Get:90 http://ftpmaster.internal/ubuntu bionic/main ppc64el libheimntlm0-heimdal ppc64el 7.5.0+dfsg-1 [16.4 kB] Get:91 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgssapi3-heimdal ppc64el 7.5.0+dfsg-1 [92.6 kB] Get:92 http://ftpmaster.internal/ubuntu bionic/main ppc64el libssl1.0.0 ppc64el 1.0.2g-1ubuntu14 [880 kB] Get:93 http://ftpmaster.internal/ubuntu bionic/main ppc64el multiarch-support ppc64el 2.26-0ubuntu2 [6832 B] Get:94 http://ftpmaster.internal/ubuntu bionic/main ppc64el openssl ppc64el 1.0.2g-1ubuntu14 [520 kB] Get:95 http://ftpmaster.internal/ubuntu bionic/main ppc64el tzdata all 2017c-1 [188 kB] Get:96 http://ftpmaster.internal/ubuntu bionic/main ppc64el libidn2-0 ppc64el 2.0.4-1 [95.7 kB] Get:97 http://ftpmaster.internal/ubuntu bionic/main ppc64el libkeyutils1 ppc64el 1.5.9-9.2ubuntu1 [9736 B] Get:98 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpng16-16 ppc64el 1.6.34-1 [200 kB] Get:99 http://ftpmaster.internal/ubuntu bionic/universe ppc64el apt-transport-https all 1.6~alpha5 [1692 B] Get:100 http://ftpmaster.internal/ubuntu bionic/main ppc64el dpkg-dev all 1.19.0.4ubuntu1 [607 kB] Get:101 http://ftpmaster.internal/ubuntu bionic/main ppc64el libdpkg-perl all 1.19.0.4ubuntu1 [211 kB] Get:102 http://ftpmaster.internal/ubuntu bionic/main ppc64el build-essential ppc64el 12.4ubuntu1 [4754 B] Get:103 http://ftpmaster.internal/ubuntu bionic/main ppc64el libnghttp2-14 ppc64el 1.28.0-1 [84.7 kB] Get:104 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpsl5 ppc64el 0.19.1-4 [43.0 kB] Get:105 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcurl3-gnutls ppc64el 7.57.0-1ubuntu1 [215 kB] Get:106 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblockfile-bin ppc64el 1.14-1.1 [12.0 kB] Get:107 http://ftpmaster.internal/ubuntu bionic/main ppc64el liblockfile1 ppc64el 1.14-1.1 [6988 B] Get:108 http://ftpmaster.internal/ubuntu bionic/main ppc64el optipng ppc64el 0.7.6-1.1 [86.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.6 MB in 1s (31.5 MB/s) (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../base-files_10ubuntu1_ppc64el.deb ... Unpacking base-files (10ubuntu1) over (9.6ubuntu101) ... Setting up base-files (10ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.30.2-0.1ubuntu1_ppc64el.deb ... Unpacking bsdutils (1:2.30.2-0.1ubuntu1) over (1:2.30.1-0ubuntu4) ... Setting up bsdutils (1:2.30.2-0.1ubuntu1) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../coreutils_8.26-3ubuntu4_ppc64el.deb ... Unpacking coreutils (8.26-3ubuntu4) over (8.26-3ubuntu3) ... Setting up coreutils (8.26-3ubuntu4) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.3_ppc64el.deb ... Unpacking debianutils (4.8.3) over (4.8.2) ... Setting up debianutils (4.8.3) ... (Reading database ... 12537 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.4ubuntu1_ppc64el.deb ... Unpacking dpkg (1.19.0.4ubuntu1) over (1.18.24ubuntu1) ... Setting up dpkg (1.19.0.4ubuntu1) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (Reading database ... 12539 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.26-0ubuntu2_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../1-libc-dev-bin_2.26-0ubuntu2_ppc64el.deb ... Unpacking libc-dev-bin (2.26-0ubuntu2) over (2.26-0ubuntu1) ... Preparing to unpack .../2-linux-libc-dev_4.13.0-17.20_ppc64el.deb ... 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Universal Time is now: Sun Dec 24 01:08:43 UTC 2017. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (235-3ubuntu2) ... Setting up libubsan0:ppc64el (7.2.0-18ubuntu2) ... Setting up libtsan0:ppc64el (7.2.0-18ubuntu2) ... Setting up liblockfile1:ppc64el (1.14-1.1) ... Setting up linux-libc-dev:ppc64el (4.13.0-17.20) ... Setting up libroken18-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up perl-modules-5.26 (5.26.1-3) ... Setting up optipng (0.7.6-1.1) ... Setting up cpp-7 (7.2.0-18ubuntu2) ... Setting up lsb-base (9.20170808ubuntu1) ... Setting up liblsan0:ppc64el (7.2.0-18ubuntu2) ... Setting up binutils-common:ppc64el (2.29.1-12ubuntu1) ... Setting up sensible-utils (0.0.11) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up libperl5.26:ppc64el (5.26.1-3) ... Setting up libheimbase1-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up openssl (1.0.2g-1ubuntu14) ... Setting up libsqlite3-0:ppc64el (3.21.0-1) ... Setting up libc-dev-bin (2.26-0ubuntu2) ... Setting up libkeyutils1:ppc64el (1.5.9-9.2ubuntu1) ... Setting up libc6-dev:ppc64el (2.26-0ubuntu2) ... Setting up libassuan0:ppc64el (2.5.1-1) ... Setting up libitm1:ppc64el (7.2.0-18ubuntu2) ... Setting up libwind0-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libbinutils:ppc64el (2.29.1-12ubuntu1) ... Setting up libcurl3-gnutls:ppc64el (7.57.0-1ubuntu1) ... Setting up libasn1-8-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up binutils-powerpc64le-linux-gnu (2.29.1-12ubuntu1) ... Setting up libhcrypto4-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libhx509-5-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up libgcc-7-dev:ppc64el (7.2.0-18ubuntu2) ... Setting up libstdc++-7-dev:ppc64el (7.2.0-18ubuntu2) ... Setting up perl (5.26.1-3) ... Setting up pinentry-curses (1.0.0-3) ... Setting up binutils (2.29.1-12ubuntu1) ... Setting up libkrb5-26-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up gnupg-agent (2.1.15-1ubuntu8) ... Setting up libheimntlm0-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up gcc-7 (7.2.0-18ubuntu2) ... Setting up g++-7 (7.2.0-18ubuntu2) ... Setting up gnupg (2.1.15-1ubuntu8) ... Setting up libdpkg-perl (1.19.0.4ubuntu1) ... Setting up dpkg-dev (1.19.0.4ubuntu1) ... Setting up libgssapi3-heimdal:ppc64el (7.5.0+dfsg-1) ... Setting up build-essential (12.4ubuntu1) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-13900887 ppc64el bionic -c chroot:build-PACKAGEBUILD-13900887 --arch=ppc64el --dist=bionic --nolog fastml_3.1-3.dsc Initiating build PACKAGEBUILD-13900887 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-104-generic #127-Ubuntu SMP Mon Dec 11 12:16:48 UTC 2017 ppc64le sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-ppc64el-008.buildd +==============================================================================+ | fastml 3.1-3 (ppc64el) 24 Dec 2017 01:08 | +==============================================================================+ Package: fastml Version: 3.1-3 Source Version: 3.1-3 Distribution: bionic Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el I: NOTICE: Log filtering will replace 'build/fastml-4ZI98G/fastml-3.1' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-4ZI98G' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-13900887/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- fastml_3.1-3.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-HcxhMU/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-HcxhMU/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HcxhMU/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-HcxhMU/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HcxhMU/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-HcxhMU/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (140 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libunistring0 libwind0-heimdal Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-HcxhMU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12553 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9) Filtered Build-Depends: debhelper (>= 9) dpkg-deb: building package 'sbuild-build-depends-fastml-dummy' in '/<>/resolver-Nbaj1m/apt_archive/sbuild-build-depends-fastml-dummy.deb'. Ign:1 copy:/<>/resolver-Nbaj1m/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Nbaj1m/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Nbaj1m/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Nbaj1m/apt_archive ./ Sources [207 B] Get:5 copy:/<>/resolver-Nbaj1m/apt_archive ./ Packages [527 B] Fetched 2853 B in 0s (141 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install fastml build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libasn1-8-heimdal libcurl3-gnutls libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn2-0 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnghttp2-14 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libwind0-heimdal Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser apparmor libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-fastml-dummy 0 upgraded, 34 newly installed, 1 to remove and 0 not upgraded. Need to get 17.9 MB of archives. After this operation, 72.0 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Nbaj1m/apt_archive ./ sbuild-build-depends-fastml-dummy 0.invalid.0 [852 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main ppc64el groff-base ppc64el 1.22.3-9 [1361 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main ppc64el libbsd0 ppc64el 0.8.6-3 [50.0 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main ppc64el bsdmainutils ppc64el 9.0.14ubuntu1 [183 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main ppc64el libpipeline1 ppc64el 1.5.0-1 [24.7 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main ppc64el man-db ppc64el 2.7.6.1-4 [913 kB] Get:7 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmagic-mgc ppc64el 1:5.32-1 [184 kB] Get:8 http://ftpmaster.internal/ubuntu bionic/main ppc64el libmagic1 ppc64el 1:5.32-1 [76.6 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main ppc64el file ppc64el 1:5.32-1 [22.7 kB] Get:10 http://ftpmaster.internal/ubuntu bionic/main ppc64el libglib2.0-0 ppc64el 2.54.1-1ubuntu1 [1160 kB] Get:11 http://ftpmaster.internal/ubuntu bionic/main ppc64el libfreetype6 ppc64el 2.8-0.2ubuntu2 [385 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main ppc64el libgraphite2-3 ppc64el 1.3.10-8 [67.0 kB] Get:13 http://ftpmaster.internal/ubuntu bionic/main ppc64el libharfbuzz0b ppc64el 1.7.2-1 [237 kB] Get:14 http://ftpmaster.internal/ubuntu bionic/main ppc64el libicu-le-hb0 ppc64el 1.0.3+git161113-4 [17.7 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main ppc64el libicu60 ppc64el 60.2-1ubuntu1 [8363 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main ppc64el libxml2 ppc64el 2.9.4+dfsg1-5.2ubuntu1 [621 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main ppc64el gettext-base ppc64el 0.19.8.1-4ubuntu2 [49.7 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main ppc64el libsigsegv2 ppc64el 2.11-1 [13.3 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main ppc64el m4 ppc64el 1.4.18-1 [202 kB] Get:20 http://ftpmaster.internal/ubuntu bionic/main ppc64el autoconf all 2.69-11 [322 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main ppc64el autotools-dev all 20171216.1 [39.7 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main ppc64el automake all 1:1.15.1-3ubuntu1 [509 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main ppc64el autopoint all 0.19.8.1-4ubuntu2 [412 kB] Get:24 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtool all 2.4.6-2 [194 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-autoreconf all 15 [15.8 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main ppc64el libarchive-zip-perl all 1.60-1 [83.9 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main ppc64el libfile-stripnondeterminism-perl all 0.040-1 [13.9 kB] Get:28 http://ftpmaster.internal/ubuntu bionic/main ppc64el libtimedate-perl all 2.3000-2 [37.5 kB] Get:29 http://ftpmaster.internal/ubuntu bionic/main ppc64el dh-strip-nondeterminism all 0.040-1 [5196 B] Get:30 http://ftpmaster.internal/ubuntu bionic/main ppc64el libcroco3 ppc64el 0.6.12-2 [82.5 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main ppc64el gettext ppc64el 0.19.8.1-4ubuntu2 [1147 kB] Get:32 http://ftpmaster.internal/ubuntu bionic/main ppc64el intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/main ppc64el po-debconf all 1.0.20 [232 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main ppc64el debhelper all 11ubuntu1 [887 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.9 MB in 0s (67.3 MB/s) (Reading database ... 12553 files and directories currently installed.) Removing pkg-create-dbgsym (0.73) ... Selecting previously unselected package groff-base. (Reading database ... 12544 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_ppc64el.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package libbsd0:ppc64el. Preparing to unpack .../01-libbsd0_0.8.6-3_ppc64el.deb ... Unpacking libbsd0:ppc64el (0.8.6-3) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_9.0.14ubuntu1_ppc64el.deb ... Unpacking bsdmainutils (9.0.14ubuntu1) ... Selecting previously unselected package libpipeline1:ppc64el. Preparing to unpack .../03-libpipeline1_1.5.0-1_ppc64el.deb ... Unpacking libpipeline1:ppc64el (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.7.6.1-4_ppc64el.deb ... Unpacking man-db (2.7.6.1-4) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.32-1_ppc64el.deb ... Unpacking libmagic-mgc (1:5.32-1) ... Selecting previously unselected package libmagic1:ppc64el. Preparing to unpack .../06-libmagic1_1%3a5.32-1_ppc64el.deb ... Unpacking libmagic1:ppc64el (1:5.32-1) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.32-1_ppc64el.deb ... Unpacking file (1:5.32-1) ... Selecting previously unselected package libglib2.0-0:ppc64el. Preparing to unpack .../08-libglib2.0-0_2.54.1-1ubuntu1_ppc64el.deb ... Unpacking libglib2.0-0:ppc64el (2.54.1-1ubuntu1) ... Selecting previously unselected package libfreetype6:ppc64el. Preparing to unpack .../09-libfreetype6_2.8-0.2ubuntu2_ppc64el.deb ... Unpacking libfreetype6:ppc64el (2.8-0.2ubuntu2) ... Selecting previously unselected package libgraphite2-3:ppc64el. Preparing to unpack .../10-libgraphite2-3_1.3.10-8_ppc64el.deb ... Unpacking libgraphite2-3:ppc64el (1.3.10-8) ... Selecting previously unselected package libharfbuzz0b:ppc64el. Preparing to unpack .../11-libharfbuzz0b_1.7.2-1_ppc64el.deb ... Unpacking libharfbuzz0b:ppc64el (1.7.2-1) ... Selecting previously unselected package libicu-le-hb0:ppc64el. Preparing to unpack .../12-libicu-le-hb0_1.0.3+git161113-4_ppc64el.deb ... Unpacking libicu-le-hb0:ppc64el (1.0.3+git161113-4) ... Selecting previously unselected package libicu60:ppc64el. Preparing to unpack .../13-libicu60_60.2-1ubuntu1_ppc64el.deb ... Unpacking libicu60:ppc64el (60.2-1ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../14-libxml2_2.9.4+dfsg1-5.2ubuntu1_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.4+dfsg1-5.2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../15-gettext-base_0.19.8.1-4ubuntu2_ppc64el.deb ... Unpacking gettext-base (0.19.8.1-4ubuntu2) ... Selecting previously unselected package libsigsegv2:ppc64el. 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Unpacking libcroco3:ppc64el (0.6.12-2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-4ubuntu2_ppc64el.deb ... Unpacking gettext (0.19.8.1-4ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-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 .../31-po-debconf_1.0.20_all.deb ... Unpacking po-debconf (1.0.20) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_11ubuntu1_all.deb ... Unpacking debhelper (11ubuntu1) ... Selecting previously unselected package sbuild-build-depends-fastml-dummy. Preparing to unpack .../33-sbuild-build-depends-fastml-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-fastml-dummy (0.invalid.0) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:ppc64el (2.11-1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:ppc64el (2.54.1-1ubuntu1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-4ubuntu2) ... Setting up libpipeline1:ppc64el (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:ppc64el (0.8.6-3) ... Setting up libfreetype6:ppc64el (2.8-0.2ubuntu2) ... Setting up libmagic-mgc (1:5.32-1) ... Setting up libmagic1:ppc64el (1:5.32-1) ... Setting up libgraphite2-3:ppc64el (1.3.10-8) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... Setting up autotools-dev (20171216.1) ... Setting up bsdmainutils (9.0.14ubuntu1) ... 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 autopoint (0.19.8.1-4ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1) ... Setting up libharfbuzz0b:ppc64el (1.7.2-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-1) ... Setting up automake (1:1.15.1-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-4) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libicu-le-hb0:ppc64el (1.0.3+git161113-4) ... Setting up dh-strip-nondeterminism (0.040-1) ... Setting up libicu60:ppc64el (60.2-1ubuntu1) ... Setting up libxml2:ppc64el (2.9.4+dfsg1-5.2ubuntu1) ... Setting up libcroco3:ppc64el (0.6.12-2) ... Setting up gettext (0.19.8.1-4ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.20) ... Setting up debhelper (11ubuntu1) ... Setting up dh-autoreconf (15) ... Setting up sbuild-build-depends-fastml-dummy (0.invalid.0) ... (Reading database ... 14393 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.26-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-104-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.29.1-12ubuntu1 dpkg-dev_1.19.0.4ubuntu1 g++-7_7.2.0-18ubuntu2 gcc-7_7.2.0-18ubuntu2 libc6-dev_2.26-0ubuntu2 libstdc++-7-dev_7.2.0-18ubuntu2 libstdc++6_7.2.0-18ubuntu2 linux-libc-dev_4.13.0-17.20 Package versions: adduser_3.116ubuntu1 advancecomp_2.0-1 apt_1.6~alpha5 apt-transport-https_1.6~alpha5 autoconf_2.69-11 automake_1:1.15.1-3ubuntu1 autopoint_0.19.8.1-4ubuntu2 autotools-dev_20171216.1 base-files_10ubuntu1 base-passwd_3.5.44 bash_4.4-5ubuntu1 binutils_2.29.1-12ubuntu1 binutils-common_2.29.1-12ubuntu1 binutils-powerpc64le-linux-gnu_2.29.1-12ubuntu1 bsdmainutils_9.0.14ubuntu1 bsdutils_1:2.30.2-0.1ubuntu1 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 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libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-8 libperl5.26_5.26.1-3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.19.1-4 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu1 libseccomp2_2.3.1-2.1ubuntu3 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.30.2-0.1ubuntu1 libsqlite3-0_3.21.0-1 libss2_1.43.7-1 libssl1.0.0_1.0.2g-1ubuntu14 libstdc++-7-dev_7.2.0-18ubuntu2 libstdc++6_7.2.0-18ubuntu2 libsystemd0_235-3ubuntu2 libtasn1-6_4.12-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.2.0-18ubuntu2 libubsan0_7.2.0-18ubuntu2 libudev1_235-3ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-5.2ubuntu1 linux-libc-dev_4.13.0-17.20 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu4 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-4 mawk_1.3.3-17ubuntu2 mount_2.30.2-0.1ubuntu1 multiarch-support_2.26-0ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu14 optipng_0.7.6-1.1 passwd_1:4.2-3.2ubuntu4 patch_2.7.5-1build1 perl_5.26.1-3 perl-base_5.26.1-3 perl-modules-5.26_5.26.1-3 pinentry-curses_1.0.0-3 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastml-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.11 systemd_235-3ubuntu2 systemd-sysv_235-3ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2017c-1 ubuntu-keyring_2016.10.27 util-linux_2.30.2-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue May 10 10:12:32 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fastml_3.1-3.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_3.1-3.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 dpkg-source: info: applying remove-template-depth.patch dpkg-source: info: applying g++-6.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-13900887 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-13900887 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-13900887 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.1-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build fastml-3.1 dpkg-buildpackage: info: host architecture ppc64el fakeroot debian/rules clean dh clean 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_update_autotools_config -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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:107:36: warning: ‘minRaw’ may be used uninitialized in this function [-Wmaybe-uninitialized] UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] //* for (i=1;i>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp sequence.cpp: In constructor ‘sequence::sequence(const sequence&, const alphabet*)’: sequence.cpp:76:28: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp someUtil.cpp: In function ‘void createDir(const string&, const string&)’: someUtil.cpp:516:16: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(sysCall.c_str()); ~~~~~~^~~~~~~~~~~~~~~~~ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp tree.cpp: In constructor ‘tree::tree(const string&)’: tree.cpp:180:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (in.is_open()) ^~ tree.cpp:182:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ create_names_to_internal_nodes(); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp treeUtil.cpp: In function ‘std::vector getNexusTreesFromFile(const string&)’: treeUtil.cpp:371:25: warning: variable ‘itStrStart’ set but not used [-Wunused-but-set-variable] string::const_iterator itStrStart = it->begin(); ^~~~~~~~~~ treeUtil.cpp:372:25: warning: variable ‘itStrEnd’ set but not used [-Wunused-but-set-variable] string::const_iterator itStrEnd = it->end(); ^~~~~~~~ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::rates(int) const’: mixtureDistribution.cpp:210:6: warning: ‘componentNum’ may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~ mixtureDistribution.cpp:221:41: warning: ‘categoryInComponent’ may be used uninitialized in this function [-Wmaybe-uninitialized] return _components[componentNum]->rates(categoryInComponent) * _globalRate; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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, ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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() { ^~~~~~~~~~~~~~~~~~~ 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); ^ g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -Wl,-z,now -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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:1245:38: note: add parentheses around left hand side expression to silence this warning 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:4382:7: note: add parentheses around left hand side expression to silence this warning 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; ^~~~~~ In file included from gainLoss.h:35:0, from gainLoss.cpp:20: gainLossModel.h: In member function ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’: gainLossModel.h:173:14: warning: ‘currM2’ may be used uninitialized in this function [-Wmaybe-uninitialized] _Q[1][1] = -_loss; ^~~~~~ gainLoss.cpp:1842:10: note: ‘currM2’ was declared here MDOUBLE currM2; ^~~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:2035:44: warning: ‘bestLossProbInvariant’ 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::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::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::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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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’ [-Wdangling-else] if(probs) ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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:894:5: note: add parentheses around left hand side expression to silence this warning 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 { } [-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>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:35:0, from gainLoss4site.h:24, from gainLoss4site.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 gainLoss4site.cpp:17:0: gainLoss4site.h: In constructor ‘gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, 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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -Wl,-z,now -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -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 -Wl,-z,now -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -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 -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThem.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThem ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThemGamma.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThemGamma ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep ./doubleRep > doubleRep.out.tmp diff doubleRep.out.tmp doubleRep.out.standard g++ -g -O3 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -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_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 131 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 pkgstripfiles: Running PNG optimization (using 4 cpus) for package fastml ... pkgstripfiles: No PNG files. dpkg-deb: building package 'fastml' in '../fastml_3.1-3_ppc64el.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../fastml_3.1-3_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build fastml-3.1 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20171224-0114 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.1-3_ppc64el.changes: ----------------------------- Format: 1.8 Date: Tue, 10 May 2016 09:46:15 +0000 Source: fastml Binary: fastml Architecture: ppc64el Version: 3.1-3 Distribution: bionic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gert Wollny Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Closes: 811944 Changes: fastml (3.1-3) unstable; urgency=medium . * Team upload . [ Gert Wollny ] * d/p/remove-template-depth.patch add patch to not restrict template depth. (Default with g++-6 is 900) * d/p/g++-6.patch: fix compilation with g++-6, Closes: #811944 * d/control: Update standards version to 3.9.8 . [ Andreas Tille ] * cme fix dpkg-control * Better hardening Checksums-Sha1: 37937030d75b253134609c9d2ca15f82bd910aad 4752 fastml_3.1-3_ppc64el.buildinfo 69e01f811a7ee32c391b7ecc550065c1f46aeada 931276 fastml_3.1-3_ppc64el.deb Checksums-Sha256: eb84be3f8e112ef6fcf2b76defb334135be8876cae841fc94accbaabf8b19559 4752 fastml_3.1-3_ppc64el.buildinfo 1b848418e5dfc9ef82c9693a0d2ebe2c5842719499a09b5929ca21603e6e4ea6 931276 fastml_3.1-3_ppc64el.deb Files: b73a2bacb4f722595d0dbfdd99d84c9f 4752 science optional fastml_3.1-3_ppc64el.buildinfo 3e033dfb37a2a5677e9e0b39f9f1a372 931276 science optional fastml_3.1-3_ppc64el.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml_3.1-3_ppc64el.deb ------------------------ new debian package, version 2.0. size 931276 bytes: control archive=1276 bytes. 1515 bytes, 27 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.1-3 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4250 Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.4.4), 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 2016-05-10 09:46 ./ drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/ drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/bin/ -rwxr-xr-x root/root 1575112 2016-05-10 09:46 ./usr/bin/fastml -rwxr-xr-x root/root 2361544 2016-05-10 09:46 ./usr/bin/gainLoss -rwxr-xr-x root/root 395464 2016-05-10 09:46 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/share/ drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/share/doc/fastml/ -rw-r--r-- root/root 438 2016-05-10 09:46 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2936 2016-05-10 09:46 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/share/man/ drwxr-xr-x root/root 0 2016-05-10 09:46 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2016-05-10 09:46 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2016-05-10 09:46 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2016-05-10 09:46 ./usr/share/man/man1/indelCoder.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build-Space: 480100 Build-Time: 362 Distribution: bionic Host Architecture: ppc64el Install-Time: 7 Job: fastml_3.1-3.dsc Machine Architecture: ppc64el Package: fastml Package-Time: 371 Source-Version: 3.1-3 Space: 480100 Status: successful Version: 3.1-3 -------------------------------------------------------------------------------- Finished at 20171224-0114 Build needed 00:06:11, 480100k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 Scanning for processes to kill in build PACKAGEBUILD-13900887 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 Stopping target for build PACKAGEBUILD-13900887 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=ppc64el PACKAGEBUILD-13900887 Removing build PACKAGEBUILD-13900887