DC-Build-Header: fastml 3.11-2 / 2020-05-03 04:32:13 +0000 DC-Task: type:rebuild-binarch-only source:fastml version:3.11-2 chroot:unstable esttime:230 logfile:/tmp/fastml_3.11-2_unstable_clang10.log modes:clang10:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 fastml_3.11-2' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-5-247.eu-central-1.compute.internal +==============================================================================+ | fastml 3.11-2 (amd64) Sun, 03 May 2020 04:32:13 +0000 | +==============================================================================+ Package: fastml Version: 3.11-2 Source Version: 3.11-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-95aab226-569e-4972-8338-f8174e2e0750' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang10 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=10 + echo 'Install of clang-10' Install of clang-10 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6185 kB] Fetched 6480 kB in 2s (3928 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: gcc-10-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libatomic1 libbsd0 libc6-i386 libcc1-0 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libgcc-s1 libgomp1 libitm1 libllvm10 liblsan0 libobjc4 libomp5-10 libquadmath0 libstdc++6 libtsan0 libubsan1 libz3-4 Suggested packages: clang-10-doc libomp-10-doc Recommended packages: llvm-10-dev python3 The following NEW packages will be installed: clang-10 lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 11 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After this operation, 259 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libatomic1 amd64 10-20200502-1 [9048 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libubsan1 amd64 10-20200502-1 [134 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libtsan0 amd64 10-20200502-1 [313 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 gcc-10-base amd64 10-20200502-1 [197 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libstdc++6 amd64 10-20200502-1 [492 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libquadmath0 amd64 10-20200502-1 [145 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblsan0 amd64 10-20200502-1 [141 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libitm1 amd64 10-20200502-1 [25.7 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgomp1 amd64 10-20200502-1 [99.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libcc1-0 amd64 10-20200502-1 [39.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libgcc-s1 amd64 10-20200502-1 [41.2 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200502-1 [41.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200502-1 [49.4 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200502-1 [1100 B] Get:23 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200502-1 [510 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.4 MB in 0s (139 MB/s) (Reading database ... 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W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-10 g++-4.6 + ln -s clang-10 gcc-4.6 + ln -s clang-10 cpp-4.6 + ln -s clang-10 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-10 g++-4.7 + ln -s clang-10 gcc-4.7 + ln -s clang-10 cpp-4.7 + ln -s clang-10 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-10 g++-4.8 + ln -s clang-10 gcc-4.8 + ln -s clang-10 cpp-4.8 + ln -s clang-10 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-10 g++-4.9 + ln -s clang-10 gcc-4.9 + ln -s clang-10 cpp-4.9 + ln -s clang-10 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-10 g++-5 + ln -s clang-10 gcc-5 + ln -s clang-10 cpp-5 + ln -s clang-10 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-10 g++-6 + ln -s clang-10 gcc-6 + ln -s clang-10 cpp-6 + ln -s clang-10 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-10 g++-7 + ln -s clang-10 gcc-7 + ln -s clang-10 cpp-7 + ln -s clang-10 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-10 g++-8 + ln -s clang-10 gcc-8 + ln -s clang-10 cpp-8 + ln -s clang-10 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-10 g++-9 + ln -s clang-10 gcc-9 + ln -s clang-10 cpp-9 + ln -s clang-10 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-10 g++-10 + ln -s clang-10 gcc-10 + ln -s clang-10 cpp-10 + ln -s clang-10 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/fastml-Q2N1Ey + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-10 clang++ + ln -s clang-10 clang + clang++ --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/fastml-Q2N1Ey + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 1270 kB of archives. After this operation, 4788 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.12.5+dfsg-10 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1270 kB in 0s (53.8 MB/s) Selecting previously unselected package qt5-qmake-bin. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12968 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ... Setting up qt5-qmake-bin (5.12.5+dfsg-10) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 May 3 04:32 . drwxr-xr-x 75 root root 4096 May 3 04:32 .. -rw-r--r-- 1 root root 276 May 3 04:32 qmake.conf -rw-r--r-- 1 root root 3218 May 3 04:32 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang10'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/fastml-Q2N1Ey/resolver-YKO8Q5' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'fastml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastml.git Please use: git clone https://salsa.debian.org/med-team/fastml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 861 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main fastml 3.11-2 (dsc) [1892 B] Get:2 http://127.0.0.1:12990/debian sid/main fastml 3.11-2 (tar) [849 kB] Get:3 http://127.0.0.1:12990/debian sid/main fastml 3.11-2 (diff) [9860 B] Fetched 861 kB in 0s (8265 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-Q2N1Ey/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-Q2N1Ey' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12~), build-essential, fakeroot Filtered Build-Depends: debhelper (>= 12~), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [368 B] Get:5 copy:/<>/apt_archive ./ Packages [450 B] Fetched 1775 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 19.2 MB of archives. After this operation, 70.4 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [868 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-1 [775 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.2 MB in 0s (106 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 13685 files and directories currently installed.) Preparing to unpack .../00-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... 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Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_13_all.deb ... Unpacking debhelper (13) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../33-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-3) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... 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 (0.19.8.1-10) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libtool (2.4.6-14) ... Setting up m4 (1.4.18-4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-10_1:10.0.0-4 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200502-1 lib32gcc1_1:10-20200502-1 lib32stdc++6_10-20200502-1 libacl1_2.2.53-8 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libatomic1_10-20200502-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-6 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200502-1 libllvm10_1:10.0.0-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libobjc-9-dev_9.3.0-11 libobjc4_10-20200502-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libquadmath0_10-20200502-1 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200502-1 libubsan1_10-20200502-1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-5 libz3-4_4.8.7-4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.3 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 po-debconf_1.0.21 qt5-qmake_5.12.5+dfsg-10 qt5-qmake-bin_5.12.5+dfsg-10 qtchooser_66-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper (>= 12~) Package-List: fastml deb science optional arch=any Checksums-Sha1: 2bc5d72d636c37c0890c36b7e426d24131bfac8d 849058 fastml_3.11.orig.tar.gz 536a5ece528ac397cb19cec322fd167a4d7b5b11 9860 fastml_3.11-2.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz 9fe4d255bbf723df1c08821b5cba0de5399cadffc5904a80024f76b0cab09fee 9860 fastml_3.11-2.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz 174551c75f7fb35adb706053129142cc 9860 fastml_3.11-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl1AULwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGPmxAAleh4yCwkmApYIOJwSf2DXk/olkmmjKfD RwQm0Mafo+kxagkVpal+C5R6Pdc4lRPu8H9aYzMSI50SCS1/qqcN/XTHc66ju9xv CiDUTygJ3VN7PPkWRcRTMIH7BADQCpLIsyy1mFEAtE6HiXz93KrGcXOqAtW+xThi 1C1WD77SC+wQoN4eQsTAqI0ykRzSVNeziPseBo2A277Phtwup+nSOdkEU4RmUvuy DTUt3zaotIZRFM5HWv0PXiZEqjLIDISC84q1TM6RRm59o2UU28xgqqWxVlWbvOv4 CFFFpmkhUe5eAxmVMr9VN/6EZkuYSN5shyLLmz6WyxqcP0YG1n8+sdNRpJg12WFk QhMBa4U7SllEL0snE8aUKQPbxsVVygFmD7vT1UDIlWp5Ja6Ajk+q63lHHB478gSk udtWH1u48stJr4WE5lk/wsAyWt0jMKfbMbV90smxE9kEQwOhFsbkjvOOjv/72s2j fqhjsd96g9YaSOo83NqxtcTEEF3r2zZfcuCx68Or8Xmdd+YoworPGIkhJpko6pVJ 4bQdgMaor8OUfJHXU3HhojFY8m5KgNGAmd/rrCFsnKzD3jzBxV46NayWb1eo2zJq yFcWwYxOCWm63HFm3odL2xLi97WGhDuVrZMNNvD+Y26KyrsuNdIFauvwB+Ey30+G PSZgcot3aDc= =KjKB -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Jul 30 14:14:20 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fastml_3.11-2.dsc dpkg-source: info: extracting fastml in /<> dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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 cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-95aab226-569e-4972-8338-f8174e2e0750 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 clean make[2]: Entering directory '/<>' cd libs;make clean cd programs;make clean make[3]: Entering directory '/<>/libs' cd phylogeny && make clean make[3]: Entering directory '/<>/programs' cd fastml && make clean cd gainLoss && make clean cd indelCoder && make clean make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/<>/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/libs/phylogeny' make[4]: Leaving directory '/<>/programs/fastml' make[3]: Leaving directory '/<>/libs' make[4]: Leaving directory '/<>/programs/gainLoss' 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 dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' making depend g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp In file included from bestAlpha.cpp:6: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp In file included from bestAlphaManyTrees.cpp:7: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from bestHKYparam.cpp:3: ./bestHKYparam.h:82:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from bestHKYparam.cpp:12: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp 2 warnings generated. g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp 3 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp computeSubstitutionCounts.cpp:16:50: warning: field '_LpostPerSpPerCat' will be initialized after field '_simulationsIterNum' [-Wreorder-ctor] _tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent) ^ computeSubstitutionCounts.cpp:16:128: warning: field '_probCutOffSum' will be initialized after field '_isSilent' [-Wreorder-ctor] _tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent) ^ g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp In file included from fastStartTree.cpp:8: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp In file included from fromCountTableComponentToDistance.cpp:4: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from fromCountTableComponentToDistancefixRoot.cpp:4: ./likeDistfixRoot.h:113:21: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp 1 warning generated. g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp fromCountTableComponentToDistancePropEB.cpp:12:60: warning: field '_nodeID' will be initialized after field '_pProportionDist' [-Wreorder-ctor] const MDOUBLE brLenIntialGuess ) : _msp(msp), _ctc(ctc), _nodeID(nodeID), _pProportionDist(pProportionDist){ ^ 1 warning generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 goldmanYangModel.cpp:9:28: warning: field '_globalV' is uninitialized when used here [-Wuninitialized] _v(inV),_k(inK),_globalV(_globalV),_codonAlph(inCodonAlph){ ^ goldmanYangModel.cpp:19:40: warning: field '_globalV' is uninitialized when used here [-Wuninitialized] _freq(freq),_v(inV),_k(inK),_globalV(_globalV),_codonAlph(inCodonAlph){ ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp In file included from likeDist.cpp:3: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp In file included from likeDistfixRoot.cpp:3: ./likeDistfixRoot.h:113:21: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from likeDistProp.cpp:3: ./likeDistProp.h:13:12: warning: private field '_alphabetSize' is not used [-Wunused-private-field] const int _alphabetSize; ^ 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp 2 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 block 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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp 3 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp sequence.cpp:76:28: warning: '&&' within '||' [-Wlogical-op-parentheses] || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ~~ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cpp:76:28: note: place parentheses around the '&&' expression to silence this warning || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ^ ( ) g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp sequenceContainer.cpp:259:27: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((_seqDataVec[j][i] == -3)) { ~~~~~~~~~~~~~~~~~~^~~~~ sequenceContainer.cpp:259:27: note: remove extraneous parentheses around the comparison to silence this warning if ((_seqDataVec[j][i] == -3)) { ~ ^ ~ sequenceContainer.cpp:259:27: note: use '=' to turn this equality comparison into an assignment if ((_seqDataVec[j][i] == -3)) { ^~ = sequenceContainer.cpp:452:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^ sequenceContainer.cpp:467:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^ 1 warning generated. g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp 3 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp tree.cpp:182:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] create_names_to_internal_nodes(); ^ tree.cpp:180:4: note: previous statement is here if (in.is_open()) ^ g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp treeUtil.cpp:371:25: warning: unused variable 'itStrStart' [-Wunused-variable] string::const_iterator itStrStart = it->begin(); ^ treeUtil.cpp:372:25: warning: unused variable 'itStrEnd' [-Wunused-variable] string::const_iterator itStrEnd = it->end(); ^ g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp In file included from givenRatesMLDistance.cpp:2: In file included from ./givenRatesMLDistance.h:8: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from distanceBasedSeqs2Tree.cpp:3: ./distanceBasedSeqs2Tree.h:105:18: warning: 'commonAlphaDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, const Vdouble *weights, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ 2 warnings generated. ./distanceBasedSeqs2Tree.h:137:18: warning: 'rate4siteDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble &rates, const Vdouble *weights, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:173:18: warning: 'posteriorDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const VVdoubleRep &posterior, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp In file included from distanceBasedSeqs2Tree.cpp:12: ./bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder-ctor] :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){}; ^ 1 warning generated. In file included from posteriorDistance.cpp:3: In file included from ./posteriorDistance.h:7: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp In file included from distanceBasedSeqs2Tree.cpp:3: In file included from ./distanceBasedSeqs2Tree.h:9: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from distanceBasedSeqs2Tree.cpp:6: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from distanceBasedSeqs2Tree.cpp:11: ./bestTamura92param.h:163:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestTamura92param.h:194:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from distanceBasedSeqs2Tree.cpp:12: ./bestGtrModelParams.h:174:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from pairwiseGammaDistance.cpp:3: ./pairwiseGammaDistance.h:32:19: warning: 'pairwiseGammaDistance::giveDistance' hides overloaded virtual function [-Woverloaded-virtual] const MDOUBLE giveDistance(const sequence& s1, ^ ./likeDist.h:51:19: note: hidden overloaded virtual function 'likeDist::giveDistance' declared here: different number of parameters (4 vs 5) const MDOUBLE giveDistance(const sequence& s1, ^ ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp 3 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp 11 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp In file included from bestAlphaAndNu.cpp:5: In file included from ./bestAlphaAndNu.h:15: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp betaDistribution.cpp:24:2: warning: field '_boundary' will be initialized after field '_alpha' [-Wreorder-ctor] _boundary(other._boundary), ^ 1 warning generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp In file included from bestParamUSSRV.cpp:2: In file included from ./bestParamUSSRV.h:13: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp 2 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp In file included from fromCountTableComponentToDistance2USSRV.cpp:4: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ 2 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp In file included from bestTamura92param.cpp:3: ./bestTamura92param.h:163:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestTamura92param.h:194:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from bestTamura92param.cpp:12: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp In file included from ssrvDistanceSeqs2Tree.cpp:3: In file included from ./ssrvDistanceSeqs2Tree.h:6: ./distanceBasedSeqs2Tree.h:105:18: warning: 'commonAlphaDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, const Vdouble *weights, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:137:18: warning: 'rate4siteDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble &rates, const Vdouble *weights, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:173:18: warning: 'posteriorDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const VVdoubleRep &posterior, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 4) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ In file included from ssrvDistanceSeqs2Tree.cpp:3: ./ssrvDistanceSeqs2Tree.h:41:18: warning: 'ssrvDistanceSeqs2Tree::seqs2TreeBootstrap' hides overloaded virtual function [-Woverloaded-virtual] tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, MDOUBLE nu, const Vdouble *weights, const tree* constraintTreePtr=NULL); ^ ./distanceBasedSeqs2Tree.h:50:16: note: hidden overloaded virtual function 'iterativeDistanceSeqs2Tree::seqs2TreeBootstrap' declared here: different number of parameters (3 vs 5) virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp In file included from ssrvDistanceSeqs2Tree.cpp:3: In file included from ./ssrvDistanceSeqs2Tree.h:6: In file included from ./distanceBasedSeqs2Tree.h:9: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from ssrvDistanceSeqs2Tree.cpp:5: In file included from ./bestParamUSSRV.h:13: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ 8 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp 4 warnings generated. g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp simulateJumps.cpp:149:37: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if ((iterTerm->second[termState]==0)){ //never reached these terminal states ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ simulateJumps.cpp:149:37: note: remove extraneous parentheses around the comparison to silence this warning if ((iterTerm->second[termState]==0)){ //never reached these terminal states ~ ^ ~ simulateJumps.cpp:149:37: note: use '=' to turn this equality comparison into an assignment if ((iterTerm->second[termState]==0)){ //never reached these terminal states ^~ = computeJumps.cpp:257:22: warning: field '_Lambda2' will be initialized after field '_r' [-Wreorder-ctor] : _Lambda1(Lambda1), _Lambda2(Lambda2), _r(r) ^ seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] const alphabet* pAlph = sc.getAlphabet(); ^ 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp mixtureDistribution.cpp:211:18: warning: variable 'componentNum' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:221:21: note: uninitialized use occurs here return _components[componentNum]->rates(categoryInComponent) * _globalRate; ^~~~~~~~~~~~ mixtureDistribution.cpp:211:18: note: remove the condition if it is always true for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:210:18: note: initialize the variable 'componentNum' to silence this warning int componentNum, categoryInComponent, totalCat = 0; ^ = 0 mixtureDistribution.cpp:211:18: warning: variable 'categoryInComponent' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:221:42: note: uninitialized use occurs here return _components[componentNum]->rates(categoryInComponent) * _globalRate; ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:211:18: note: remove the condition if it is always true for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:210:39: note: initialize the variable 'categoryInComponent' to silence this warning int componentNum, categoryInComponent, totalCat = 0; ^ = 0 mixtureDistribution.cpp:229:18: warning: variable 'componentNum' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:239:27: note: uninitialized use occurs here return getComponentProb(componentNum) * _components[componentNum]->ratesProb(categoryInComponent); ^~~~~~~~~~~~ mixtureDistribution.cpp:229:18: note: remove the condition if it is always true for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:228:18: note: initialize the variable 'componentNum' to silence this warning int componentNum, categoryInComponent, totalCat = 0; ^ = 0 mixtureDistribution.cpp:229:18: warning: variable 'categoryInComponent' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:239:80: note: uninitialized use occurs here return getComponentProb(componentNum) * _components[componentNum]->ratesProb(categoryInComponent); ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:229:18: note: remove the condition if it is always true for (int i = 0; i < getComponentsNum(); ++i) ^~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:228:39: note: initialize the variable 'categoryInComponent' to silence this warning int componentNum, categoryInComponent, totalCat = 0; ^ = 0 g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable] MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); ^ 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: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); ^ In file included from GamMixtureOptimizer.cpp:3: ./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: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))); ^ 1 warning generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp 4 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp 5 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp In file included from optGammaMixtureEM.cpp:1: ./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:87:11: warning: unused variable 'debugRes' [-Wunused-variable] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp 2 warnings generated. g++ -g -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 -O2 -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 fromCountTableComponentToDistance2Codon.cpp:5: ./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ 2 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp gtrModel.cpp:12:59: warning: field '_g2t' will be initialized after field '_freq' [-Wreorder-ctor] :_a2c(a2c),_a2g(a2g),_a2t(a2t),_c2g(c2g),_c2t(c2t),_g2t(g2t),_freq(freq) ^ gtrModel.cpp:134:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:139:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:134:3: note: remove the 'if' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:134:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:139:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:134:6: note: remove the '||' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:131:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:139:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:131:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:130:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 gtrModel.cpp:148:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:153:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:148:3: note: remove the 'if' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:148:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:153:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:148:6: note: remove the '||' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:145:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:153:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:145:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:144:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 gtrModel.cpp:162:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:167:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:162:3: note: remove the 'if' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:162:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:167:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:162:6: note: remove the '||' if its condition is always false if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:159:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:167:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:159:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:158:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 gtrModel.cpp:176:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:181:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:176:3: note: remove the 'if' if its condition is always false if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:176:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:181:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:176:6: note: remove the '||' if its condition is always false if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:173:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:181:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:173:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:172:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 gtrModel.cpp:190:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:195:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:190:3: note: remove the 'if' if its condition is always false if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:190:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:195:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:190:6: note: remove the '||' if its condition is always false if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:187:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:195:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:187:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:186:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 gtrModel.cpp:204:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:209:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:204:3: note: remove the 'if' if its condition is always false if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:204:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized] if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:209:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:204:6: note: remove the '||' if its condition is always false if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize())) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:201:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:209:9: note: uninitialized use occurs here return result; ^~~~~~ gtrModel.cpp:201:2: note: remove the 'if' if its condition is always false if(_Q.size() < alphabetSize()) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp:200:16: note: initialize the variable 'result' to silence this warning MDOUBLE result; ^ = 0.0 g++ -g -O2 -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 -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp In file included from bestGtrModelParams.cpp:3: ./bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder-ctor] :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){}; ^ In file included from simulateRateShiftJumps.cpp:1: ./simulateRateShiftJumps.h:16:7: warning: 'simulateRateShiftJumps::runSimulation' hides overloaded virtual function [-Woverloaded-virtual] void runSimulation(int iterNum, vector inputNodes); ^ ./simulateJumpsAbstract.h:30:15: note: hidden overloaded virtual function 'simulateJumpsAbstract::runSimulation' declared here: different number of parameters (1 vs 2) virtual void runSimulation(int iterNum = 10000); ^ 19 warnings generated. ./bestGtrModelParams.h:174:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from bestGtrModelParams.cpp:12: ./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ 1 warning generated. 4 warnings generated. 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 cd gainLoss && make all cd indelCoder && make all make[3]: Entering directory '/<>/programs/indelCoder' making depend make[3]: Entering directory '/<>/programs/fastml' make[3]: Entering directory '/<>/programs/gainLoss' making depend making depend g++ -g -O2 -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 g++ -g -O2 -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 -O2 -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 indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; ^ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^ indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; ^ g++ -g -O2 -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 In file included from fastml.cpp:254: In file included from ./bbAlg.h:8: ./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder-ctor] : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;} ^ In file included from fastml.cpp:1: In file included from ./mainbb.h:4: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -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 2 warnings generated. g++ -g -O2 -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 g++ -g -O2 -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 In file included from bbAlg.cpp:1: In file included from ./bbAlg.h:8: ./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder-ctor] : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;} ^ gainLossOptions.cpp:2060:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (str=="Vhigh") ^~~~~~~~~~~~ gainLossOptions.cpp:2064:9: note: uninitialized use occurs here return returnType; ^~~~~~~~~~ gainLossOptions.cpp:2060:7: note: remove the 'if' if its condition is always true else if (str=="Vhigh") ^~~~~~~~~~~~~~~~~ gainLossOptions.cpp:2047:2: note: variable 'returnType' is declared here optimizationLevel returnType; ^ gainLossOptions.cpp:2107:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (str=="gainLossCost") ^~~~~~~~~~~~~~~~~~~ gainLossOptions.cpp:2111:9: note: uninitialized use occurs here return returnType; ^~~~~~~~~~ gainLossOptions.cpp:2107:7: note: remove the 'if' if its condition is always true else if (str=="gainLossCost") ^~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptions.cpp:2098:2: note: variable 'returnType' is declared here costMatrixType returnType; ^ gainLossOptions.cpp:2415:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (str=="Gam_gVrl") ^~~~~~~~~~~~~~~ gainLossOptions.cpp:2419:9: note: uninitialized use occurs here return returnType; ^~~~~~~~~~ gainLossOptions.cpp:2415:7: note: remove the 'if' if its condition is always true else if (str=="Gam_gVrl") ^~~~~~~~~~~~~~~~~~~~ gainLossOptions.cpp:2396:2: note: variable 'returnType' is declared here simulationType returnType; ^ bbAlg.cpp:14:2: warning: field '_reportFileName' will be initialized after field 'BandBReportAllPos1' [-Wreorder-ctor] _reportFileName(reportFileName), ^ bbAlg.cpp:15:2: warning: field 'BandBReportAllPos1' will be initialized after field '_et' [-Wreorder-ctor] BandBReportAllPos1(reportFileName,et.getInternalNodesNum()*spVec[0].alphabetSize()*sc.seqLen()), ^ In file included from bbAlg.cpp:1: In file included from ./bbAlg.h:5: In file included from ./bbNodeOrderAlg.h:5: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ g++ -g -O2 -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 3 warnings generated. g++ -g -O2 -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 4 warnings generated. g++ -g -O2 -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 -O2 -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 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,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' g++ -g -O2 -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 bbEvaluateSpecificAV.cpp:6:53: warning: field '_sc' will be initialized after field '_bbcpij' [-Wreorder-ctor] const computePijGam& cpij) : _et(et), _sp(sp), _sc(sc), _bbcpij(cpij) { ^ bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] MDOUBLE rate = _sp.rates(categor); // the r. ^ g++ -g -O2 -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 bbEvaluateSpecificAV.cpp:1: In file included from ./bbEvaluateSpecificAV.h:4: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ In file included from bbEvaluateSpecificAV.cpp:1: ./bbEvaluateSpecificAV.h:33:6: warning: private field '_pos' is not used [-Wunused-private-field] int _pos; ^ g++ -g -O2 -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 4 warnings generated. g++ -g -O2 -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 bbfindBestAVDynProg.cpp:1: In file included from ./bbfindBestAVDynProg.h:5: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ In file included from bbfindBestAVDynProg.cpp:1: ./bbfindBestAVDynProg.h:31:6: warning: private field '_pos' is not used [-Wunused-private-field] int _pos; ^ bbNodeOrderAlg.cpp:12:64: warning: field '_sc' will be initialized after field '_cpij' [-Wreorder-ctor] const MDOUBLE computeAgainExactTreshold) :_et(et),_sp(sp),_sc(sc),_cpij(cpij){ ^ bb_options.cpp:11:2: warning: field 'reportFile' will be initialized after field 'outFile_seq_joint' [-Wreorder-ctor] reportFile("log.txt"), ^ bb_options.cpp:13:2: warning: field 'outFile_seq_marginal' will be initialized after field 'outFile_prob_joint' [-Wreorder-ctor] outFile_seq_marginal("seq.marginal.txt"), ^ bb_options.cpp:15:2: warning: field 'outFile_prob_marginal' will be initialized after field 'seqfile' [-Wreorder-ctor] outFile_prob_marginal("prob.marginal.txt"), ^ bb_options.cpp:17:5: warning: field 'distributionName' will be initialized after field 'seqOutputFormat' [-Wreorder-ctor] distributionName(hom), ^ bb_options.cpp:20:5: warning: field 'outTreeFileAncestor' will be initialized after field 'boundMethod' [-Wreorder-ctor] outTreeFileAncestor("tree.ancestor.txt"), ^ bb_options.cpp:22:2: warning: field 'gammaPar' will be initialized after field 'userProvideAlpha' [-Wreorder-ctor] gammaPar(1.0), ^ bb_options.cpp:24:2: warning: field 'gammaCategies' will be initialized after field 'modelName' [-Wreorder-ctor] gammaCategies(8), ^ bb_options.cpp:28:2: warning: field 'useChebyshev' will be initialized after field 'treeOutFile' [-Wreorder-ctor] useChebyshev(true), ^ In file included from bb_options.cpp:2: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ In file included from bbNodeOrderAlg.cpp:1: In file included from ./bbNodeOrderAlg.h:5: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ In file included from bbNodeOrderAlg.cpp:1: ./bbNodeOrderAlg.h:40:6: warning: private field '_pos' is not used [-Wunused-private-field] int _pos; ^ 2 warnings generated. g++ -g -O2 -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 9 warnings generated. g++ -g -O2 -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 In file included from bbReport.cpp:1: ./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder-ctor] : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;} ^ bbReport.cpp:11:2: warning: field '_reportFileName' will be initialized after field '_position' [-Wreorder-ctor] _reportFileName(reportFileName), _position(position), _alphabetSize(alphabetSize) ^ 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; ^ 3 warnings generated. g++ -g -O2 -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 2 warnings generated. g++ -g -O2 -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 3 warnings generated. g++ -g -O2 -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 jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^ jointNoGamma.cpp:108:12: warning: unused variable 'maxL' [-Wunused-variable] MDOUBLE maxL = VERYSMALL; ^ In file included from mainbb.cpp:5: In file included from ./bbAlg.h:8: ./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder-ctor] : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;} ^ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder-ctor] :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){}; ^ mainbb.cpp:426:11: warning: variable 'bm' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (_options->boundMethod == bb_options::both) bm=bbAlg::both; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mainbb.cpp:428:30: note: uninitialized use occurs here bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); ^~ mainbb.cpp:426:7: note: remove the 'if' if its condition is always true else if (_options->boundMethod == bb_options::both) bm=bbAlg::both; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mainbb.cpp:423:2: note: variable 'bm' is declared here bbAlg::boundMethod bm; ^ In file included from gainLoss.cpp:20: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ In file included from gainLoss.cpp:41: ./bblLS.h:50:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion] MDOUBLE curL =NULL); ~^~~~ 0.0 ./bblLS.h:58:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion] MDOUBLE curL =NULL); ~^~~~ 0.0 ./bblLS.h:99:92: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor] :_pNode(pNode),_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights) ^ ./bblLS.h:155:78: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor] :_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights) ^ gainLoss.cpp:63:33: warning: field '_unObservableData_p' will be initialized after field '_lossDist' [-Wreorder-ctor] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ gainLoss.cpp:63:59: warning: field '_lossDist' will be initialized after field '_gainDist' [-Wreorder-ctor] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ gainLoss.cpp:63:93: warning: field '_refSeq' will be initialized after field '_weightsUniqPatterns' [-Wreorder-ctor] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^ In file included from mainbb.cpp:1: In file included from ./mainbb.h:4: ./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function] static const string usege_splash_screen() { ^ In file included from mainbb.cpp:6: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from mainbb.cpp:15: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h:174:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from mainbb.cpp:32: ../../libs/phylogeny/bestTamura92param.h:163:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestTamura92param.h:194:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from mainbb.cpp:33: ../../libs/phylogeny/bestHKYparam.h:82:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] char missigDataChar = -2; ^ gainLoss.cpp:1121:5: warning: variable 'rateDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ gainLoss.cpp:1124:50: note: uninitialized use occurs here stochasticProcess* sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); ^~~~~~~~ gainLoss.cpp:1105:26: note: initialize the variable 'rateDist' to silence this warning distribution* rateDist; ^ = nullptr gainLoss.cpp:1245:38: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^ ~~ gainLoss.cpp:1245:38: note: add parentheses after the '!' to evaluate the comparison first 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:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(sp); ^ gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); ^ 2 warnings generated. g++ -g -O2 -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 gainLoss.cpp:2331:3: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] _correlationsPerSitePerPosVec = computeCorrel->getcorrelationPerSitePerPosVec(); ^ gainLoss.cpp:2327:2: note: previous statement is here if(gainLossOptions::_isPrintCorrelationsOfAllPairs_Corr) ^ gainLoss.cpp:2467:5: warning: variable 'countsGL' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if(!gainLossOptions::_gainLossDist){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:2484:2: note: uninitialized use occurs here countsGL->run(); ^~~~~~~~ gainLoss.cpp:2467:2: note: remove the 'if' if its condition is always true if(!gainLossOptions::_gainLossDist){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:2466:27: note: initialize the variable 'countsGL' to silence this warning computeCountsGL* countsGL; ^ = nullptr 2 warnings generated. g++ -g -O2 -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 gainLoss.cpp:4382:7: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^ ~ gainLoss.cpp:4382:7: note: add parentheses after the '!' to evaluate the comparison first 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){ ^ ( ) g++ -g -O2 -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 g++ -g -O2 -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 gainLossUtils.cpp:19: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossUtils.cpp:75:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else //print losses ^ 12 warnings generated. gainLossUtils.cpp:91:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else //print losses ^ 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 In file included from gainLoss.cpp:20: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from gainLoss.cpp:20: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from gainLoss.cpp:20: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ gainLossUtils.cpp:306:11: warning: variable 'res' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (dynamic_cast(dist)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp:312:9: note: uninitialized use occurs here return res; ^~~ gainLossUtils.cpp:306:7: note: remove the 'if' if its condition is always true else if (dynamic_cast(dist)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp:285:13: note: initialize the variable 'res' to silence this warning MDOUBLE res; ^ = 0.0 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,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] MDOUBLE scale; ^ In file included from optimizeGainLossModel.cpp:17: In file included from ./optimizeGainLossModel.h:27: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ optimizeGainLossModel.cpp:25:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights), _unObservableData_p(unObservableData_p) ^ make[3]: Leaving directory '/<>/programs/fastml' g++ -g -O2 -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 optimizeGainLossModel.cpp:17: In file included from ./optimizeGainLossModel.h:23: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ 5 warnings generated. g++ -g -O2 -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 optimizeGainLossModelVV.cpp:17: In file included from ./optimizeGainLossModelVV.h:27: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ optimizeGainLossModelVV.cpp:32:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights),_unObservableData_p(unObservableData_p) ^ optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); ^ In file included from optimizeGainLossModelVV.cpp:17: In file included from ./optimizeGainLossModelVV.h:23: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from optimizeGainLossModelVV.cpp:17: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ In file included from gainLossModel.cpp:17: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.cpp:25:1: warning: field '_gain' will be initialized after field '_freq' [-Wreorder-ctor] _gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){ ^ gainLossModel.cpp:25:23: warning: field '_isRootFreqEQstationary' will be initialized after field '_isReversible' [-Wreorder-ctor] _gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){ ^ gainLossModel.cpp:25:135: warning: field '_isHGT_with_Q' will be initialized after field '_q2pt' [-Wreorder-ctor] _gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){ ^ 6 warnings generated. g++ -g -O2 -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 7 warnings generated. g++ -g -O2 -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 5 warnings generated. g++ -g -O2 -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 siteSpecificGL.cpp:24: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ In file included from computePosteriorExpectationOfChange.cpp:25: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ In file included from gainLossProject.cpp:17: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ 2 warnings generated. g++ -g -O2 -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 gainLossProject.cpp:17: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from gainLossProject.cpp:17: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from gainLossProject.cpp:17: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ 7 warnings generated. g++ -g -O2 -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 In file included from gainLossOptimizer.cpp:17: In file included from ./gainLossOptimizer.h:24: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ In file included from gainLossOptimizer.cpp:20: ./bblLS.h:50:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion] MDOUBLE curL =NULL); ~^~~~ 0.0 ./bblLS.h:58:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion] MDOUBLE curL =NULL); ~^~~~ 0.0 ./bblLS.h:99:92: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor] :_pNode(pNode),_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights) ^ ./bblLS.h:155:78: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor] :_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights) ^ gainLossOptimizer.cpp:31:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc), ^ gainLossOptimizer.cpp:31:17: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc), ^ gainLossOptimizer.cpp:35:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights), ^ gainLossOptimizer.cpp:57:45: warning: field '_lossDist' will be initialized after field '_sc' [-Wreorder-ctor] _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist), ^ gainLossOptimizer.cpp:58:1: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder-ctor] _sc(sc),//_spSimple(spSimple), // ignore sent model, make new one ^ gainLossOptimizer.cpp:62:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights), ^ 2 warnings generated. g++ -g -O2 -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 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: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:827:11: warning: variable 'res' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (dynamic_cast(dist)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:833:9: note: uninitialized use occurs here return res; ^~~ gainLossOptimizer.cpp:827:7: note: remove the 'if' if its condition is always true else if (dynamic_cast(dist)){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:820:2: note: variable 'res' is declared here gainLossOptions::distributionType res; ^ In file included from gainLossOptimizer.cpp:17: In file included from ./gainLossOptimizer.h:24: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from gainLossOptimizer.cpp:17: In file included from ./gainLossOptimizer.h:24: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from gainLossOptimizer.cpp:17: In file included from ./gainLossOptimizer.h:24: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ In file included from rate4siteGL.cpp:17: In file included from ./rate4siteGL.h:24: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ rate4siteGL.cpp:25:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p) ^ 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; ^ In file included from rate4siteGL.cpp:17: In file included from ./rate4siteGL.h:24: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warningg++ -g -O2 -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 : private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from rate4siteGL.cpp:17: In file included from ./rate4siteGL.h:24: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from rate4siteGL.cpp:17: In file included from ./rate4siteGL.h:24: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ In file included from computeCountsGL.cpp:17: In file included from ./computeCountsGL.h:24: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ 10 warnings generated. g++ -g -O2 -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 computeCountsGL.cpp:29:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^ computeCountsGL.cpp:29:85: warning: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^ computeCountsGL.cpp:34:47: warning: field '_lossDist' will be initialized after field '_sc' [-Wreorder-ctor] _tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^ computeCountsGL.cpp:34:145: warning: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' [-Wreorder-ctor] _tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^ In file included from computeCountsGL.cpp:17: In file included from ./computeCountsGL.h:24: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from computeCountsGL.cpp:17: In file included from ./computeCountsGL.h:24: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from computeCountsGL.cpp:17: In file included from ./computeCountsGL.h:24: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ In file included from computeCorrelations.cpp:17: In file included from ./computeCorrelations.h:25: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^ 22 warnings generated. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp 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:559:21: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic] if(!simCorrelStream==NULL) ~~~~~~~~~~~~~~~~^ ~~~~ computeCorrelations.cpp:559:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!simCorrelStream==NULL) ^ ~~ computeCorrelations.cpp:559:5: note: add parentheses after the '!' to evaluate the comparison first if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:559:5: note: add parentheses around left hand side expression to silence this warning if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:569:22: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic] if(!simCorrelStream==NULL) ~~~~~~~~~~~~~~~~^ ~~~~ computeCorrelations.cpp:569:6: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!simCorrelStream==NULL) ^ ~~ computeCorrelations.cpp:569:6: note: add parentheses after the '!' to evaluate the comparison first if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:569:6: note: add parentheses around left hand side expression to silence this warning if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:579:22: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic] if(!simCorrelStream==NULL) ~~~~~~~~~~~~~~~~^ ~~~~ computeCorrelations.cpp:579:6: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!simCorrelStream==NULL) ^ ~~ computeCorrelations.cpp:579:6: note: add parentheses after the '!' to evaluate the comparison first if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:579:6: note: add parentheses around left hand side expression to silence this warning if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:584:21: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic] if(!simCorrelStream==NULL) ~~~~~~~~~~~~~~~~^ ~~~~ computeCorrelations.cpp:584:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!simCorrelStream==NULL) ^ ~~ computeCorrelations.cpp:584:5: note: add parentheses after the '!' to evaluate the comparison first if(!simCorrelStream==NULL) ^ ( ) computeCorrelations.cpp:584:5: note: add parentheses around left hand side expression to silence this warning if(!simCorrelStream==NULL) ^ ( ) 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:894:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if(!numOfSites_A == numOfSites_B){ ^ ~~ computeCorrelations.cpp:894:5: note: add parentheses after the '!' to evaluate the comparison first 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: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:1347:36: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing] float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:1347:36: note: insert an explicit cast to silence this issue float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ static_cast( ) computeCorrelations.cpp:1300:7: warning: unused variable 'it_siteB' [-Wunused-variable] it_B it_siteB = it_siteA->second.begin(); ^ In file included from gainLoss4site.cpp:17: In file included from ./gainLoss4site.h:24: In file included from ./gainLoss.h:35: ./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual] void updateQ(){ ^ ./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0) virtual MDOUBLE updateQ(bool isReversible); ^ ./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ In file included from computeCorrelations.cpp:17: In file included from ./computeCorrelations.h:25: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from computeCorrelations.cpp:17: In file included from ./computeCorrelations.h:25: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from computeCorrelations.cpp:17: In file included from ./computeCorrelations.h:25: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ 24 warnings and 1 error generated. make[3]: *** [: computeCorrelations.o] Error 1 make[3]: *** Waiting for unfinished jobs.... gainLoss4site.cpp:25:1: warning: field '_tr' will be initialized after field '_spVVec' [-Wreorder-ctor] _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf) ^ gainLoss4site.cpp:25:89: warning: field '_unObservableData_p' will be initialized after field '_alphaConf' [-Wreorder-ctor] _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf) ^ In file included from gainLoss4site.cpp:17: In file included from ./gainLoss4site.h:24: In file included from ./gainLoss.h:24: ../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ ../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field] const Vdouble * _weights; ^ In file included from gainLoss4site.cpp:17: In file included from ./gainLoss4site.h:24: In file included from ./gainLoss.h:42: ../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ ../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field] unObservableData* _unObservableData_p; ^ In file included from gainLoss4site.cpp:17: In file included from ./gainLoss4site.h:24: In file included from ./gainLoss.h:51: ./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field] bool _isReversible; ^ 9 warnings generated. 11 warnings generated. 22 warnings generated. make[3]: Leaving directory '/<>/programs/gainLoss' make[2]: *** [Makefile:30: gainLoss.all] Error 2 make[2]: Leaving directory '/<>/programs' make[1]: *** [Makefile:29: programs.all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:8: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T04:34:00Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 188636 Build-Time: 87 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 5 Job: fastml_3.11-2 Machine Architecture: amd64 Package: fastml Package-Time: 107 Source-Version: 3.11-2 Space: 188636 Status: attempted Version: 3.11-2 -------------------------------------------------------------------------------- Finished at 2020-05-03T04:34:00Z Build needed 00:01:47, 188636k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 108.61148151s DC-Time-Estimation: 108.61148151 versus expected 230 (r/m: 1.1176398369892744 ; m: 108.61148151)