DC-Build-Header: fastml 3.11-3 / 2021-10-26 21:42:38 +0000 DC-Task: type:rebuild-binarch-only source:fastml version:3.11-3 chroot:unstable esttime:321 logfile:/tmp/fastml_3.11-3_unstable_clang13.log modes:clang13:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang13 fastml_3.11-3' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-2-57.eu-central-1.compute.internal +==============================================================================+ | fastml 3.11-3 (amd64) Tue, 26 Oct 2021 21:42:38 +0000 | +==============================================================================+ Package: fastml Version: 3.11-3 Source Version: 3.11-3 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-c6aea9a8-07cf-45c2-8fab-09d441927790' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang13 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=13 + echo 'Install of clang-13' Install of clang-13 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [165 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Translation-en [6586 kB] Fetched 6981 kB in 3s (2773 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-13 libomp-13-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc4 libomp5-13 libxml2 libz3-4 Suggested packages: clang-13-doc libomp-13-doc Recommended packages: llvm-13-dev python3 The following NEW packages will be installed: clang-13 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc-9-dev libobjc4 libomp-13-dev libomp5-13 libxml2 libz3-4 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 68.5 MB of archives. After this operation, 379 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libmd0 amd64 1.0.4-1 [29.6 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20210910-1 [97.5 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.12-1+b1 [6997 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libllvm13 amd64 1:13.0.0-8 [19.7 MB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp13 amd64 1:13.0.0-8 [10.5 MB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgc1 amd64 1:8.0.4-3 [239 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 11.2.0-10 [43.2 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libobjc-11-dev amd64 11.2.0-10 [170 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.32-4 [2624 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 11.2.0-10 [49.9 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 11.2.0-10 [601 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-13-dev amd64 1:13.0.0-8 [5730 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang1-13 amd64 1:13.0.0-8 [6093 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 clang-13 amd64 1:13.0.0-8 [119 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.4.0-3 [2734 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.4.0-3 [2343 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.4.0-3 [219 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libomp5-13 amd64 1:13.0.0-8 [377 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libomp-13-dev amd64 1:13.0.0-8 [482 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.5 MB in 0s (155 MB/s) Selecting previously unselected package libmd0:amd64. (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 ... 12431 files and directories currently installed.) Preparing to unpack .../00-libmd0_1.0.4-1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20210910-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20210910-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../03-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../04-libxml2_2.9.12+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.12+dfsg-5) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../05-libz3-4_4.8.12-1+b1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-1+b1) ... Selecting previously unselected package libllvm13:amd64. Preparing to unpack .../06-libllvm13_1%3a13.0.0-8_amd64.deb ... Unpacking libllvm13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libclang-cpp13. Preparing to unpack .../07-libclang-cpp13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-cpp13 (1:13.0.0-8) ... Selecting previously unselected package libgc1:amd64. Preparing to unpack .../08-libgc1_1%3a8.0.4-3_amd64.deb ... Unpacking libgc1:amd64 (1:8.0.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_11.2.0-10_amd64.deb ... Unpacking libobjc4:amd64 (11.2.0-10) ... Selecting previously unselected package libobjc-11-dev:amd64. Preparing to unpack .../10-libobjc-11-dev_11.2.0-10_amd64.deb ... Unpacking libobjc-11-dev:amd64 (11.2.0-10) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../11-libc6-i386_2.32-4_amd64.deb ... Unpacking libc6-i386 (2.32-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../12-lib32gcc-s1_11.2.0-10_amd64.deb ... Unpacking lib32gcc-s1 (11.2.0-10) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../13-lib32stdc++6_11.2.0-10_amd64.deb ... Unpacking lib32stdc++6 (11.2.0-10) ... Selecting previously unselected package libclang-common-13-dev. Preparing to unpack .../14-libclang-common-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-common-13-dev (1:13.0.0-8) ... Selecting previously unselected package libclang1-13. Preparing to unpack .../15-libclang1-13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang1-13 (1:13.0.0-8) ... Selecting previously unselected package clang-13. Preparing to unpack .../16-clang-13_1%3a13.0.0-8_amd64.deb ... Unpacking clang-13 (1:13.0.0-8) ... Selecting previously unselected package libasan5:amd64. Preparing to unpack .../17-libasan5_9.4.0-3_amd64.deb ... Unpacking libasan5:amd64 (9.4.0-3) ... Selecting previously unselected package libgcc-9-dev:amd64. Preparing to unpack .../18-libgcc-9-dev_9.4.0-3_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../19-libobjc-9-dev_9.4.0-3_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libomp5-13:amd64. Preparing to unpack .../20-libomp5-13_1%3a13.0.0-8_amd64.deb ... Unpacking libomp5-13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libomp-13-dev. Preparing to unpack .../21-libomp-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libomp-13-dev (1:13.0.0-8) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libasan5:amd64 (9.4.0-3) ... Setting up libz3-4:amd64 (4.8.12-1+b1) ... Setting up libgc1:amd64 (1:8.0.4-3) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libc6-i386 (2.32-4) ... Setting up libomp5-13:amd64 (1:13.0.0-8) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up libobjc4:amd64 (11.2.0-10) ... Setting up libgcc-9-dev:amd64 (9.4.0-3) ... Setting up lib32gcc-s1 (11.2.0-10) ... Setting up lib32stdc++6 (11.2.0-10) ... Setting up libllvm13:amd64 (1:13.0.0-8) ... Setting up libobjc-9-dev:amd64 (9.4.0-3) ... Setting up libclang-common-13-dev (1:13.0.0-8) ... Setting up libomp-13-dev (1:13.0.0-8) ... Setting up libobjc-11-dev:amd64 (11.2.0-10) ... Setting up libclang1-13 (1:13.0.0-8) ... Setting up libclang-cpp13 (1:13.0.0-8) ... Setting up clang-13 (1:13.0.0-8) ... Processing triggers for libc-bin (2.32-4) ... 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 11' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-13 g++-4.6 + ln -s clang-13 gcc-4.6 + ln -s clang-13 cpp-4.6 + ln -s clang-13 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++-13 g++-4.7 + ln -s clang-13 gcc-4.7 + ln -s clang-13 cpp-4.7 + ln -s clang-13 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++-13 g++-4.8 + ln -s clang-13 gcc-4.8 + ln -s clang-13 cpp-4.8 + ln -s clang-13 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++-13 g++-4.9 + ln -s clang-13 gcc-4.9 + ln -s clang-13 cpp-4.9 + ln -s clang-13 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++-13 g++-5 + ln -s clang-13 gcc-5 + ln -s clang-13 cpp-5 + ln -s clang-13 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++-13 g++-6 + ln -s clang-13 gcc-6 + ln -s clang-13 cpp-6 + ln -s clang-13 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++-13 g++-7 + ln -s clang-13 gcc-7 + ln -s clang-13 cpp-7 + ln -s clang-13 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++-13 g++-8 + ln -s clang-13 gcc-8 + ln -s clang-13 cpp-8 + ln -s clang-13 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++-13 g++-9 + ln -s clang-13 gcc-9 + ln -s clang-13 cpp-9 + ln -s clang-13 gcc + echo 'gcc-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-10 gcc-10 cpp-10 gcc + ln -s clang++-13 g++-10 + ln -s clang-13 gcc-10 + ln -s clang-13 cpp-10 + ln -s clang-13 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 + for VERSION in $VERSIONS + rm -f g++-11 gcc-11 cpp-11 gcc + ln -s clang++-13 g++-11 + ln -s clang-13 gcc-11 + ln -s clang-13 cpp-11 + ln -s clang-13 gcc + echo 'gcc-11 hold' + dpkg --set-selections + echo 'g++-11 hold' + dpkg --set-selections + cd - /build/fastml-goJgjO + 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-13 clang++ + ln -s clang-13 clang + clang++ --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/fastml-goJgjO + 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 1322 kB of archives. After this operation, 4914 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.15.2+dfsg-12 [1046 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 5.15.2+dfsg-12 [249 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1322 kB in 0s (58.0 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 ... 13528 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake-bin (5.15.2+dfsg-12) ... 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_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake:amd64 (5.15.2+dfsg-12) ... Setting up qt5-qmake-bin (5.15.2+dfsg-12) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.15.2+dfsg-12) ... 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 Oct 26 21:42 . drwxr-xr-x 76 root root 4096 Oct 26 21:42 .. -rw-r--r-- 1 root root 276 Oct 26 21:42 qmake.conf -rw-r--r-- 1 root root 3218 Oct 26 21:42 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/clang13'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/fastml-goJgjO/resolver-5kXRdf' 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 3.11-3 (dsc) [1897 B] Get:2 http://127.0.0.1:12990/debian sid/main fastml 3.11-3 (tar) [849 kB] Get:3 http://127.0.0.1:12990/debian sid/main fastml 3.11-3 (diff) [9984 B] Fetched 861 kB in 0s (9373 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-goJgjO/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-goJgjO' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), 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 [370 B] Get:5 copy:/<>/apt_archive ./ Packages [453 B] Fetched 1780 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 bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc 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 libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 8981 kB of archives. After this operation, 31.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [872 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdextrautils amd64 2.37.2-4 [143 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.5-1 [823 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.21-4 [510 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-15 [513 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 20 [17.1 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 1.12.0-2 [26.3 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.21-4 [1311 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13.5.2 [1056 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8981 kB in 0s (87.4 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14273 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.37.2-4_amd64.deb ... Unpacking bsdextrautils (2.37.2-4) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-7_amd64.deb ... Unpacking groff-base (1.22.4-7) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. 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Setting up bsdextrautils (2.37.2-4) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.5.2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:amd64 (0.185-2) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.5.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... +------------------------------------------------------------------------------+ | 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_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 clang-13_1:13.0.0-8 coreutils_8.32-4+b1 cpp_4:11.2.0-2 cpp-11_11.2.0-10 dash_0.5.11+git20210120+802ebd4-2 debconf_1.5.78 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-dev_1.20.9 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.26-1 file_1:5.39-3 findutils_4.8.0-1 g++_4:11.2.0-2 g++-11_11.2.0-10 gcc_4:11.2.0-2 gcc-10-base_10.3.0-11 gcc-11_11.2.0-10 gcc-11-base_11.2.0-10 gcc-9-base_9.4.0-3 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_11.2.0-10 lib32stdc++6_11.2.0-10 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan5_9.4.0-3 libasan6_11.2.0-10 libatomic1_11.2.0-10 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7 libblkid1_2.37.2-4 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4 libc-dev-bin_2.32-4 libc6_2.32-4 libc6-dev_2.32-4 libc6-i386_2.32-4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10 libclang-common-13-dev_1:13.0.0-8 libclang-cpp13_1:13.0.0-8 libclang1-13_1:13.0.0-8 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9 libedit2_3.1-20210910-1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.26-1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgc1_1:8.0.4-3 libgcc-11-dev_11.2.0-10 libgcc-9-dev_9.4.0-3 libgcc-s1_11.2.0-10 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libitm1_11.2.0-10 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libllvm13_1:13.0.0-8 liblsan0_11.2.0-10 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libobjc-11-dev_11.2.0-10 libobjc-9-dev_9.4.0-3 libobjc4_11.2.0-10 libomp-13-dev_1:13.0.0-8 libomp5-13_1:13.0.0-8 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libquadmath0_11.2.0-10 libseccomp2_2.5.2-2 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 libsub-override-perl_0.09-2 libsystemd0_249.5-1 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-10 libubsan1_11.2.0-10 libuchardet0_0.0.7-1 libudev1_249.5-1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libz3-4_4.8.12-1+b1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.14.12-1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 qt5-qmake_5.15.2+dfsg-12 qt5-qmake-bin_5.15.2+dfsg-12 qtchooser_66-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 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: 3.11-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper-compat (= 13) Package-List: fastml deb science optional arch=any Checksums-Sha1: 2bc5d72d636c37c0890c36b7e426d24131bfac8d 849058 fastml_3.11.orig.tar.gz 048ab93c1c1d67bea8c949b2026e9a25dc117a1c 9984 fastml_3.11-3.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz f9a00304da244a0bc0561a3723a633bc9690766687c46c11ea8af18aa5223617 9984 fastml_3.11-3.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz ba33f9cb4200207ddb91e8e805b80ae8 9984 fastml_3.11-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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14:38:59 2020 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_3.11-3.dsc dpkg-source: info: extracting fastml in /<> dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-3.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-c6aea9a8-07cf-45c2-8fab-09d441927790 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 3.11-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Entering directory '/<>/programs/gainLoss' make[4]: Leaving directory '/<>/libs/phylogeny' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/<>/programs/fastml' make[3]: Leaving directory '/<>/libs' make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/programs/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 binary dh binary 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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlpha.cpp:371:10: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] MDOUBLE oldA=0; ^ g++ -g -O2 -ffile-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; ^ bestAlphaManyTrees.cpp:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ bestAlphaManyTrees.cpp:184:13: warning: variable 'bx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ bestAlphaManyTrees.cpp:184:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^ g++ -g -O2 -ffile-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; ^ 5 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp 3 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp computeSubstitutionCounts.cpp:16:50: warning: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ _isSilent(isSilent) _LpostPerSpPerCat(LpostPerSpPerCat) computeSubstitutionCounts.cpp:16:50: note: field '_LpostPerSpPerCat' will be initialized after field '_simulationsIterNum' _tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:16:128: note: field '_probCutOffSum' will be initialized after field '_isSilent' _tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp 1 warning generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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. 2 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -ffile-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 -ffile-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 -ffile-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){ ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _pProportionDist(pProportionDist) _nodeID(nodeID) 1 warning generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] MDOUBLE oldIntervalSize = currentIntervalSize; ^ likeDistfixRoot.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] MDOUBLE oldIntervalSize = currentIntervalSize; ^ 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; ^ In file included from likeDistProp.cpp:3: ./likeDistProp.h:13:12: warning: private field '_alphabetSize' is not used [-Wunused-private-field] const int _alphabetSize; ^ 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; ^ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp 1 warning generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp 2 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp 3 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^ sequenceContainer.cpp:199:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^ 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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp 5 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp 2 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp g++ -g -O2 -ffile-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); ^ ./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); ^ 1 warning generated. g++ -g -O2 -ffile-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){}; ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _pProportionDist(pProportionDist) _weights(weights) _sp(sp) 2 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 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; ^ 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; ^ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp 2 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp 3 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp matrixUtils.cpp:220:10: warning: variable 'squareSum' set but not used [-Wunused-but-set-variable] MDOUBLE squareSum=0.0; ^ g++ -g -O2 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp betaDistribution.cpp:24:2: warning: field '_boundary' will be initialized after field '_alpha' [-Wreorder-ctor] _boundary(other._boundary), ^~~~~~~~~~~~~~~~~~~~~~~~~~ _alpha(other._alpha) g++ -g -O2 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp 1 warning generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp 1 warning generated. g++ -g -O2 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp 4 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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) ~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~ ~~~~~ _r(r) _Lambda1(Lambda1) _Lambda2(Lambda2) seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] const alphabet* pAlph = sc.getAlphabet(); ^ 1 warning generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp suffStatGammaMixture.cpp:123:12: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] MDOUBLE Exp_Rk, Exp_LogRk, sum; ^ 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:228:11: warning: unused variable 'fifth' [-Wunused-variable] MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); ^ suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable] MDOUBLE fourth = -_AkVec[comp]*beta_k; ^ suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable] MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); ^ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] MDOUBLE res2 = 0.0; ^ 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. 4 warnings generated. g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp 7 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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) ~~~~~~~~~ ~~~~~~~~~ ~~~~~~~~~ ~~~~~~~~~ ~~~~~~~~~ ^~~~~~~~~ ~~~~~~~~~~~ _freq(freq) _a2c(a2c) _a2g(a2g) _a2t(a2t) _c2g(c2g) _c2t(c2t) _g2t(g2t) 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 -ffile-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 -ffile-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){}; ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _pProportionDist(pProportionDist) _weights(weights) _sp(sp) 19 warnings generated. 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); ^ ./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/fastml' making depend make[3]: Entering directory '/<>/programs/indelCoder' make[3]: Entering directory '/<>/programs/gainLoss' making depend making depend g++ -g -O2 -ffile-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 -ffile-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 -ffile-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:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; ^ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^ g++ -g -O2 -ffile-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;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _minNumOfNodesToVisit(minNumOfNodesToVisit) _reportFileName(reportFileName) 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 -ffile-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 -ffile-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 -ffile-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;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _minNumOfNodesToVisit(minNumOfNodesToVisit) _reportFileName(reportFileName) 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; ^~~~~~~~~~ bbAlg.cpp:14:2: warning: initializer order does not match the declaration order [-Wreorder-ctor] gainLossOptions.cpp _reportFileName(reportFileName), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _et(et) bbAlg.cpp:14:2: note: field '_reportFileName' will be initialized after field 'BandBReportAllPos1' _reportFileName(reportFileName), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bbAlg.cpp:15:2: note: field 'BandBReportAllPos1' will be initialized after field '_et' BandBReportAllPos1(reportFileName,et.getInternalNodesNum()*spVec[0].alphabetSize()*sc.seqLen()), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :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; ^ 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 -ffile-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 -ffile-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 3 warnings generated. g++ -g -O2 -ffile-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 -ffile-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 -ffile-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 g++ -g -O2 -ffile-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 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) { ^~~~~~~ ~~~~~~~~~~~~~ _bbcpij(cpij) _sc(sc) bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] MDOUBLE rate = _sp.rates(categor); // the r. ^ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from 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; ^ 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){ ^~~~~~~ ~~~~~~~~~~~ _cpij(cpij) _sc(sc) 4 warnings generated. g++ -g -O2 -ffile-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 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 -ffile-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 bb_options.cpp:11:2: warning: initializer order does not match the declaration order [-Wreorder-ctor] reportFile("log.txt"), ^~~~~~~~~~~~~~~~~~~~~ seqfile("") bb_options.cpp:11:2: note: field 'reportFile' will be initialized after field 'outFile_seq_joint' reportFile("log.txt"), ^~~~~~~~~~~~~~~~~~~~~ bb_options.cpp:13:2: note: field 'outFile_seq_marginal' will be initialized after field 'outFile_prob_joint' outFile_seq_marginal("seq.marginal.txt"), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bb_options.cpp:15:2: note: field 'outFile_prob_marginal' will be initialized after field 'seqfile' outFile_prob_marginal("prob.marginal.txt"), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bb_options.cpp:17:5: note: field 'distributionName' will be initialized after field 'seqOutputFormat' distributionName(hom), ^~~~~~~~~~~~~~~~~~~~~ bb_options.cpp:20:5: note: field 'outTreeFileAncestor' will be initialized after field 'boundMethod' outTreeFileAncestor("tree.ancestor.txt"), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bb_options.cpp:22:2: note: field 'gammaPar' will be initialized after field 'userProvideAlpha' gammaPar(1.0), ^~~~~~~~~~~~~ bb_options.cpp:24:2: note: field 'gammaCategies' will be initialized after field 'modelName' gammaCategies(8), ^~~~~~~~~~~~~~~~ bb_options.cpp:28:2: note: field 'useChebyshev' will be initialized after field 'treeOutFile' 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() { ^ 2 warnings generated. g++ -g -O2 -ffile-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;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _minNumOfNodesToVisit(minNumOfNodesToVisit) _reportFileName(reportFileName) bbReport.cpp:11:2: warning: field '_reportFileName' will be initialized after field '_position' [-Wreorder-ctor] _reportFileName(reportFileName), _position(position), _alphabetSize(alphabetSize) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ _position(position) _alphabetSize(alphabetSize) _reportFileName(reportFileName) 3 warnings generated. 3 warnings generated. g++ -g -O2 -ffile-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 g++ -g -O2 -ffile-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 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; ^ 2 warnings generated. g++ -g -O2 -ffile-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 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 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _weights(weights) _unObservableData_p(unObservableData_p) ./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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _weights(weights) _unObservableData_p(unObservableData_p) gainLoss.cpp:63:33: warning: initializer order does not match the declaration order [-Wreorder-ctor] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ _gainDist(NULL) _unObservableData_p(NULL) _weightsUniqPatterns(NULL) _refSeq(NULL) gainLoss.cpp:63:33: note: field '_unObservableData_p' will be initialized after field '_lossDist' gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:63:59: note: field '_lossDist' will be initialized after field '_gainDist' gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~~~~~~~~ gainLoss.cpp:63:93: note: field '_refSeq' will be initialized after field '_weightsUniqPatterns' gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~~~~~~ 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;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _minNumOfNodesToVisit(minNumOfNodesToVisit) _reportFileName(reportFileName) gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] char missigDataChar = -2; ^ 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){}; ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _pProportionDist(pProportionDist) _weights(weights) _sp(sp) 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()){ ^ ( ) 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; ^ 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); ^ 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 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; ^ 2 warnings generated. g++ -g -O2 -ffile-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:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^ gainLoss.cpp:4283:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^ 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){ ^ ( ) gainLoss.cpp:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^ 2 warnings generated. g++ -g -O2 -ffile-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 g++ -g -O2 -ffile-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 -ffile-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 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; ^ 12 warnings generated. ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) gainLossUtils.cpp:75:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else //print losses ^ gainLossUtils.cpp:91:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else //print losses ^ 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 gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] MDOUBLE normFactor; ^ 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) optimizeGainLossModel.cpp:25:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights), _unObservableData_p(unObservableData_p) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _unObservableData_p(unObservableData_p) _weightsUniqPatterns(weights) optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^ make[3]: Leaving directory '/<>/programs/fastml' g++ -g -O2 -ffile-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; ^ 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) optimizeGainLossModelVV.cpp:32:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor] _weightsUniqPatterns(weights),_unObservableData_p(unObservableData_p) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _unObservableData_p(unObservableData_p) _weightsUniqPatterns(weights) optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); ^ 6 warnings generated. g++ -g -O2 -ffile-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 optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^ 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(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) gainLossModel.cpp:25:1: warning: initializer order does not match the declaration order [-Wreorder-ctor] _gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){ ^~~~~~~~~ ~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ _freq(freq) _gain(m1) _q2pt(NULL) _isRootFreqEQstationary(isRootFreqEQstationary) _isHGT_normal_Pij(isHGT_normal_Pij) _isHGT_with_Q(isHGT_with_Q) gainLossModel.cpp:25:1: note: field '_gain' will be initialized after field '_freq' _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: note: field '_isRootFreqEQstationary' will be initialized after field '_isReversible' _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: note: field '_isHGT_with_Q' will be initialized after field '_q2pt' _gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. g++ -g -O2 -ffile-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 8 warnings generated. g++ -g -O2 -ffile-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 3 warnings generated. g++ -g -O2 -ffile-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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 2 warnings generated. g++ -g -O2 -ffile-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 -ffile-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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _weights(weights) _unObservableData_p(unObservableData_p) ./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) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ _weights(weights) _unObservableData_p(unObservableData_p) gainLossOptimizer.cpp:31:1: warning: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc), ^~~~~~~ ~~~~~~~ ~~~~~~~ _epsilonOptimization(epsilonOptimization) _maxNumOfIterations(numIterations) _epsilonOptimizationModel(epsilonOptimizationModel) gainLossOptimizer.cpp:31:1: note: field '_tr' will be initialized after field '_sp' _tr(tr),_sp(sp),_sc(sc), ^~~~~~~ gainLossOptimizer.cpp:31:17: note: field '_sc' will be initialized after field '_epsilonOptimization' _tr(tr),_sp(sp),_sc(sc), ^~~~~~~ gainLossOptimizer.cpp:35:1: note: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' _weightsUniqPatterns(weights), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:57:45: warning: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist), ~~~~~~~ ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~ _epsilonOptimization(epsilonOptimization) _maxNumOfIterations(numIterations) _epsilonOptimizationModel(epsilonOptimizationModel) _maxNumOfIterationsModel(numIterationsModel) gainLossOptimizer.cpp:57:45: note: field '_lossDist' will be initialized after field '_sc' _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist), ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:58:1: note: field '_sc' will be initialized after field '_epsilonOptimization' _sc(sc),//_spSimple(spSimple), // ignore sent model, make new one ^~~~~~~ gainLossOptimizer.cpp:62:1: note: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' _weightsUniqPatterns(weights), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. g++ -g -O2 -ffile-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:487:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^ gainLossOptimizer.cpp:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^ gainLossOptimizer.cpp: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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 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) ^~~~~~~ ~~~~~~~ _sp(sp) _tr(tr) 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: 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 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; ^ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from 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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 10 warnings generated. g++ -g -O2 -ffile-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: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^~~~~~~ ~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ _sp(sp) _tr(tr) _isSilent(isSilent) _postProbPerCatPerPos(logLpostPerCatPerPos) _distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent) computeCountsGL.cpp:29:1: note: field '_tr' will be initialized after field '_sp' _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^~~~~~~ computeCountsGL.cpp:29:85: note: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' _tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.cpp:34:47: warning: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~ ~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ _sc(sc) _spVVec(spVVec) _gainDist(gainDist) _lossDist(lossDist) _isSilent(isSilent) _postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos) _distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent) computeCountsGL.cpp:34:47: note: field '_lossDist' will be initialized after field '_sc' _tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent) ^~~~~~~~~~~~~~~~~~~ computeCountsGL.cpp:34:145: note: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' _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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) 20 warnings generated. g++ -g -O2 -ffile-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:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^ 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:676:9: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationsInRange = 1; ^ computeCorrelations.cpp:677:9: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; ^ computeCorrelations.cpp:679:9: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin ^ computeCorrelations.cpp:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] bool isNextLowerBinAllowed = true; ^ computeCorrelations.cpp: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) ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) _loss(m2) gainLoss4site.cpp:25:1: warning: initializer order does not match the declaration order [-Wreorder-ctor] _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf) ^~~~~~~ ~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ _spVVec(spVVec) _gainDist(gainDist) _lossDist(lossDist) _tr(tr) _alphaConf(alphaConf) _unObservableData_p(unObservableData_p) gainLoss4site.cpp:25:1: note: field '_tr' will be initialized after field '_spVVec' _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf) ^~~~~~~ gainLoss4site.cpp:25:89: note: field '_unObservableData_p' will be initialized after field '_alphaConf' _tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; ^ 26 warnings and 1 error generated. make[3]: *** [: computeCorrelations.o] Error 1 make[3]: *** Waiting for unfinished jobs.... 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; ^ 8 warnings generated. 9 warnings generated. 23 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: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-10-26T21:44:21Z 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: 144340 Build-Time: 78 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 4 Job: fastml_3.11-3 Machine Architecture: amd64 Package: fastml Package-Time: 103 Source-Version: 3.11-3 Space: 144340 Status: attempted Version: 3.11-3 -------------------------------------------------------------------------------- Finished at 2021-10-26T21:44:21Z Build needed 00:01:43, 144340k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 103.903456478s DC-Time-Estimation: 103.903456478 versus expected 321 (r/m: 2.0894063670342566 ; m: 103.903456478)