DC-Build-Header: fastml 3.11-3 / 2021-10-26 21:42:55 +0000
DC-Task: type:rebuild-binarch-only source:fastml version:3.11-3 chroot:unstable esttime:321 logfile:/tmp/fastml_3.11-3_unstable_clang12.log modes:clang12:binarch-only
DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang12 fastml_3.11-3'
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-5-178.eu-central-1.compute.internal

+==============================================================================+
| fastml 3.11-3 (amd64)                        Tue, 26 Oct 2021 21:42:55 +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-61d48247-4722-44fc-9cfd-49992a1c2e92' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


/tmp/clang12
------------

+ echo 'Entering customization script...'
Entering customization script...
+ CLANG_VERSION=12
+ echo 'Install of clang-12'
Install of clang-12
+ 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 (2681 kB/s)
Reading package lists...
+ apt-get install --yes --no-install-recommends --force-yes clang-12 libomp-12-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-12-dev
  libclang-cpp12 libclang1-12 libedit2 libelf1 libgc1 libgcc-9-dev libicu67
  libllvm12 libmd0 libobjc-11-dev libobjc4 libomp5-12 libunwind-12 libxml2
  libz3-4 llvm-12-linker-tools
Suggested packages:
  clang-12-doc libomp-12-doc
Recommended packages:
  llvm-12-dev python3
The following NEW packages will be installed:
  clang-12 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386
  libclang-common-12-dev libclang-cpp12 libclang1-12 libedit2 libelf1 libgc1
  libgcc-9-dev libicu67 libllvm12 libmd0 libobjc-11-dev libobjc-9-dev libobjc4
  libomp-12-dev libomp5-12 libunwind-12 libxml2 libz3-4 llvm-12-linker-tools
0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded.
Need to get 67.6 MB of archives.
After this operation, 349 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 libllvm12 amd64 1:12.0.1-15 [19.4 MB]
Get:8 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp12 amd64 1:12.0.1-15 [9996 kB]
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-12-dev amd64 1:12.0.1-15 [4819 kB]
Get:16 http://127.0.0.1:12990/debian sid/main amd64 llvm-12-linker-tools amd64 1:12.0.1-15 [1222 kB]
Get:17 http://127.0.0.1:12990/debian sid/main amd64 libclang1-12 amd64 1:12.0.1-15 [5644 kB]
Get:18 http://127.0.0.1:12990/debian sid/main amd64 clang-12 amd64 1:12.0.1-15 [117 kB]
Get:19 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.4.0-3 [2734 kB]
Get:20 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.185-2 [172 kB]
Get:21 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.4.0-3 [2343 kB]
Get:22 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.4.0-3 [219 kB]
Get:23 http://127.0.0.1:12990/debian sid/main amd64 libunwind-12 amd64 1:12.0.1-15 [63.9 kB]
Get:24 http://127.0.0.1:12990/debian sid/main amd64 libomp5-12 amd64 1:12.0.1-15 [405 kB]
Get:25 http://127.0.0.1:12990/debian sid/main amd64 libomp-12-dev amd64 1:12.0.1-15 [104 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.6 MB in 0s (152 MB/s)
Selecting previously unselected package libmd0:amd64.
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(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.
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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) ...
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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 libllvm12:amd64.
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Unpacking libllvm12:amd64 (1:12.0.1-15) ...
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Preparing to unpack .../07-libclang-cpp12_1%3a12.0.1-15_amd64.deb ...
Unpacking libclang-cpp12 (1:12.0.1-15) ...
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) ...
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Unpacking lib32stdc++6 (11.2.0-10) ...
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Unpacking libgcc-9-dev:amd64 (9.4.0-3) ...
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Unpacking libobjc-9-dev:amd64 (9.4.0-3) ...
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Setting up libasan5:amd64 (9.4.0-3) ...
Setting up libz3-4:amd64 (4.8.12-1+b1) ...
Setting up libunwind-12:amd64 (1:12.0.1-15) ...
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 libbsd0:amd64 (0.11.3-1) ...
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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 libllvm12:amd64 (1:12.0.1-15) ...
Setting up libobjc-9-dev:amd64 (9.4.0-3) ...
Setting up libclang-common-12-dev (1:12.0.1-15) ...
Setting up libomp5-12:amd64 (1:12.0.1-15) ...
Setting up libobjc-11-dev:amd64 (11.2.0-10) ...
Setting up llvm-12-linker-tools (1:12.0.1-15) ...
Setting up libclang1-12 (1:12.0.1-15) ...
Setting up libclang-cpp12 (1:12.0.1-15) ...
Setting up libomp-12-dev (1:12.0.1-15) ...
Setting up clang-12 (1:12.0.1-15) ...
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++-12 g++-4.6
+ ln -s clang-12 gcc-4.6
+ ln -s clang-12 cpp-4.6
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc
+ ln -s clang++-12 g++-4.7
+ ln -s clang-12 gcc-4.7
+ ln -s clang-12 cpp-4.7
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc
+ ln -s clang++-12 g++-4.8
+ ln -s clang-12 gcc-4.8
+ ln -s clang-12 cpp-4.8
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc
+ ln -s clang++-12 g++-4.9
+ ln -s clang-12 gcc-4.9
+ ln -s clang-12 cpp-4.9
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-5 gcc-5 cpp-5 gcc
+ ln -s clang++-12 g++-5
+ ln -s clang-12 gcc-5
+ ln -s clang-12 cpp-5
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-6 gcc-6 cpp-6 gcc
+ ln -s clang++-12 g++-6
+ ln -s clang-12 gcc-6
+ ln -s clang-12 cpp-6
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-7 gcc-7 cpp-7 gcc
+ ln -s clang++-12 g++-7
+ ln -s clang-12 gcc-7
+ ln -s clang-12 cpp-7
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-8 gcc-8 cpp-8 gcc
+ ln -s clang++-12 g++-8
+ ln -s clang-12 gcc-8
+ ln -s clang-12 cpp-8
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-9 gcc-9 cpp-9 gcc
+ ln -s clang++-12 g++-9
+ ln -s clang-12 gcc-9
+ ln -s clang-12 cpp-9
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-10 gcc-10 cpp-10 gcc
+ ln -s clang++-12 g++-10
+ ln -s clang-12 gcc-10
+ ln -s clang-12 cpp-10
+ ln -s clang-12 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 <https://wiki.debian.org/Teams/Dpkg/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 <https://wiki.debian.org/Teams/Dpkg/FAQ>
+ for VERSION in $VERSIONS
+ rm -f g++-11 gcc-11 cpp-11 gcc
+ ln -s clang++-12 g++-11
+ ln -s clang-12 gcc-11
+ ln -s clang-12 cpp-11
+ ln -s clang-12 gcc
+ echo 'gcc-11 hold'
+ dpkg --set-selections
+ echo 'g++-11 hold'
+ dpkg --set-selections
+ cd -
/build/fastml-oAGIok
+ 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-12 clang++
+ ln -s clang-12 clang
+ clang++ --version
Debian clang version 12.0.1-15
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
+ clang --version
Debian clang version 12.0.1-15
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
+ cd -
/build/fastml-oAGIok
+ 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 (57.3 MB/s)
Selecting previously unselected package qt5-qmake-bin.
(Reading database ... 
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(Reading database ... 13527 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 21:43 .
drwxr-xr-x 76 root root 4096 Oct 26 21:43 ..
-rw-r--r--  1 root root  276 Oct 26 21:43 qmake.conf
-rw-r--r--  1 root root 3218 Oct 26 21:43 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/clang12'.

Finished processing commands.
--------------------------------------------------------------------------------
I: NOTICE: Log filtering will replace 'build/fastml-oAGIok/resolver-AsV0dX' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| 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 (8789 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fastml-oAGIok/fastml-3.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fastml-oAGIok' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| 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 '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [370 B]
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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
  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
  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, 29 newly installed, 0 to remove and 0 not upgraded.
Need to get 8809 kB of archives.
After this operation, 30.8 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [876 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 dwz amd64 0.14-1 [98.3 kB]
Get:26 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.21-4 [1311 kB]
Get:27 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:28 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:29 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
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Setting up libpipeline1:amd64 (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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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 dwz (0.14-1) ...
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 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 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-12_1:12.0.1-15 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-12-dev_1:12.0.1-15 libclang-cpp12_1:12.0.1-15 libclang1-12_1:12.0.1-15 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 libllvm12_1:12.0.1-15 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-12-dev_1:12.0.1-15 libomp5-12_1:12.0.1-15 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 libunwind-12_1:12.0.1-15 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 llvm-12-linker-tools_1:12.0.1-15 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.VvKAVTND/trustedkeys.kbx': General error
gpgv: Signature made Thu Dec 17 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 /<<PKGBUILDDIR>>
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-61d48247-4722-44fc-9cfd-49992a1c2e92
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 <tille@debian.org>
 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 '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd libs;make clean
cd programs;make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make clean
cd gainLoss && make clean
cd indelCoder && make clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml  fastml.debug fastml.doubleRep *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
make[4]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a   *.o
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder  indelCoder.debug indelCoder.doubleRep *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss  gainLoss.debug gainLoss.doubleRep *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f libs/phylogeny/make.dep \
      programs/fastml/make.dep \
      programs/gainLoss/make.dep \
      programs/indelCoder/make.dep
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules 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 '/<<PKGBUILDDIR>>'
cd libs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
making depend
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestHKYparam.o bestHKYparam.cpp
In file included from bestAlpha.cpp:6:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bootstrap.o bootstrap.cpp
In file included from bestAlphaManyTrees.cpp:7:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from bestHKYparam.cpp:3:
./bestHKYparam.h:82:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from bestHKYparam.cpp:12:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEM.o bblEM.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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: field '_LpostPerSpPerCat' will be initialized after field '_simulationsIterNum' [-Wreorder-ctor]
_tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent)
                                                 ^
computeSubstitutionCounts.cpp:16:128: warning: field '_probCutOffSum' will be initialized after field '_isSilent' [-Wreorder-ctor]
_tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent)
                                                                                                                               ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fastaFormat.o fastaFormat.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o findRateOfGene.o findRateOfGene.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp
In file included from fromCountTableComponentToDistance.cpp:4:
./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from fromCountTableComponentToDistancefixRoot.cpp:4:
./likeDistfixRoot.h:113:21: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData*  _unObservableData_p;
                           ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromQtoPt.o fromQtoPt.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaDistribution.o gammaDistribution.cpp
fromCountTableComponentToDistancePropEB.cpp:12:60: warning: field '_nodeID' will be initialized after field '_pProportionDist' [-Wreorder-ctor]
                const MDOUBLE brLenIntialGuess ) : _msp(msp), _ctc(ctc), _nodeID(nodeID), _pProportionDist(pProportionDist){
                                                                         ^
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDistProp.o likeDistProp.cpp
In file included from likeDist.cpp:3:
./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDistPropEB.o likeDistPropEB.cpp
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;
                           ^
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputation.o likelihoodComputation.cpp
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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<n;i++) e[i-1]=e[i];
 ^
numRec.cpp:307:2: warning: '/*' within block comment [-Wcomment]
//*     e[n-1]=0.0;
 ^
numRec.cpp:308:2: warning: '/*' within block comment [-Wcomment]
//*     e.push_back(0);//since in my algorithm I return an n-1 sized e
 ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateTree.o simulateTree.cpp
sequenceContainer.cpp:259:27: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                        if ((_seqDataVec[j][i] == -3)) {
                             ~~~~~~~~~~~~~~~~~~^~~~~
sequenceContainer.cpp:259:27: note: remove extraneous parentheses around the comparison to silence this warning
                        if ((_seqDataVec[j][i] == -3)) {
                            ~                  ^    ~
sequenceContainer.cpp:259:27: note: use '=' to turn this equality comparison into an assignment
                        if ((_seqDataVec[j][i] == -3)) {
                                               ^~
                                               =
sequenceContainer.cpp:452:12: warning: unused variable 'len' [-Wunused-variable]
        const int len = _seqDataVec[0].seqLen();
                  ^
sequenceContainer.cpp:467:12: warning: unused variable 'len' [-Wunused-variable]
        const int len = _seqDataVec[0].seqLen();
                  ^
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o someUtil.o someUtil.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o split.o split.cpp
3 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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){};
                                                ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o matrixUtils.o matrixUtils.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp
In file included from bestAlphaAndNu.cpp:5:
In file included from ./bestAlphaAndNu.h:15:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o geneticCodeHolder.o geneticCodeHolder.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o samplingSequences.o samplingSequences.cpp
betaDistribution.cpp:24:2: warning: field '_boundary' will be initialized after field '_alpha' [-Wreorder-ctor]
        _boundary(other._boundary),
        ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestParamUSSRV.o bestParamUSSRV.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o ussrvModel.o ussrvModel.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
In file included from bestParamUSSRV.cpp:2:
In file included from ./bestParamUSSRV.h:13:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateCodonsJumps.o simulateCodonsJumps.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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp
computeJumps.cpp:257:22: warning: field '_Lambda2' will be initialized after field '_r' [-Wreorder-ctor]
: _Lambda1(Lambda1), _Lambda2(Lambda2), _r(r)
                     ^
seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable]
        const alphabet* pAlph = sc.getAlphabet();
                        ^
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
                                                                ^~
                                                                =
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o GamMixtureOptimizer.o GamMixtureOptimizer.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
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:224:11: warning: unused variable 'first' [-Wunused-variable]
                MDOUBLE first = _MkVec[comp] * log(P_k);
                        ^
suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable]
                MDOUBLE third = -_MkVec[comp] * gammln(alpha_k);
                        ^
suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable]
                MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0);
                        ^
In file included from GamMixtureOptimizer.cpp:3:
./optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable]
                MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); 
                        ^
./optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable]
                MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); 
                        ^
1 warning generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
4 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gainLossAlphabet.o gainLossAlphabet.cpp
5 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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))); 
                        ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o codonUtils.o codonUtils.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestGtrModelParams.o bestGtrModelParams.cpp
gtrModel.cpp:12:59: warning: field '_g2t' will be initialized after field '_freq' [-Wreorder-ctor]
                                          :_a2c(a2c),_a2g(a2g),_a2t(a2t),_c2g(c2g),_c2t(c2t),_g2t(g2t),_freq(freq)
                                                                                             ^
gtrModel.cpp:134:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:139:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:134:3: note: remove the 'if' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:134:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:139:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:134:6: note: remove the '||' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[c].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:131:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:139:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:131:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:130:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
gtrModel.cpp:148:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:153:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:148:3: note: remove the 'if' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:148:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:153:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:148:6: note: remove the '||' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:145:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:153:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:145:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:144:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
gtrModel.cpp:162:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:167:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:162:3: note: remove the 'if' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:162:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:167:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:162:6: note: remove the '||' if its condition is always false
                if((_Q[a].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:159:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:167:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:159:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:158:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
gtrModel.cpp:176:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:181:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:176:3: note: remove the 'if' if its condition is always false
                if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:176:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:181:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:176:6: note: remove the '||' if its condition is always false
                if((_Q[c].size() < alphabetSize())||(_Q[g].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:173:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:181:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:173:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:172:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
gtrModel.cpp:190:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:195:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:190:3: note: remove the 'if' if its condition is always false
                if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:190:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:195:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:190:6: note: remove the '||' if its condition is always false
                if((_Q[c].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:187:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:195:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:187:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:186:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
gtrModel.cpp:204:6: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
                if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:209:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:204:3: note: remove the 'if' if its condition is always false
                if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:204:6: warning: variable 'result' is used uninitialized whenever '||' condition is true [-Wsometimes-uninitialized]
                if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:209:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:204:6: note: remove the '||' if its condition is always false
                if((_Q[g].size() < alphabetSize())||(_Q[t].size() < alphabetSize()))
                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:201:5: warning: variable 'result' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
        if(_Q.size() < alphabetSize())
           ^~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:209:9: note: uninitialized use occurs here
        return result;
               ^~~~~~
gtrModel.cpp:201:2: note: remove the 'if' if its condition is always false
        if(_Q.size() < alphabetSize())
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gtrModel.cpp:200:16: note: initialize the variable 'result' to silence this warning
        MDOUBLE result;
                      ^
                       = 0.0
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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){};
                                                ^
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 <tree::nodeP> 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 '/<<PKGBUILDDIR>>/libs/phylogeny'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
cd programs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make all
cd gainLoss && make all
cd indelCoder && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
making depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
making depend
making depend
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o fastml.o fastml.cpp
indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable]
        int gapNum = 1;
            ^
indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable]
        int seqLeng = _sc.seqLen();
            ^
indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable]
        bool isSIC  = indelCoderOptions::_codingType == indelCoderOptions::SIC;
             ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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;}
                  ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossOptions.o gainLossOptions.cpp
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() {
                    ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o indelCoderUtils.o indelCoderUtils.cpp
gainLossOptions.cpp:2060:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="Vhigh")
                 ^~~~~~~~~~~~
gainLossOptions.cpp:2064:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2060:7: note: remove the 'if' if its condition is always true
        else if (str=="Vhigh")
             ^~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2047:2: note: variable 'returnType' is declared here
        optimizationLevel returnType;
        ^
In file included from bbAlg.cpp:1:
In file included from ./bbAlg.h:8:
./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder-ctor]
                : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;}
                  ^
gainLossOptions.cpp:2107:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="gainLossCost")
                 ^~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2111:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2107:7: note: remove the 'if' if its condition is always true
        else if (str=="gainLossCost")
             ^~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2098:2: note: variable 'returnType' is declared here
        costMatrixType returnType;
        ^
gainLossOptions.cpp:2415:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="Gam_gVrl")
                 ^~~~~~~~~~~~~~~
gainLossOptions.cpp:2419:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2415:7: note: remove the 'if' if its condition is always true
        else if (str=="Gam_gVrl")
             ^~~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2396:2: note: variable 'returnType' is declared here
        simulationType returnType;
        ^
bbAlg.cpp:14:2: warning: field '_reportFileName' will be initialized after field 'BandBReportAllPos1' [-Wreorder-ctor]
        _reportFileName(reportFileName),
        ^
bbAlg.cpp:15:2: warning: field 'BandBReportAllPos1' will be initialized after field '_et' [-Wreorder-ctor]
        BandBReportAllPos1(reportFileName,et.getInternalNodesNum()*spVec[0].alphabetSize()*sc.seqLen()),
        ^
In file included from bbAlg.cpp:1:
In file included from ./bbAlg.h:5:
In file included from ./bbNodeOrderAlg.h:5:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gaps.o gaps.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbComputeDownAlg.o bbComputeDownAlg.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
4 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp
bbEvaluateSpecificAV.cpp:6:53: warning: field '_sc' will be initialized after field '_bbcpij' [-Wreorder-ctor]
                                        const computePijGam& cpij) : _et(et), _sp(sp), _sc(sc), _bbcpij(cpij) {
                                                                                       ^
bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable]
                        MDOUBLE rate = _sp.rates(categor); // the r.
                                ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp
In file included from bbEvaluateSpecificAV.cpp:1:
In file included from ./bbEvaluateSpecificAV.h:4:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
In file included from bbEvaluateSpecificAV.cpp:1:
./bbEvaluateSpecificAV.h:33:6: warning: private field '_pos' is not used [-Wunused-private-field]
        int _pos;
            ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp
4 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bb_options.o bb_options.cpp
In file included from bbfindBestAVDynProg.cpp:1:
In file included from ./bbfindBestAVDynProg.h:5:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
In file included from bbfindBestAVDynProg.cpp:1:
./bbfindBestAVDynProg.h:31:6: warning: private field '_pos' is not used [-Wunused-private-field]
        int _pos;
            ^
bbNodeOrderAlg.cpp:12:64: warning: field '_sc' will be initialized after field '_cpij' [-Wreorder-ctor]
                                        const MDOUBLE computeAgainExactTreshold) :_et(et),_sp(sp),_sc(sc),_cpij(cpij){
                                                                                                  ^
bb_options.cpp:11:2: warning: field 'reportFile' will be initialized after field 'outFile_seq_joint' [-Wreorder-ctor]
        reportFile("log.txt"),
        ^
bb_options.cpp:13:2: warning: field 'outFile_seq_marginal' will be initialized after field 'outFile_prob_joint' [-Wreorder-ctor]
        outFile_seq_marginal("seq.marginal.txt"),
        ^
bb_options.cpp:15:2: warning: field 'outFile_prob_marginal' will be initialized after field 'seqfile' [-Wreorder-ctor]
        outFile_prob_marginal("prob.marginal.txt"),
        ^
bb_options.cpp:17:5: warning: field 'distributionName' will be initialized after field 'seqOutputFormat' [-Wreorder-ctor]
    distributionName(hom),
    ^
bb_options.cpp:20:5: warning: field 'outTreeFileAncestor' will be initialized after field 'boundMethod' [-Wreorder-ctor]
    outTreeFileAncestor("tree.ancestor.txt"),
    ^
bb_options.cpp:22:2: warning: field 'gammaPar' will be initialized after field 'userProvideAlpha' [-Wreorder-ctor]
        gammaPar(1.0),
        ^
bb_options.cpp:24:2: warning: field 'gammaCategies' will be initialized after field 'modelName' [-Wreorder-ctor]
        gammaCategies(8),
        ^
bb_options.cpp:28:2: warning: field 'useChebyshev' will be initialized after field 'treeOutFile' [-Wreorder-ctor]
        useChebyshev(true),
        ^
In file included from bb_options.cpp:2:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
In file included from bbNodeOrderAlg.cpp:1:
In file included from ./bbNodeOrderAlg.h:5:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
In file included from bbNodeOrderAlg.cpp:1:
./bbNodeOrderAlg.h:40:6: warning: private field '_pos' is not used [-Wunused-private-field]
        int _pos;
            ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbReport.o bbReport.cpp
9 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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;}
                  ^
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;
                ^
bbReport.cpp:11:2: warning: field '_reportFileName' will be initialized after field '_position' [-Wreorder-ctor]
        _reportFileName(reportFileName), _position(position), _alphabetSize(alphabetSize)
        ^
3 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o jointNoGamma.o jointNoGamma.cpp
3 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLoss.o gainLoss.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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)   
                 ^
In file included from gainLoss.cpp:41:
./bblLS.h:50:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion]
                MDOUBLE curL =NULL);
                             ~^~~~
                              0.0
./bblLS.h:58:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion]
                MDOUBLE curL =NULL);    
                             ~^~~~
                              0.0
./bblLS.h:99:92: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor]
                :_pNode(pNode),_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights)
                                                                                                         ^
./bblLS.h:155:78: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor]
                :_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights)
                                                                                           ^
gainLoss.cpp:63:33: warning: field '_unObservableData_p' will be initialized after field '_lossDist' [-Wreorder-ctor]
gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
                                ^
gainLoss.cpp:63:59: warning: field '_lossDist' will be initialized after field '_gainDist' [-Wreorder-ctor]
gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
                                                          ^
gainLoss.cpp:63:93: warning: field '_refSeq' will be initialized after field '_weightsUniqPatterns' [-Wreorder-ctor]
gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
                                                                                            ^
In file included from mainbb.cpp: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;}
                  ^
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){};
                                                ^
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o sequenceDataDiff.o sequenceDataDiff.cpp
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp
gainLoss.cpp:4382:7: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
                        if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){
                           ^           ~
gainLoss.cpp:4382:7: note: add parentheses after the '!' to evaluate the comparison first
                        if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){
                           ^
                             (                                    )
gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning
                        if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){
                           ^
                           (          )
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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;
             ^
In file included from gainLossUtils.cpp:19:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
gainLossUtils.cpp:75:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                        else //print losses
                        ^
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<generalGammaDistribution*>(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<generalGammaDistribution*>(dist)){
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossUtils.cpp:285:13: note: initialize the variable 'res' to silence this warning
        MDOUBLE res;
                   ^
                    = 0.0
gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable]
        MDOUBLE scale;
                ^
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
In file included from optimizeGainLossModel.cpp:17:
In file included from ./optimizeGainLossModel.h:27:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
optimizeGainLossModel.cpp:25:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor]
_weightsUniqPatterns(weights), _unObservableData_p(unObservableData_p)
^
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 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;
                        ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp
5 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossModel.o gainLossModel.cpp
In file included from optimizeGainLossModelVV.cpp:17:
In file included from ./optimizeGainLossModelVV.h:27:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
optimizeGainLossModelVV.cpp:32:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor]
_weightsUniqPatterns(weights),_unObservableData_p(unObservableData_p)
^
optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable]
                                MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p);
                                        ^
In file included from optimizeGainLossModelVV.cpp:17:
In file included from ./optimizeGainLossModelVV.h:23:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from optimizeGainLossModelVV.cpp:17:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
In file included from gainLossModel.cpp:17:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
gainLossModel.cpp:25:1: warning: field '_gain' will be initialized after field '_freq' [-Wreorder-ctor]
_gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){
^
gainLossModel.cpp:25:23: warning: field '_isRootFreqEQstationary' will be initialized after field '_isReversible' [-Wreorder-ctor]
_gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){
                      ^
gainLossModel.cpp:25:135: warning: field '_isHGT_with_Q' will be initialized after field '_q2pt' [-Wreorder-ctor]
_gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){
                                                                                                                                      ^
6 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o siteSpecificGL.o siteSpecificGL.cpp
7 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp
5 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossProject.o gainLossProject.cpp
In file included from siteSpecificGL.cpp:24:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
In file included from computePosteriorExpectationOfChange.cpp:25:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
In file included from gainLossProject.cpp:17:
In file included from ./gainLoss.h:35:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp
In file included from gainLossOptimizer.cpp:17:
In file included from ./gainLossOptimizer.h:24:
In file included from ./gainLoss.h:35:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
In file included from gainLossOptimizer.cpp:20:
./bblLS.h:50:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion]
                MDOUBLE curL =NULL);
                             ~^~~~
                              0.0
./bblLS.h:58:17: warning: implicit conversion of NULL constant to 'double' [-Wnull-conversion]
                MDOUBLE curL =NULL);    
                             ~^~~~
                              0.0
./bblLS.h:99:92: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor]
                :_pNode(pNode),_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights)
                                                                                                         ^
./bblLS.h:155:78: warning: field '_unObservableData_p' will be initialized after field '_weights' [-Wreorder-ctor]
                :_tr(tr),_sc(sc),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_unObservableData_p(unObservableData_p),_weights(weights)
                                                                                           ^
gainLossOptimizer.cpp:31:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor]
_tr(tr),_sp(sp),_sc(sc),
^
gainLossOptimizer.cpp:31:17: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder-ctor]
_tr(tr),_sp(sp),_sc(sc),
                ^
gainLossOptimizer.cpp:35:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor]
_weightsUniqPatterns(weights),
^
gainLossOptimizer.cpp:57:45: warning: field '_lossDist' will be initialized after field '_sc' [-Wreorder-ctor]
_tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),
                                            ^
gainLossOptimizer.cpp:58:1: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder-ctor]
_sc(sc),//_spSimple(spSimple), // ignore sent model, make new one
^
gainLossOptimizer.cpp:62:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder-ctor]
_weightsUniqPatterns(weights),
^
gainLossOptimizer.cpp:498:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
                        MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL);
                                ^
gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
                        MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL);
                                ^
gainLossOptimizer.cpp:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
                        MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL);
                                ^
gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable]
                        MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL);
                                ^
gainLossOptimizer.cpp:827:11: warning: variable 'res' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (dynamic_cast<generalGammaDistribution*>(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<generalGammaDistribution*>(dist)){
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptimizer.cpp:820:2: note: variable 'res' is declared here
        gainLossOptions::distributionType res;
        ^
2 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o rate4siteGL.o rate4siteGL.cpp
In file included from gainLossOptimizer.cpp:17:
In file included from ./gainLossOptimizer.h:24:
In file included from ./gainLoss.h:24:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from gainLossOptimizer.cpp:17:
In file included from ./gainLossOptimizer.h:24:
In file included from ./gainLoss.h:42:
../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from gainLossOptimizer.cpp:17:
In file included from ./gainLossOptimizer.h:24:
In file included from ./gainLoss.h:51:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
In file included from rate4siteGL.cpp:17:
In file included from ./rate4siteGL.h:24:
In file included from ./gainLoss.h:35:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
rate4siteGL.cpp:25:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor]
_tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p)
^
rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable]
        int precisionLow = 3;
            ^
rate4siteGL.cpp:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable]
        int precisionHigh = 5;
            ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 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;
             ^
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)   
                 ^
computeCountsGL.cpp:29:1: warning: field '_tr' will be initialized after field '_sp' [-Wreorder-ctor]
_tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent)
^
computeCountsGL.cpp:29:85: warning: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' [-Wreorder-ctor]
_tr(tr),_sp(sp),_sc(sc),_outDir(outDir),_postProbPerCatPerPos(logLpostPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent)
                                                                                    ^
computeCountsGL.cpp:34:47: warning: field '_lossDist' will be initialized after field '_sc' [-Wreorder-ctor]
_tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent)
                                              ^
computeCountsGL.cpp:34:145: warning: field '_distanceFromNearestOTUForRecent' will be initialized after field '_isSilent' [-Wreorder-ctor]
_tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent)
                                                                                                                                                ^
10 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o computeCorrelations.o computeCorrelations.cpp
22 warnings generated.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLoss4site.o gainLoss4site.cpp
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:24:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:42:
../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:51:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
In file included from computeCorrelations.cpp:17:
In file included from ./computeCorrelations.h:25:
In file included from ./gainLoss.h:35:
./gainLossModel.h:171:7: warning: 'gainLossModelNonReversible::updateQ' hides overloaded virtual function [-Woverloaded-virtual]
        void updateQ(){
             ^
./gainLossModel.h:95:18: note: hidden overloaded virtual function 'gainLossModel::updateQ' declared here: different number of parameters (1 vs 0)
        virtual MDOUBLE updateQ(bool isReversible);
                        ^
./gainLossModel.h:128:4: warning: field '_loss' will be initialized after base 'gainLossModel' [-Wreorder-ctor]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable]
        int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node
            ^
computeCorrelations.cpp:408:8: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable]
                        int isHigherNminReducedFreqOfHighCorr = false;
                            ^
computeCorrelations.cpp:348:7: warning: unused variable 'typeIndex' [-Wunused-variable]
                int typeIndex = corIndex % _EventTypes.size();  // in case both Spearman and pearson are used
                    ^
computeCorrelations.cpp:559:21: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic]
        if(!simCorrelStream==NULL)
           ~~~~~~~~~~~~~~~~^ ~~~~
computeCorrelations.cpp:559:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
        if(!simCorrelStream==NULL)
           ^               ~~
computeCorrelations.cpp:559:5: note: add parentheses after the '!' to evaluate the comparison first
        if(!simCorrelStream==NULL)
           ^
            (                    )
computeCorrelations.cpp:559:5: note: add parentheses around left hand side expression to silence this warning
        if(!simCorrelStream==NULL)
           ^
           (               )
computeCorrelations.cpp:569:22: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic]
                if(!simCorrelStream==NULL)
                   ~~~~~~~~~~~~~~~~^ ~~~~
computeCorrelations.cpp:569:6: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
                if(!simCorrelStream==NULL)
                   ^               ~~
computeCorrelations.cpp:569:6: note: add parentheses after the '!' to evaluate the comparison first
                if(!simCorrelStream==NULL)
                   ^
                    (                    )
computeCorrelations.cpp:569:6: note: add parentheses around left hand side expression to silence this warning
                if(!simCorrelStream==NULL)
                   ^
                   (               )
computeCorrelations.cpp:579:22: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic]
                if(!simCorrelStream==NULL)
                   ~~~~~~~~~~~~~~~~^ ~~~~
computeCorrelations.cpp:579:6: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
                if(!simCorrelStream==NULL)
                   ^               ~~
computeCorrelations.cpp:579:6: note: add parentheses after the '!' to evaluate the comparison first
                if(!simCorrelStream==NULL)
                   ^
                    (                    )
computeCorrelations.cpp:579:6: note: add parentheses around left hand side expression to silence this warning
                if(!simCorrelStream==NULL)
                   ^
                   (               )
computeCorrelations.cpp:584:21: warning: comparison between NULL and non-pointer ('bool' and NULL) [-Wnull-arithmetic]
        if(!simCorrelStream==NULL)
           ~~~~~~~~~~~~~~~~^ ~~~~
computeCorrelations.cpp:584:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
        if(!simCorrelStream==NULL)
           ^               ~~
computeCorrelations.cpp:584:5: note: add parentheses after the '!' to evaluate the comparison first
        if(!simCorrelStream==NULL)
           ^
            (                    )
computeCorrelations.cpp:584:5: note: add parentheses around left hand side expression to silence this warning
        if(!simCorrelStream==NULL)
           ^
           (               )
computeCorrelations.cpp:679:9: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable]
                                int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin
                                    ^
computeCorrelations.cpp:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable]
                                bool isNextLowerBinAllowed = true;
                                     ^
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)   
                 ^
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
            ^
gainLoss4site.cpp:25:1: warning: field '_tr' will be initialized after field '_spVVec' [-Wreorder-ctor]
_tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf)
^
gainLoss4site.cpp:25:89: warning: field '_unObservableData_p' will be initialized after field '_alphaConf' [-Wreorder-ctor]
_tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),_sc(sc),_outDir(outDir),_unObservableData_p(unObservableData_p),_alphaConf(alphaConf)
                                                                                        ^
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<float>(                       )
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: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;
             ^
In file included from computeCorrelations.cpp:17:
In file included from ./computeCorrelations.h:25:
In file included from ./gainLoss.h:24:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from computeCorrelations.cpp:17:
In file included from ./computeCorrelations.h:25:
In file included from ./gainLoss.h:42:
../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from computeCorrelations.cpp:17:
In file included from ./computeCorrelations.h:25:
In file included from ./gainLoss.h:51:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
24 warnings and 1 error generated.
make[3]: *** [<builtin>: computeCorrelations.o] Error 1
make[3]: *** Waiting for unfinished jobs....
9 warnings generated.
11 warnings generated.
22 warnings generated.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[2]: *** [Makefile:30: gainLoss.all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/programs'
make[1]: *** [Makefile:29: programs.all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 2021-10-26T21:44:54Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: binary
Build-Space: 157772
Build-Time: 93
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 4
Job: fastml_3.11-3
Machine Architecture: amd64
Package: fastml
Package-Time: 119
Source-Version: 3.11-3
Space: 157772
Status: attempted
Version: 3.11-3
--------------------------------------------------------------------------------
Finished at 2021-10-26T21:44:54Z
Build needed 00:01:59, 157772k disk space
E: Build failure (dpkg-buildpackage died)
DC-Status: Failed 119.571024223s
DC-Time-Estimation: 119.571024223 versus expected 321 (r/m: 1.6845968919805765 ; m: 119.571024223)