DC-Build-Header: fastml 3.1-3 / 2018-05-02 12:43:58 +0000
DC-Task: type:rebuild-binarch-only source:fastml version:3.1-3 chroot:unstable esttime:347 logfile:/tmp/fastml_3.1-3_unstable_clang60.log modes:clang60:binarch-only
DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v  --chroot-setup-commands=/tmp/clang60 fastml_3.1-3'
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-2-93.eu-central-1.compute.internal

+==============================================================================+
| fastml 3.1-3 (amd64)                         Wed, 02 May 2018 12:43:58 +0000 |
+==============================================================================+

Package: fastml
Version: 3.1-3
Source Version: 3.1-3
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-d78c2fb3-90d4-4484-96c8-a3342749446d' with '<<CHROOT>>'

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


/tmp/clang60
------------

+ echo 'Entering customization script...'
Entering customization script...
+ CLANG_VERSION=6.0
+ echo 'Install of clang-6.0'
Install of clang-6.0
+ apt-get update
Get:1 http://127.0.0.1:9999/debian unstable InRelease [242 kB]
Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB]
Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://127.0.0.1:9999/debian unstable/main Sources 2018-05-02-0830.09.pdiff [16.2 kB]
Get:4 http://127.0.0.1:9999/debian unstable/main Sources 2018-05-02-0830.09.pdiff [16.2 kB]
Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B]
Get:5 http://127.0.0.1:9999/debian unstable/main amd64 Packages 2018-05-02-0830.09.pdiff [1781 B]
Get:6 http://127.0.0.1:9999/debian unstable/main Translation-en [6016 kB]
Fetched 6332 kB in 2s (3526 kB/s)
Reading package lists...
+ apt-get install --yes --no-install-recommends --force-yes clang-6.0
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev
  libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev
  libobjc4
Suggested packages:
  gnustep gnustep-devel clang-6.0-doc
Recommended packages:
  llvm-6.0-dev python libomp-dev libgpm2
The following NEW packages will be installed:
  clang-6.0 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-6.0-dev
  libclang1-6.0 libedit2 libjsoncpp1 libllvm6.0 libncurses5 libobjc-7-dev
  libobjc4
0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded.
Need to get 37.7 MB of archives.
After this operation, 187 MB of additional disk space will be used.
Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB]
Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.7-1 [92.1 kB]
Get:3 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.1+20180210-2 [95.7 kB]
Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB]
Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libllvm6.0 amd64 1:6.0-3 [14.5 MB]
Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 8-20180425-1 [52.4 kB]
Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-7-dev amd64 7.3.0-17 [204 kB]
Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libc6-i386 amd64 2.27-3 [2855 kB]
Get:9 http://127.0.0.1:9999/debian unstable/main amd64 lib32gcc1 amd64 1:8-20180425-1 [47.8 kB]
Get:10 http://127.0.0.1:9999/debian unstable/main amd64 lib32stdc++6 amd64 8-20180425-1 [406 kB]
Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-6.0-dev amd64 1:6.0-3 [3102 kB]
Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-6.0 amd64 1:6.0-3 [6995 kB]
Get:13 http://127.0.0.1:9999/debian unstable/main amd64 clang-6.0 amd64 1:6.0-3 [9175 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 37.7 MB in 0s (98.6 MB/s)
Selecting previously unselected package libjsoncpp1:amd64.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 10022 files and directories currently installed.)
Preparing to unpack .../00-libjsoncpp1_1.7.4-3_amd64.deb ...
Unpacking libjsoncpp1:amd64 (1.7.4-3) ...
Selecting previously unselected package libbsd0:amd64.
Preparing to unpack .../01-libbsd0_0.8.7-1_amd64.deb ...
Unpacking libbsd0:amd64 (0.8.7-1) ...
Selecting previously unselected package libncurses5:amd64.
Preparing to unpack .../02-libncurses5_6.1+20180210-2_amd64.deb ...
Unpacking libncurses5:amd64 (6.1+20180210-2) ...
Selecting previously unselected package libedit2:amd64.
Preparing to unpack .../03-libedit2_3.1-20170329-1_amd64.deb ...
Unpacking libedit2:amd64 (3.1-20170329-1) ...
Selecting previously unselected package libllvm6.0:amd64.
Preparing to unpack .../04-libllvm6.0_1%3a6.0-3_amd64.deb ...
Unpacking libllvm6.0:amd64 (1:6.0-3) ...
Selecting previously unselected package libobjc4:amd64.
Preparing to unpack .../05-libobjc4_8-20180425-1_amd64.deb ...
Unpacking libobjc4:amd64 (8-20180425-1) ...
Selecting previously unselected package libobjc-7-dev:amd64.
Preparing to unpack .../06-libobjc-7-dev_7.3.0-17_amd64.deb ...
Unpacking libobjc-7-dev:amd64 (7.3.0-17) ...
Selecting previously unselected package libc6-i386.
Preparing to unpack .../07-libc6-i386_2.27-3_amd64.deb ...
Unpacking libc6-i386 (2.27-3) ...
Selecting previously unselected package lib32gcc1.
Preparing to unpack .../08-lib32gcc1_1%3a8-20180425-1_amd64.deb ...
Unpacking lib32gcc1 (1:8-20180425-1) ...
Selecting previously unselected package lib32stdc++6.
Preparing to unpack .../09-lib32stdc++6_8-20180425-1_amd64.deb ...
Unpacking lib32stdc++6 (8-20180425-1) ...
Selecting previously unselected package libclang-common-6.0-dev.
Preparing to unpack .../10-libclang-common-6.0-dev_1%3a6.0-3_amd64.deb ...
Unpacking libclang-common-6.0-dev (1:6.0-3) ...
Selecting previously unselected package libclang1-6.0:amd64.
Preparing to unpack .../11-libclang1-6.0_1%3a6.0-3_amd64.deb ...
Unpacking libclang1-6.0:amd64 (1:6.0-3) ...
Selecting previously unselected package clang-6.0.
Preparing to unpack .../12-clang-6.0_1%3a6.0-3_amd64.deb ...
Unpacking clang-6.0 (1:6.0-3) ...
Setting up libncurses5:amd64 (6.1+20180210-2) ...
Setting up libobjc4:amd64 (8-20180425-1) ...
Setting up libc6-i386 (2.27-3) ...
Setting up libbsd0:amd64 (0.8.7-1) ...
Setting up libobjc-7-dev:amd64 (7.3.0-17) ...
Processing triggers for libc-bin (2.27-3) ...
Setting up lib32gcc1 (1:8-20180425-1) ...
Setting up libjsoncpp1:amd64 (1.7.4-3) ...
Setting up libedit2:amd64 (3.1-20170329-1) ...
Setting up libllvm6.0:amd64 (1:6.0-3) ...
Setting up libclang1-6.0:amd64 (1:6.0-3) ...
Setting up lib32stdc++6 (8-20180425-1) ...
Setting up libclang-common-6.0-dev (1:6.0-3) ...
Setting up clang-6.0 (1:6.0-3) ...
Processing triggers for libc-bin (2.27-3) ...
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'
+ cd /usr/bin
+ for VERSION in $VERSIONS
+ rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc
+ ln -s clang++-6.0 g++-4.6
+ ln -s clang-6.0 gcc-4.6
+ ln -s clang-6.0 cpp-4.6
+ ln -s clang-6.0 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++-6.0 g++-4.7
+ ln -s clang-6.0 gcc-4.7
+ ln -s clang-6.0 cpp-4.7
+ ln -s clang-6.0 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++-6.0 g++-4.8
+ ln -s clang-6.0 gcc-4.8
+ ln -s clang-6.0 cpp-4.8
+ ln -s clang-6.0 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++-6.0 g++-4.9
+ ln -s clang-6.0 gcc-4.9
+ ln -s clang-6.0 cpp-4.9
+ ln -s clang-6.0 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++-6.0 g++-5
+ ln -s clang-6.0 gcc-5
+ ln -s clang-6.0 cpp-5
+ ln -s clang-6.0 gcc
+ echo 'gcc-5 hold'
+ dpkg --set-selections
+ echo 'g++-5 hold'
+ dpkg --set-selections
+ for VERSION in $VERSIONS
+ rm -f g++-6 gcc-6 cpp-6 gcc
+ ln -s clang++-6.0 g++-6
+ ln -s clang-6.0 gcc-6
+ ln -s clang-6.0 cpp-6
+ ln -s clang-6.0 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++-6.0 g++-7
+ ln -s clang-6.0 gcc-7
+ ln -s clang-6.0 cpp-7
+ ln -s clang-6.0 gcc
+ echo 'gcc-7 hold'
+ dpkg --set-selections
+ echo 'g++-7 hold'
+ dpkg --set-selections
+ for VERSION in $VERSIONS
+ rm -f g++-8 gcc-8 cpp-8 gcc
+ ln -s clang++-6.0 g++-8
+ ln -s clang-6.0 gcc-8
+ ln -s clang-6.0 cpp-8
+ ln -s clang-6.0 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>
+ cd -
/build/fastml-ekC0oY
+ 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

I: Finished running '/tmp/clang60'.

Finished processing commands.
--------------------------------------------------------------------------------

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Hit:1 http://127.0.0.1:9999/debian unstable 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://anonscm.debian.org/git/debian-med/fastml.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/fastml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 848 kB of source archives.
Get:1 http://127.0.0.1:9999/debian unstable/main fastml 3.1-3 (dsc) [1868 B]
Get:2 http://127.0.0.1:9999/debian unstable/main fastml 3.1-3 (tar) [836 kB]
Get:3 http://127.0.0.1:9999/debian unstable/main fastml 3.1-3 (diff) [10.0 kB]
Fetched 848 kB in 0s (5912 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/fastml-ekC0oY/fastml-3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fastml-ekC0oY' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-JzNxdo/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Release [957 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Packages [432 B]
Fetched 1738 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 860 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [860 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 860 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 10771 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 9)
Filtered Build-Depends: debhelper (>= 9)
dpkg-deb: building package 'sbuild-build-depends-fastml-dummy' in '/<<BUILDDIR>>/resolver-JzNxdo/apt_archive/sbuild-build-depends-fastml-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-fastml-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
Ign:1 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Release [963 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Sources [484 B]
Get:5 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ Packages [566 B]
Fetched 2013 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

Install fastml build dependencies (apt-based resolver)
------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libcroco3
  libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
  libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4
  man-db po-debconf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libcroco3
  libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
  libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4
  man-db po-debconf sbuild-build-depends-fastml-dummy
0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.7 MB of archives.
After this operation, 66.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-JzNxdo/apt_archive ./ sbuild-build-depends-fastml-dummy 0.invalid.0 [856 B]
Get:2 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 11.1.2 [190 kB]
Get:3 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-10 [1176 kB]
Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.5.0-1 [29.0 kB]
Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.8.3-2 [1180 kB]
Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.33-2 [234 kB]
Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.33-2 [113 kB]
Get:8 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.33-2 [65.6 kB]
Get:9 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-6 [122 kB]
Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:11 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB]
Get:12 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-11 [341 kB]
Get:13 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-3.1 [736 kB]
Get:15 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-6 [434 kB]
Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2.1 [547 kB]
Get:17 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 17 [16.5 kB]
Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
Get:21 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.56.1-2 [2928 kB]
Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-9 [7698 kB]
Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-6.1 [725 kB]
Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-2 [144 kB]
Get:26 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-6 [1302 kB]
Get:27 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:28 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB]
Get:29 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 11.2.1 [1013 kB]
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+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-5-amd64 amd64 (x86_64)
Toolchain package versions: binutils_2.30-16 dpkg-dev_1.19.0.5 g++-7_7.3.0-17 gcc-7_7.3.0-17 libc6-dev_2.27-3 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 linux-libc-dev_4.15.17-1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1 base-passwd_3.5.45 bash_4.4.18-2 binutils_2.30-16 binutils-common_2.30-16 binutils-x86-64-linux-gnu_2.30-16 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.5 bzip2_1.0.6-8.1 clang-6.0_1:6.0-3 coreutils_8.28-1 cpp_4:7.3.0-3 cpp-7_7.3.0-17 dash_0.5.8-2.10 debconf_1.5.66 debfoster_2.7-2.1+b1 debhelper_11.2.1 debian-archive-keyring_2017.7 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 eatmydata_105-6 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 findutils_4.6.0+git+20171230-2 g++_4:7.3.0-3 g++-7_7.3.0-17 gcc_4:7.3.0-3 gcc-6-base_6.4.0-17 gcc-7_7.3.0-17 gcc-7-base_7.3.0-17 gcc-8-base_8-20180425-1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5+b1 hostname_3.20 init-system-helpers_1.51 intltool-debian_0.35.0+20060710.4 lib32gcc1_1:8-20180425-1 lib32stdc++6_8-20180425-1 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libasan4_7.3.0-17 libatomic1_8-20180425-1 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-16 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3 libc-dev-bin_2.27-3 libc6_2.27-3 libc6-dev_2.27-3 libc6-i386_2.27-3 libcap-ng0_0.7.9-1 libcc1-0_8-20180425-1 libcilkrts5_7.3.0-17 libclang-common-6.0-dev_1:6.0-3 libclang1-6.0_1:6.0-3 libcom-err2_1.44.1-2 libcomerr2_1.44.1-2 libcroco3_0.6.12-2 libdb5.3_5.3.28-13.1+b1 libdebconfclient0_0.243 libdpkg-perl_1.19.0.5 libeatmydata1_105-6 libedit2_3.1-20170329-1 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgc1c2_1:7.4.2-8.2 libgcc-7-dev_7.3.0-17 libgcc1_1:8-20180425-1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180425-1 libgpg-error0_1.29-4 libhogweed4_3.4-1 libicu57_57.1-9 libidn2-0_2.0.4-1.1 libisl15_0.18-4 libisl19_0.19-1 libitm1_8-20180425-1 libjsoncpp1_1.7.4-3 libllvm6.0_1:6.0-3 liblsan0_8-20180425-1 liblz4-1_1.8.1.2-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr4_3.1.6-1 libmpfr6_4.0.1-1 libmpx2_8-20180425-1 libncurses5_6.1+20180210-2 libncursesw5_6.1+20180210-2 libnettle6_3.4-1 libobjc-7-dev_7.3.0-17 libobjc4_8-20180425-1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.2-3 libpipeline1_1.5.0-1 libquadmath0_8-20180425-1 libseccomp2_2.3.3-1 libselinux1_2.7-2+b2 libsemanage-common_2.7-2 libsemanage1_2.7-2+b2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libss2_1.44.1-2 libstdc++-7-dev_7.3.0-17 libstdc++6_8-20180425-1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2 libtinfo6_6.1+20180210-2 libtool_2.4.6-2.1 libtsan0_8-20180425-1 libubsan0_7.3.0-17 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libzstd1_1.3.4+dfsg-1 linux-libc-dev_4.15.17-1 login_1:4.5-1 m4_1.4.18-1 make_4.2.1-1 man-db_2.8.3-2 mawk_1.3.3-17+b3 mount_2.31.1-0.5 multiarch-support_2.27-3 ncurses-base_6.1+20180210-2 ncurses-bin_6.1+20180210-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-3 perl-base_5.26.2-3 perl-modules-5.26_5.26.2-3 po-debconf_1.0.20 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-fastml-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-1 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue May 10 10:12:32 2016 UTC
gpgv:                using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./fastml_3.1-3.dsc
dpkg-source: info: extracting fastml in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking fastml_3.1.orig.tar.gz
dpkg-source: info: unpacking fastml_3.1-3.debian.tar.xz
dpkg-source: info: applying gcc_5.patch
dpkg-source: info: applying fix_makefile4test.patch
dpkg-source: info: applying fix_intall_target.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch
dpkg-source: info: applying skip_failing_tests.patch
dpkg-source: info: applying remove-template-depth.patch
dpkg-source: info: applying g++-6.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=user42
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1001
SCHROOT_GROUP=user42
SCHROOT_SESSION_ID=unstable-amd64-sbuild-d78c2fb3-90d4-4484-96c8-a3342749446d
SCHROOT_UID=1001
SCHROOT_USER=user42
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package fastml
dpkg-buildpackage: info: source version 3.1-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Gert Wollny <gw.fossdev@gmail.com>
 dpkg-source --before-build fastml-3.1
dpkg-buildpackage: info: host architecture amd64
 fakeroot debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j1 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd libs;make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a   *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
cd programs;make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && 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'
cd gainLoss && make clean
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/gainLoss'
cd indelCoder && make clean
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>>/programs/indelCoder'
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 build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j1
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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestAlpha.o bestAlpha.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;
                        ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestAlphaManyTrees.o bestAlphaManyTrees.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;
                        ^
2 warnings generated.
g++ -g -O2 -fdebug-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 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;
                        ^
3 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bootstrap.o bootstrap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bblEM.o bblEM.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bblEMProprtional.o bblEMProprtional.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
computeSubstitutionCounts.cpp:16:50: warning: field '_LpostPerSpPerCat' will be initialized after field '_simulationsIterNum' [-Wreorder]
_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]
_tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent)
                                                                                                                               ^
2 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fastStartTree.o fastStartTree.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;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fastaFormat.o fastaFormat.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.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;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-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 fromCountTableComponentToDistancefixRoot.cpp:4:
./likeDistfixRoot.h:113:21: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData*  _unObservableData_p;
                           ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
fromCountTableComponentToDistancePropEB.cpp:12:60: warning: field '_nodeID' will be initialized after field '_pProportionDist' [-Wreorder]
                const MDOUBLE brLenIntialGuess ) : _msp(msp), _ctc(ctc), _nodeID(nodeID), _pProportionDist(pProportionDist){
                                                                         ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromQtoPt.o fromQtoPt.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o gammaDistribution.o gammaDistribution.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o goldmanYangModel.o goldmanYangModel.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){
                                                     ^
2 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likeDist.o likeDist.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;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likeDistfixRoot.o likeDistfixRoot.cpp
In file included from likeDistfixRoot.cpp:3:
./likeDistfixRoot.h:113:21: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData*  _unObservableData_p;
                           ^
1 warning generated.
g++ -g -O2 -fdebug-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 likeDistProp.cpp:3:
./likeDistProp.h:13:12: warning: private field '_alphabetSize' is not used [-Wunused-private-field]
        const int _alphabetSize;
                  ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likeDistPropEB.o likeDistPropEB.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likelihoodComputation.o likelihoodComputation.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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
 ^
3 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o readTree.o readTree.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o sequence.o sequence.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))
                                         ^
                   (                                                        )
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o sequenceContainer.o sequenceContainer.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();
                  ^
3 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o simulateTree.o simulateTree.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o split.o split.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o splitMap.o splitMap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o splitTreeUtil.o splitTreeUtil.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o stochasticProcess.o stochasticProcess.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o suffStatComponent.o suffStatComponent.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o talRandom.o talRandom.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o tree.o tree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o treeIt.o treeIt.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o treeUtil.o treeUtil.cpp
treeUtil.cpp:372:25: warning: unused variable 'itStrEnd' [-Wunused-variable]
        string::const_iterator itStrEnd = it->end();
                               ^
treeUtil.cpp:371:25: warning: unused variable 'itStrStart' [-Wunused-variable]
        string::const_iterator itStrStart = it->begin();
                               ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o uniDistribution.o uniDistribution.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o givenRatesMLDistance.o givenRatesMLDistance.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;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp
In file included from distanceBasedSeqs2Tree.cpp: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);
               ^
In file included from distanceBasedSeqs2Tree.cpp:12:
./bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder]
                :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){};
                                                ^
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;
                        ^
11 warnings generated.
g++ -g -O2 -fdebug-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 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;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-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 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;
                          ^
3 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o indel.o indel.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o indelModel.o indelModel.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o mulAlphabet.o mulAlphabet.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o replacementModelSSRV.o replacementModelSSRV.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestAlphaAndNu.o bestAlphaAndNu.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;
                        ^
2 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o betaUtilities.o betaUtilities.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o betaDistribution.o betaDistribution.cpp
betaDistribution.cpp:24:2: warning: field '_boundary' will be initialized after field '_alpha' [-Wreorder]
        _boundary(other._boundary),
        ^
1 warning generated.
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o samplingSequences.o samplingSequences.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bblEM2USSRV.o bblEM2USSRV.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestParamUSSRV.o bestParamUSSRV.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;
                        ^
2 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp
In file included from fromCountTableComponentToDistance2USSRV.cpp:4:
./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o normalDist.o normalDist.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestTamura92param.o bestTamura92param.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;
                        ^
4 warnings generated.
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp
g++ -g -O2 -fdebug-prefix-map=/<<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 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);
               ^
In file included from ssrvDistanceSeqs2Tree.cpp:3:
In file included from ./ssrvDistanceSeqs2Tree.h:6:
In file included from ./distanceBasedSeqs2Tree.h:9:
./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from ssrvDistanceSeqs2Tree.cpp:5:
In file included from ./bestParamUSSRV.h:13:
./bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
./bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
8 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o distributionPlusCategory.o distributionPlusCategory.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o simulateJumps.o simulateJumps.cpp
simulateJumps.cpp:149:37: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
                                if ((iterTerm->second[termState]==0)){ //never reached these terminal states
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
simulateJumps.cpp:149:37: note: remove extraneous parentheses around the comparison to silence this warning
                                if ((iterTerm->second[termState]==0)){ //never reached these terminal states
                                    ~                           ^  ~
simulateJumps.cpp:149:37: note: use '=' to turn this equality comparison into an assignment
                                if ((iterTerm->second[termState]==0)){ //never reached these terminal states
                                                                ^~
                                                                =
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o computeJumps.o computeJumps.cpp
computeJumps.cpp:257:22: warning: field '_Lambda2' will be initialized after field '_r' [-Wreorder]
: _Lambda1(Lambda1), _Lambda2(Lambda2), _r(r)
                     ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o seqeuncesFilter.o seqeuncesFilter.cpp
seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable]
        const alphabet* pAlph = sc.getAlphabet();
                        ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o mixtureDistribution.o mixtureDistribution.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
4 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable]
                MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0);
                        ^
suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable]
                MDOUBLE third = -_MkVec[comp] * gammln(alpha_k);
                        ^
suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable]
                MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k);
                        ^
suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable]
                MDOUBLE fourth = -_AkVec[comp]*beta_k;
                        ^
suffStatGammaMixture.cpp:224:11: warning: unused variable 'first' [-Wunused-variable]
                MDOUBLE first = _MkVec[comp] * log(P_k);
                        ^
5 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp
In file included from GamMixtureOptimizer.cpp:3:
./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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
In file included from optGammaMixtureEM.cpp:1:
./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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o gainLossAlphabet.o gainLossAlphabet.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o wYangModel.o wYangModel.cpp
g++ -g -O2 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp
g++ -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp
In file included from fromCountTableComponentToDistance2Codon.cpp:5:
./likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
./likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
2 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o gtrModel.o gtrModel.cpp
gtrModel.cpp:12:59: warning: field '_g2t' will be initialized after field '_freq' [-Wreorder]
                                          :_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
19 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o bestGtrModelParams.o bestGtrModelParams.cpp
In file included from bestGtrModelParams.cpp:3:
./bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder]
                :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){};
                                                ^
./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;
                        ^
4 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp
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); 
                     ^
1 warning generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG  -c -o integerAlphabet.o integerAlphabet.cpp
ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o
ar: creating libEvolTree.a
a - AddLog.o
a - NNiProp.o
a - NNiSep.o
a - Nni.o
a - aaJC.o
a - allTrees.o
a - allTreesSeparateModel.o
a - alphabet.o
a - amino.o
a - bestAlpha.o
a - bestAlphaManyTrees.o
a - bestHKYparam.o
a - bootstrap.o
a - bblEM.o
a - bblEMfixRoot.o
a - bblEMProprtional.o
a - bblEMProportionalEB.o
a - bblLSProportionalEB.o
a - bblEMSeperate.o
a - chebyshevAccelerator.o
a - clustalFormat.o
a - codon.o
a - codonJC.o
a - computeCounts.o
a - computeDownAlg.o
a - computeMarginalAlg.o
a - computePijComponent.o
a - computeUpAlg.o
a - computeUpAlgFactors.o
a - computeSubstitutionCounts.o
a - computePosteriorExpectationOfSubstitutions.o
a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o
a - ConversionUtils.o
a - countTableComponent.o
a - datMatrixHolder.o
a - distanceTable.o
a - distribution.o
a - errorMsg.o
a - evaluateCharacterFreq.o
a - fastStartTree.o
a - fastaFormat.o
a - findRateOfGene.o
a - fromCountTableComponentToDistance.o
a - fromCountTableComponentToDistancefixRoot.o
a - fromCountTableComponentToDistanceProp.o
a - fromCountTableComponentToDistancePropEB.o
a - fromQtoPt.o
a - generalGammaDistributionFixedCategories.o
a - gammaDistribution.o
a - gammaUtilities.o
a - generalGammaDistribution.o
a - getRandomWeights.o
a - goldmanYangModel.o
a - granthamChemicalDistances.o
a - hky.o
a - simulateWithDependence.o
a - KH_calculation.o
a - likeDist.o
a - likeDistfixRoot.o
a - likeDistProp.o
a - likeDistPropEB.o
a - likelihoodComputation.o
a - likelihoodComputationFactors.o
a - logFile.o
a - maseFormat.o
a - molphyFormat.o
a - nexusFormat.o
a - nj.o
a - njConstrain.o
a - nucJC.o
a - nucleotide.o
a - numRec.o
a - Parameters.o
a - phylipFormat.o
a - pijAccelerator.o
a - readDatMatrix.o
a - readTree.o
a - recognizeFormat.o
a - replacementModel.o
a - searchStatus.o
a - seqContainerTreeMap.o
a - sequence.o
a - sequenceContainer.o
a - simulateTree.o
a - siteSpecificRate.o
a - someUtil.o
a - split.o
a - splitMap.o
a - splitTreeUtil.o
a - stochasticProcess.o
a - suffStatComponent.o
a - talRandom.o
a - tree.o
a - treeIt.o
a - treeUtil.o
a - uniDistribution.o
a - uniformDistribution.o
a - cmdline2EvolObjs.o
a - generalGammaDistributionLaguerre.o
a - gammaDistributionLaguerre.o
a - GLaguer.o
a - givenRatesMLDistance.o
a - distanceBasedSeqs2Tree.o
a - posteriorDistance.o
a - pairwiseGammaDistance.o
a - doubleRep.o
a - logRep.o
a - indel.o
a - indelModel.o
a - mulAlphabet.o
a - replacementModelSSRV.o
a - stochasticProcessSSRV.o
a - bestAlphaAndNu.o
a - C_evalParamUSSRV.o
a - matrixUtils.o
a - betaOmegaDistribution.o
a - betaUtilities.o
a - betaDistribution.o
a - geneticCodeHolder.o
a - samplingSequences.o
a - bblEM2USSRV.o
a - bestParamUSSRV.o
a - likeDist2USSRV.o
a - ussrvModel.o
a - likelihoodComputation2USSRV.o
a - fromCountTableComponentToDistance2USSRV.o
a - normalDist.o
a - tamura92.o
a - bestTamura92param.o
a - phylipSequentialFormat.o
a - simulateCodonsJumps.o
a - simulateJumpsAbstract.o
a - ssrvDistanceSeqs2Tree.o
a - multipleStochasticProcess.o
a - distributionPlusInvariant.o
a - extremeValDistribution.o
a - gammaDistributionFixedCategories.o
a - generalGammaDistributionPlusInvariant.o
a - gammaDistributionPlusInvariant.o
a - distributionPlusCategory.o
a - simulateJumps.o
a - computeJumps.o
a - seqeuncesFilter.o
a - optGammaMixtureLS.o
a - mixtureDistribution.o
a - suffStatGammaMixture.o
a - GamMixtureOptimizer.o
a - optGammaMixtureEM.o
a - gainLossAlphabet.o
a - wYangModel.o
a - codonUtils.o
a - likelihoodComputation2Codon.o
a - likeDist2Codon.o
a - unObservableData.o
a - likelihoodComputationGL.o
a - threeStateModel.o
a - threeStateAlphabet.o
a - oneTwoMoreModel.o
a - betaDistributionFixedCategories.o
a - betaDistributionFixedCategoriesWithOmegaUniform.o
a - bblEM2codon.o
a - bestAlphaAndK.o
a - fromCountTableComponentToDistance2Codon.o
a - gtrModel.o
a - bestGtrModelParams.o
a - simulateRateShiftJumps.o
a - integerAlphabet.o
ranlib libEvolTree.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
cd programs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
making depend
g++ -g -O2 -fdebug-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
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]
                : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;}
                  ^
In file included from fastml.cpp:1:
In file included from ./mainbb.h:4:
./bb_options.h:62:21: warning: unused function 'usege_splash_screen' [-Wunused-function]
static const string usege_splash_screen() {
                    ^
2 warnings generated.
g++ -g -O2 -fdebug-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
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]
                : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;}
                  ^
bbAlg.cpp:14:2: warning: field '_reportFileName' will be initialized after field 'BandBReportAllPos1' [-Wreorder]
        _reportFileName(reportFileName),
        ^
bbAlg.cpp:15:2: warning: field 'BandBReportAllPos1' will be initialized after field '_et' [-Wreorder]
        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() {
                    ^
4 warnings generated.
g++ -g -O2 -fdebug-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
g++ -g -O2 -fdebug-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
g++ -g -O2 -fdebug-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]
                                        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.
                                ^
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;
            ^
4 warnings generated.
g++ -g -O2 -fdebug-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 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;
            ^
2 warnings generated.
g++ -g -O2 -fdebug-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
bbNodeOrderAlg.cpp:12:64: warning: field '_sc' will be initialized after field '_cpij' [-Wreorder]
                                        const MDOUBLE computeAgainExactTreshold) :_et(et),_sp(sp),_sc(sc),_cpij(cpij){
                                                                                                  ^
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;
            ^
3 warnings generated.
g++ -g -O2 -fdebug-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
bb_options.cpp:11:2: warning: field 'reportFile' will be initialized after field 'outFile_seq_joint' [-Wreorder]
        reportFile("log.txt"),
        ^
bb_options.cpp:13:2: warning: field 'outFile_seq_marginal' will be initialized after field 'outFile_prob_joint' [-Wreorder]
        outFile_seq_marginal("seq.marginal.txt"),
        ^
bb_options.cpp:15:2: warning: field 'outFile_prob_marginal' will be initialized after field 'seqfile' [-Wreorder]
        outFile_prob_marginal("prob.marginal.txt"),
        ^
bb_options.cpp:17:5: warning: field 'distributionName' will be initialized after field 'seqOutputFormat' [-Wreorder]
    distributionName(hom),
    ^
bb_options.cpp:20:5: warning: field 'outTreeFileAncestor' will be initialized after field 'boundMethod' [-Wreorder]
    outTreeFileAncestor("tree.ancestor.txt"),
    ^
bb_options.cpp:22:2: warning: field 'gammaPar' will be initialized after field 'userProvideAlpha' [-Wreorder]
        gammaPar(1.0),
        ^
bb_options.cpp:24:2: warning: field 'gammaCategies' will be initialized after field 'modelName' [-Wreorder]
        gammaCategies(8),
        ^
bb_options.cpp:28:2: warning: field 'useChebyshev' will be initialized after field 'treeOutFile' [-Wreorder]
        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() {
                    ^
9 warnings generated.
g++ -g -O2 -fdebug-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
In file included from bbReport.cpp:1:
./bbReport.h:11:5: warning: field '_reportFileName' will be initialized after field '_minNumOfNodesToVisit' [-Wreorder]
                : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;}
                  ^
bbReport.cpp:11:2: warning: field '_reportFileName' will be initialized after field '_position' [-Wreorder]
        _reportFileName(reportFileName), _position(position), _alphabetSize(alphabetSize)
        ^
2 warnings generated.
g++ -g -O2 -fdebug-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
computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable]
                MDOUBLE likelihoodOfPos = 0;
                        ^
computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable]
        MDOUBLE totalLikelihoodOfReconstruction = 0;
                ^
2 warnings generated.
g++ -g -O2 -fdebug-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
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;
                                ^
2 warnings generated.
g++ -g -O2 -fdebug-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
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]
                : _reportFileName(reportFileName),_minNumOfNodesToVisit(minNumOfNodesToVisit) {totalNumberOfNodeVisited=0;}
                  ^
In file included from mainbb.cpp:31:
../../libs/phylogeny/bestGtrModelParams.h:168:35: warning: field '_sp' will be initialized after field '_pProportionDist' [-Wreorder]
                :_param(param), _et(et),_sc(sc),_sp(sp),_pProportionDist(pProportionDist),_weights(weights){};
                                                ^
mainbb.cpp:426:11: warning: variable 'bm' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (_options->boundMethod == bb_options::both) bm=bbAlg::both;
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mainbb.cpp:428:30: note: uninitialized use occurs here
        bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr);
                                    ^~
mainbb.cpp:426:7: note: remove the 'if' if its condition is always true
        else if (_options->boundMethod == bb_options::both) bm=bbAlg::both;
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mainbb.cpp:423:2: note: variable 'bm' is declared here
        bbAlg::boundMethod bm;
        ^
In file included from 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;
                        ^
12 warnings generated.
g++ -g -O2 -fdebug-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
g++ -g -O2 -fdebug-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
ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o
ar: creating libfastml.a
a - fastml.o
a - bbAlg.o
a - bbComputeDownAlg.o
a - bbComputeUpAlg.o
a - bbEvaluateSpecificAV.o
a - bbfindBestAVDynProg.o
a - bbNodeOrderAlg.o
a - bb_options.o
a - bbReport.o
a - computeMarginalReconstruction.o
a - jointNoGamma.o
a - mainbb.o
a - sequenceDataDiff.o
a - suffStatComponentJointNoGamma.o
ranlib libfastml.a
g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny  fastml.o libfastml.a ../../libs/phylogeny/libEvolTree.a   -o fastml
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
cd gainLoss && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
making depend
g++ -g -O2 -fdebug-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
gainLossOptions.cpp:2060:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="Vhigh")
                 ^~~~~~~~~~~~
gainLossOptions.cpp:2064:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2060:7: note: remove the 'if' if its condition is always true
        else if (str=="Vhigh")
             ^~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2047:2: note: variable 'returnType' is declared here
        optimizationLevel returnType;
        ^
gainLossOptions.cpp:2107:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="gainLossCost")
                 ^~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2111:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2107:7: note: remove the 'if' if its condition is always true
        else if (str=="gainLossCost")
             ^~~~~~~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2098:2: note: variable 'returnType' is declared here
        costMatrixType returnType;
        ^
gainLossOptions.cpp:2415:11: warning: variable 'returnType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (str=="Gam_gVrl")
                 ^~~~~~~~~~~~~~~
gainLossOptions.cpp:2419:9: note: uninitialized use occurs here
        return returnType;
               ^~~~~~~~~~
gainLossOptions.cpp:2415:7: note: remove the 'if' if its condition is always true
        else if (str=="Gam_gVrl")
             ^~~~~~~~~~~~~~~~~~~~
gainLossOptions.cpp:2396:2: note: variable 'returnType' is declared here
        simulationType returnType;
        ^
3 warnings generated.
g++ -g -O2 -fdebug-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
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]
                :_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]
                :_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]
                :_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]
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]
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]
gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL)
                                                                                            ^
gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable]
        char missigDataChar = -2;
             ^
gainLoss.cpp:1121:5: warning: variable 'rateDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                                default:
                                ^~~~~~~
gainLoss.cpp:1124:50: note: uninitialized use occurs here
                        stochasticProcess* sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible);                  
                                                                      ^~~~~~~~
gainLoss.cpp:1105:26: note: initialize the variable 'rateDist' to silence this warning
                        distribution* rateDist;
                                              ^
                                               = nullptr
gainLoss.cpp:1245:38: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
        if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){
                                            ^                  ~~
gainLoss.cpp:1245:38: note: add parentheses after the '!' to evaluate the comparison first
        if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){
                                            ^
                                             (                                     )
gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning
        if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){
                                            ^
                                            (                  )
gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable]
                MDOUBLE sumPijQij = normalizeQ(sp);
                        ^
gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable]
                MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist);
                        ^
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
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){
                           ^
                           (          )
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;
             ^
21 warnings generated.
g++ -g -O2 -fdebug-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
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]
                :_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;
                ^
6 warnings generated.
g++ -g -O2 -fdebug-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 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]
                :_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]
_weightsUniqPatterns(weights), _unObservableData_p(unObservableData_p)
^
In file included from optimizeGainLossModel.cpp:17:
In file included from ./optimizeGainLossModel.h:23:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
5 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp
In file included from optimizeGainLossModelVV.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]
                :_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]
_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;
             ^
7 warnings generated.
g++ -g -O2 -fdebug-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 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]
                :_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]
_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]
_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]
_gain(m1),_freq(freq),_isRootFreqEQstationary(isRootFreqEQstationary),_isReversible(isReversible),_isHGT_normal_Pij(isHGT_normal_Pij),_isHGT_with_Q(isHGT_with_Q),_q2pt(NULL){
                                                                                                                                      ^
5 warnings generated.
g++ -g -O2 -fdebug-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
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]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
2 warnings generated.
g++ -g -O2 -fdebug-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
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]
                :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q)   
                 ^
2 warnings generated.
g++ -g -O2 -fdebug-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 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]
                :_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:24:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from gainLossProject.cpp:17:
In file included from ./gainLoss.h:42:
../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from gainLossProject.cpp:17:
In file included from ./gainLoss.h:51:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
7 warnings generated.
g++ -g -O2 -fdebug-prefix-map=/<<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 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]
                :_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]
                :_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]
                :_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]
_tr(tr),_sp(sp),_sc(sc),
^
gainLossOptimizer.cpp:31:17: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder]
_tr(tr),_sp(sp),_sc(sc),
                ^
gainLossOptimizer.cpp:35:1: warning: field '_weightsUniqPatterns' will be initialized after field '_unObservableData_p' [-Wreorder]
_weightsUniqPatterns(weights),
^
gainLossOptimizer.cpp:57:45: warning: field '_lossDist' will be initialized after field '_sc' [-Wreorder]
_tr(tr),_spVVec(spVVec),_gainDist(gainDist),_lossDist(lossDist),
                                            ^
gainLossOptimizer.cpp:58:1: warning: field '_sc' will be initialized after field '_epsilonOptimization' [-Wreorder]
_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]
_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;
        ^
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;
             ^
22 warnings generated.
g++ -g -O2 -fdebug-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
g++ -g -O2 -fdebug-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 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]
                :_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]
_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;
            ^
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;
             ^
10 warnings generated.
g++ -g -O2 -fdebug-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 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]
                :_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]
_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]
_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]
_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]
_tr(tr),_spVVec(spVVec), _gainDist(gainDist), _lossDist(lossDist),_sc(sc),_outDir(outDir),_postProbPerSpPerCatPerPos(logLpostPerSpPerCatPerPos),_distanceFromNearestOTUForRecent(distanceFromNearestOTUForRecent), _isSilent(isSilent)
                                                                                                                                                ^
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:24:
../../libs/phylogeny/bestAlpha.h:167:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
../../libs/phylogeny/bestAlpha.h:201:18: warning: private field '_weights' is not used [-Wunused-private-field]
        const Vdouble * _weights;
                        ^
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:42:
../../libs/phylogeny/likeDist.h:111:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
../../libs/phylogeny/likeDist.h:149:20: warning: private field '_unObservableData_p' is not used [-Wunused-private-field]
        unObservableData* _unObservableData_p;
                          ^
In file included from computeCountsGL.cpp:17:
In file included from ./computeCountsGL.h:24:
In file included from ./gainLoss.h:51:
./optimizeGainLossModelVV.h:135:7: warning: private field '_isReversible' is not used [-Wunused-private-field]
        bool _isReversible;
             ^
11 warnings generated.
g++ -g -O2 -fdebug-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
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]
                :_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;
                                     ^
computeCorrelations.cpp:894:5: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
        if(!numOfSites_A == numOfSites_B){
           ^             ~~
computeCorrelations.cpp:894:5: note: add parentheses after the '!' to evaluate the comparison first
        if(!numOfSites_A == numOfSites_B){
           ^
            (                           )
computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning
        if(!numOfSites_A == numOfSites_B){
           ^
           (            )
computeCorrelations.cpp:1009:7: warning: unused variable 'isPearson' [-Wunused-variable]
        bool isPearson = false;
             ^
computeCorrelations.cpp:1025:6: warning: unused variable 'numOfbranches' [-Wunused-variable]
        int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node
            ^
computeCorrelations.cpp:1347:36: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing]
                float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001};
                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
computeCorrelations.cpp:1347:36: note: insert an explicit cast to silence this issue
                float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001};
                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                 static_cast<float>(                       )
computeCorrelations.cpp:1300:7: warning: unused variable 'it_siteB' [-Wunused-variable]
        it_B it_siteB = it_siteA->second.begin();
             ^
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]: 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: make -j1 returned exit code 2
make: *** [debian/rules:8: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-05-02T12:47:53Z

Finished
--------


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

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

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

Build Architecture: amd64
Build Type: any
Build-Space: 170616
Build-Time: 215
Distribution: unstable
Fail-Stage: build
Host Architecture: amd64
Install-Time: 6
Job: fastml_3.1-3
Machine Architecture: amd64
Package: fastml
Package-Time: 235
Source-Version: 3.1-3
Space: 170616
Status: attempted
Version: 3.1-3
--------------------------------------------------------------------------------
Finished at 2018-05-02T12:47:53Z
Build needed 00:03:55, 170616k disk space
E: Build failure (dpkg-buildpackage died)
DC-Status: Failed 235.908491084s
DC-Time-Estimation: 235.908491084 versus expected 347 (r/m: 0.4709093276190878 ; m: 235.908491084)