I: pbuilder: network access will be disabled during build I: Current time: Fri May 22 17:35:39 -12 2020 I: pbuilder-time-stamp: 1590212139 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [fastml_3.1-4.dsc] I: copying [./fastml_3.1.orig.tar.gz] I: copying [./fastml_3.1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 11 07:30:13 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fastml_3.1-4.dsc dpkg-source: info: extracting fastml in fastml-3.1 dpkg-source: info: unpacking fastml_3.1.orig.tar.gz dpkg-source: info: unpacking fastml_3.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_5.patch dpkg-source: info: applying fix_makefile4test.patch dpkg-source: info: applying fix_intall_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch dpkg-source: info: applying skip_failing_tests.patch dpkg-source: info: applying remove-template-depth.patch dpkg-source: info: applying g++-6.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 18.2 MB of archives. After unpacking 63.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Fetched 18.2 MB in 3s (6270 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... 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Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/fastml-3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/fastml-3.1' dh_auto_clean make -j3 clean make[2]: Entering directory '/build/fastml-3.1' cd libs;make clean cd programs;make clean make[3]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make clean make[3]: Entering directory '/build/fastml-3.1/programs' cd fastml && make clean cd gainLoss && make clean make[4]: Entering directory '/build/fastml-3.1/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.1/programs/fastml' cd indelCoder && make clean make[4]: Entering directory '/build/fastml-3.1/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Entering directory '/build/fastml-3.1/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[3]: Leaving directory '/build/fastml-3.1/libs' make[4]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[4]: Entering directory '/build/fastml-3.1/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.1/programs' make[2]: Leaving directory '/build/fastml-3.1' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/build/fastml-3.1' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.1/libs/phylogeny' making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from allTrees.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from allTrees.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void allTrees::recursiveFind(tree, const stochasticProcess&, const sequenceContainer&, std::vector, const Vdouble*, int, double)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp bestAlpha.cpp: In constructor 'bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)': bestAlpha.cpp:371:10: warning: variable 'oldA' set but not used [-Wunused-but-set-variable] MDOUBLE oldA=0; ^~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlphaManyTrees.cpp: In function 'void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)': bestAlphaManyTrees.cpp:184:10: warning: variable 'ax' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^~ bestAlphaManyTrees.cpp:184:13: warning: variable 'bx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^~ bestAlphaManyTrees.cpp:184:16: warning: variable 'cx' set but not used [-Wunused-but-set-variable] MDOUBLE ax,bx,cx; // left, midle, right limit on alpha ^~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from bestAlpha.h:6, from bestAlpha.cpp:6: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from bestAlpha.h:6, from bestAlpha.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In constructor 'bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::__cxx11::string, bool, bool, const Vdouble*, double, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::__cxx11::string, bool, bool, const Vdouble*, double, double, double, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from bblEM.h:5, from bblEMProportionalEB.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from bblEM.h:5, from bblEMProportionalEB.cpp:2: /usr/include/c++/8/bits/stl_vector.h: In member function 'void bblEMProportionalEB::allocatePlacePropEB()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from codon.h:6, from codon.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from codon.h:6, from codon.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void codonUtility::readCodonUsage(const string&, Vdouble&, const codon&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp /usr/include/c++/8/bits/stl_vector.h: In static member function 'static double codonUtility::calcCodonAdaptationIndex(const sequenceContainer&, const Vdouble&, Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from computeUpAlgFactors.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor 'computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::__cxx11::string&, VVVdouble&, int, double, bool)': computeSubstitutionCounts.h:57:12: warning: 'computeSubstitutionCounts::_LpostPerSpPerCat' will be initialized after [-Wreorder] VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:6: warning: 'int computeSubstitutionCounts::_simulationsIterNum' [-Wreorder] int _simulationsIterNum; ^~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h:54:10: warning: 'computeSubstitutionCounts::_probCutOffSum' will be initialized after [-Wreorder] MDOUBLE _probCutOffSum; ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:7: warning: 'bool computeSubstitutionCounts::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from computeUpAlgFactors.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from computeSubstitutionCounts.h:4, from computeSubstitutionCounts.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from computeSubstitutionCounts.h:4, from computeSubstitutionCounts.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeSubstitutionCounts::run()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from distanceTable.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from distanceTable.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In function 'void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from fastStartTree.cpp:15: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from fastStartTree.cpp:15: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor 'fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)': fromCountTableComponentToDistancePropEB.h:29:12: warning: 'fromCountTableComponentToDistancePropEB::_nodeID' will be initialized after [-Wreorder] const int _nodeID; ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:27: warning: 'const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, from generalGammaDistributionFixedCategories.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, from generalGammaDistributionFixedCategories.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void generalGammaDistributionFixedCategories::setDefaultBoundaries(int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void generalGammaDistributionFixedCategories::fill_mean()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'generalGammaDistributionFixedCategories::generalGammaDistributionFixedCategories(double, double, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from fromQtoPt.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from fromQtoPt.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In function 'VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from generalGammaDistribution.h:11, from generalGammaDistribution.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from generalGammaDistribution.h:11, from generalGammaDistribution.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'generalGammaDistribution::generalGammaDistribution(double, double, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void generalGammaDistribution::setGammaParameters(int, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void generalGammaDistribution::setBeta(double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void generalGammaDistribution::setAlpha(double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': goldmanYangModel.cpp:8:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): ^~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': goldmanYangModel.cpp:18:1: warning: 'goldmanYangModel::_globalV' is initialized with itself [-Winit-self] goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from goldmanYangModel.h:6, from goldmanYangModel.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from goldmanYangModel.h:6, from goldmanYangModel.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp likeDist.cpp: In instantiation of 'double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]': likeDist.cpp:274:18: required from here likeDist.cpp:210:13: warning: variable 'oldIntervalSize' set but not used [-Wunused-but-set-variable] MDOUBLE oldIntervalSize = currentIntervalSize; ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from tree.h:6, from simulateWithDependence.h:29, from simulateWithDependence.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'double sim_with_dep::simulate_with_dependence(std::__cxx11::string, double, double, int, int, double, int, double, double, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In function 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In function 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from nj.h:8, from nj.cpp:6: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from nj.h:8, from nj.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In member function 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&, njConstraint&)': nj.cpp:122:13: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] int minRaw,minCol; ^~~~~~ nj.cpp:133:36: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] UpdateDistanceTableAndCurrentNodes(currentNodes,distanceTable,nodeI,nodeJ,theNewNode,minRaw,minCol); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nj.cpp: In member function 'void NJalg::NJiterate(tree&, std::vector&, VVdouble&)': nj.cpp:100:41: warning: 'minCol' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeJ = currentNodes[minCol]; ^ nj.cpp:99:41: warning: 'minRaw' may be used uninitialized in this function [-Wmaybe-uninitialized] tree::nodeP nodeI = currentNodes[minRaw]; ^ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] //* for (i=1;i >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from numRec.cpp:6: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'double performKSTest(const uniformDistribution&, Vdouble&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from numRec.h:13, from numRec.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from numRec.h:13, from numRec.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In function 'void houseHolder(VVdouble&, VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from readDatMatrix.h:6, from readDatMatrix.cpp:14: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from readDatMatrix.h:6, from readDatMatrix.cpp:14: /usr/include/c++/8/bits/stl_vector.h: In function 'VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void readDatMatrixFromFile(const string&, VVdouble&, Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp /usr/include/c++/8/bits/stl_vector.h: In function 'void readDatMatrixFromString(const string&, VVdouble&, Vdouble&, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ sequence.cpp: In constructor 'sequence::sequence(const sequence&, const alphabet*)': sequence.cpp:76:28: warning: suggest parentheses around '&&' within '||' [-Wparentheses] || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void pupAll::fillMatrices(const string&, const Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositions()': sequenceContainer.cpp:187:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^~~~~~ sequenceContainer.cpp: In member function 'void sequenceContainer::removeGapPositionsAllSeqs()': sequenceContainer.cpp:199:7: warning: variable 'gapCol' set but not used [-Wunused-but-set-variable] bool gapCol; ^~~~~~ sequenceContainer.cpp: In member function 'int sequenceContainer::getNumOfOccurancesPerPos(int, char)': sequenceContainer.cpp:452:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^~~ sequenceContainer.cpp: In member function 'std::vector > sequenceContainer::getSeqNamesThatMatchPos(int, char)': sequenceContainer.cpp:467:12: warning: unused variable 'len' [-Wunused-variable] const int len = _seqDataVec[0].seqLen(); ^~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from someUtil.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from someUtil.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from someUtil.cpp:9: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = vecElem; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from someUtil.cpp:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp /usr/include/c++/8/bits/stl_algo.h: In function 'double computeFDRthreshold(Vdouble&, double, bool)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp /usr/include/c++/8/bits/stl_algo.h: In function 'double computeMedian(const std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'double computeQuantileFrac(const std::vector&, double)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'double computeQuantile(const std::vector&, double)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp /usr/include/c++/8/bits/stl_algo.h: In function 'double orderVec(const std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void orderRankNoTies(const std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void orderVec(const Vdouble&, std::vector >&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ tree.cpp: In constructor 'tree::tree(const string&)': tree.cpp:180:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (in.is_open()) ^~ tree.cpp:182:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' create_names_to_internal_nodes(); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp treeUtil.cpp: In function 'std::vector getNexusTreesFromFile(const string&)': treeUtil.cpp:371:25: warning: variable 'itStrStart' set but not used [-Wunused-but-set-variable] string::const_iterator itStrStart = it->begin(); ^~~~~~~~~~ treeUtil.cpp:372:25: warning: variable 'itStrEnd' set but not used [-Wunused-but-set-variable] string::const_iterator itStrEnd = it->end(); ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from uniformDistribution.h:22, from uniformDistribution.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from uniformDistribution.h:22, from uniformDistribution.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void uniformDistribution::setUniformParameters(int, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'uniformDistribution::uniformDistribution(int, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void uniformDistribution::change_number_of_categories(int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from generalGammaDistributionLaguerre.h:26, from generalGammaDistributionLaguerre.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void generalGammaDistributionLaguerre::fillRatesAndProbs(int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In constructor 'generalGammaDistributionLaguerre::generalGammaDistributionLaguerre(double, double, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from GLaguer.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from GLaguer.cpp:2: /usr/include/c++/8/bits/stl_vector.h: In constructor 'GLaguer::GLaguer(int, double, Vdouble&, Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void GLaguer::GetPhylipLaguer(int, double, Vdouble&, Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void GLaguer::gaulag(Vdouble&, Vdouble&, double, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^~~ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from replacementModel.h:6, from replacementModelSSRV.h:6, from replacementModelSSRV.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from replacementModel.h:6, from replacementModelSSRV.h:6, from replacementModelSSRV.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In member function 'void replacementModelSSRV::updateQ()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'replacementModelSSRV::replacementModelSSRV(const distribution*, const replacementModel*, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'Vdouble getSubDiagonalFromMatrix(VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'void appendVectors(VVdouble&, const VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In function 'Vdouble getDiagonalFromMatrix(VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor 'betaDistribution::betaDistribution(const betaDistribution&)': betaDistribution.h:54:18: warning: 'betaDistribution::_boundary' will be initialized after [-Wreorder] vector _boundary; ^~~~~~~~~ betaDistribution.h:47:10: warning: 'double betaDistribution::_alpha' [-Wreorder] MDOUBLE _alpha; ^~~~~~ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] betaDistribution::betaDistribution(const betaDistribution& other) : ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In function 'void readDoubleVecFromFile(Vdouble&, std::__cxx11::string)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from betaDistribution.h:10, from betaDistribution.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp /usr/include/c++/8/bits/vector.tcc: In function 'void readMatrixFromFile(VVdouble&, std::__cxx11::string)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from betaDistribution.h:10, from betaDistribution.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'betaDistribution::betaDistribution(double, double, int, betaDistribution::discretizationType)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistribution::setBetaParameters(int, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistribution::change_number_of_categories(int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistribution::setAlpha(double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistribution::setBeta(double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from likelihoodComputation2USSRV.h:5, from likelihoodComputation2USSRV.cpp:2: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'double likelihoodComputation2USSRV::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const sequenceContainer&, const ussrvModel&, const suffStatGlobalGam&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateCodonsJumps.h:4, from simulateCodonsJumps.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateCodonsJumps.h:4, from simulateCodonsJumps.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void simulateCodonsJumps::init()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from bestTamura92param.h:6, from bestTamura92param.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from bestTamura92param.h:6, from bestTamura92param.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'bestTamura92ParamAlphaAndBBLProportional::bestTamura92ParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::__cxx11::string, bool, bool, const Vdouble*, double, double, double, double, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor 'computeJumps::gFunc::gFunc(double, double, double)': computeJumps.h:59:11: warning: 'computeJumps::gFunc::_Lambda2' will be initialized after [-Wreorder] MDOUBLE _Lambda2; ^~~~~~~~ computeJumps.h:57:11: warning: 'double computeJumps::gFunc::_r' [-Wreorder] MDOUBLE _r; ^~ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateJumps.h:4, from simulateJumps.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ seqeuncesFilter.cpp: In static member function 'static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)': seqeuncesFilter.cpp:141:18: warning: unused variable 'pAlph' [-Wunused-variable] const alphabet* pAlph = sc.getAlphabet(); ^~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateJumps.h:4, from simulateJumps.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void simulateJumps::init()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: sequenceContainer.h: In static member function 'static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const string&, std::__cxx11::string)': sequenceContainer.h:31:81: warning: 'refID' may be used uninitialized in this function [-Wmaybe-uninitialized] const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} ^ seqeuncesFilter.cpp:165:6: note: 'refID' was declared here int refID; ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::rates(int) const': mixtureDistribution.cpp:210:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~ mixtureDistribution.cpp:221:41: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] return _components[componentNum]->rates(categoryInComponent) * _globalRate; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp: In member function 'virtual const double mixtureDistribution::ratesProb(int) const': mixtureDistribution.cpp:228:6: warning: 'componentNum' may be used uninitialized in this function [-Wmaybe-uninitialized] int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~ In file included from mixtureDistribution.h:12, from mixtureDistribution.cpp:1: generalGammaDistribution.h:28:73: warning: 'categoryInComponent' may be used uninitialized in this function [-Wmaybe-uninitialized] virtual const MDOUBLE ratesProb(const int i) const {return _ratesProb[i];} ^ mixtureDistribution.cpp:228:20: note: 'categoryInComponent' was declared here int componentNum, categoryInComponent, totalCat = 0; ^~~~~~~~~~~~~~~~~~~ suffStatGammaMixture.cpp: In member function 'void suffStatGammaMixture::computeStatistics()': suffStatGammaMixture.cpp:123:12: warning: variable 'Exp_Rk' set but not used [-Wunused-but-set-variable] MDOUBLE Exp_Rk, Exp_LogRk, sum; ^~~~~~ suffStatGammaMixture.cpp: In member function 'double suffStatGammaMixture::computeQ()': suffStatGammaMixture.cpp:224:11: warning: unused variable 'first' [-Wunused-variable] MDOUBLE first = _MkVec[comp] * log(P_k); ^~~~~ suffStatGammaMixture.cpp:225:11: warning: unused variable 'second' [-Wunused-variable] MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); ^~~~~~ suffStatGammaMixture.cpp:226:11: warning: unused variable 'third' [-Wunused-variable] MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); ^~~~~ suffStatGammaMixture.cpp:227:11: warning: unused variable 'fourth' [-Wunused-variable] MDOUBLE fourth = -_AkVec[comp]*beta_k; ^~~~~~ suffStatGammaMixture.cpp:228:11: warning: unused variable 'fifth' [-Wunused-variable] MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); ^~~~~ suffStatGammaMixture.cpp:216:10: warning: variable 'res2' set but not used [-Wunused-but-set-variable] MDOUBLE res2 = 0.0; ^~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from mixtureDistribution.h:11, from mixtureDistribution.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from mixtureDistribution.h:11, from mixtureDistribution.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void mixtureDistribution::change_number_of_components(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from suffStatGammaMixture.h:16, from suffStatGammaMixture.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from suffStatGammaMixture.h:16, from suffStatGammaMixture.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void suffStatGammaMixture::allocatePlaceForSuffStat()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); ^~~~ optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^~~~~~~~ In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGammaPlus(double) const': optGammaMixtureEM.h:76:11: warning: unused variable 'res1' [-Wunused-variable] MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); ^~~~ optGammaMixtureEM.h: In member function 'double C_evalAlphaEM::diGamma(double) const': optGammaMixtureEM.h:87:11: warning: unused variable 'debugRes' [-Wunused-variable] MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from GamMixtureOptimizer.cpp:7: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from GamMixtureOptimizer.cpp:7: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mixtureDistribution&}; _Tp = mixtureDistribution; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {mixtureDistribution}; _Tp = mixtureDistribution; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from replacementModel.h:6, from wYangModel.h:4, from wYangModel.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from codonUtils.cpp:3: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from codonUtils.cpp:3: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'Vdouble freqCodonF3x4(const sequenceContainer&, codon*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from replacementModel.h:6, from wYangModel.h:4, from wYangModel.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In constructor 'wYangModel::wYangModel(double, double, bool, codon*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'wYangModel::wYangModel(double, double, const Vdouble&, bool, codon*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::__cxx11::string, codon*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from codonUtils.cpp:3: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from likelihoodComputation2Codon.h:6, from likelihoodComputation2Codon.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In function 'double likelihoodComputation2Codon::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, Vdouble&, const distribution*, const Vdouble*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from betaDistributionFixedCategories.h:9, from betaDistributionFixedCategories.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from betaDistributionFixedCategories.h:9, from betaDistributionFixedCategories.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void betaDistributionFixedCategories::fill_mean()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'betaDistributionFixedCategories::betaDistributionFixedCategories()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In constructor 'betaDistributionFixedCategories::betaDistributionFixedCategories(double, double, int)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from gtrModel.cpp:1: gtrModel.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': gtrModel.h:54:10: warning: 'gtrModel::_g2t' will be initialized after [-Wreorder] MDOUBLE _g2t; ^~~~ gtrModel.h:47:10: warning: 'Vdouble gtrModel::_freq' [-Wreorder] Vdouble _freq; ^~~~~ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] gtrModel::gtrModel(const Vdouble& freq, ^~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2c() const': gtrModel.cpp:139:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2g() const': gtrModel.cpp:153:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_a2t() const': gtrModel.cpp:167:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2g() const': gtrModel.cpp:181:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ In file included from bestGtrModelParams.cpp:3: bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^~~ bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_c2t() const': gtrModel.cpp:195:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ gtrModel.cpp: In member function 'double gtrModel::get_g2t() const': gtrModel.cpp:209:9: warning: 'result' may be used uninitialized in this function [-Wmaybe-uninitialized] return result; ^~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from replacementModel.h:6, from gtrModel.h:4, from gtrModel.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from replacementModel.h:6, from gtrModel.h:4, from gtrModel.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In constructor 'gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from definitions.h:18, from bestGtrModelParams.h:6, from bestGtrModelParams.cpp:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void simulateRateShiftJumps::init(std::vector)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from definitions.h:18, from bestGtrModelParams.h:6, from bestGtrModelParams.cpp:3: /usr/include/c++/8/bits/stl_vector.h: In constructor 'bestGtrModelProportional::bestGtrModelProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::__cxx11::string, bool, bool, const Vdouble*, double, double, double, double, double)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ 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 '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' cd programs;make all make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make all cd gainLoss && make all cd indelCoder && make all make[3]: Entering directory '/build/fastml-3.1/programs/fastml' make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' making depend making depend making depend g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp indelCoder.cpp: In member function 'void indelCoder::printGapsInfo()': indelCoder.cpp:422:6: warning: unused variable 'gapNum' [-Wunused-variable] int gapNum = 1; ^~~~~~ indelCoder.cpp: In member function 'void indelCoder::printIndelSummary()': indelCoder.cpp:587:7: warning: unused variable 'isSIC' [-Wunused-variable] bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; ^~~~~ indelCoder.cpp:597:6: warning: unused variable 'seqLeng' [-Wunused-variable] int seqLeng = _sc.seqLen(); ^~~~~~~ In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ In file included from bbAlg.cpp:1: bbAlg.h: In constructor 'bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, bbAlg::boundMethod, const string&, double, const distribution*)': bbAlg.h:61:16: warning: 'bbAlg::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbAlg.h:60:20: warning: 'BandBReportAllPos bbAlg::BandBReportAllPos1' [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^~~~~~~~~~~~~~~~~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^~~~~ In file included from bbAlg.cpp:1: bbAlg.h:60:20: warning: 'bbAlg::BandBReportAllPos1' will be initialized after [-Wreorder] BandBReportAllPos BandBReportAllPos1; // report for all positions. ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:14: warning: 'const tree& bbAlg::_et' [-Wreorder] const tree& _et; ^~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] bbAlg::bbAlg(const tree& et, ^~~~~ In file included from bbNodeOrderAlg.h:5, from bbAlg.h:5, from bbAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ indelCoder.cpp: In member function 'void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)': indelCoder.cpp:175:19: warning: 'condition' may be used uninitialized in this function [-Wmaybe-uninitialized] while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const string&)': gainLossOptions.cpp:2064:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^~~~~~~~~~ gainLossOptions.cpp: In static member function 'static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const string&)': gainLossOptions.cpp:2111:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/computePijComponent.h:6, from bbAlg.h:4, from bbAlg.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/computePijComponent.h:6, from bbAlg.h:4, from bbAlg.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'double bbAlg::bbReconstructAllPositions(sequenceContainer&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp gainLossOptions.cpp: In static member function 'static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const string&)': gainLossOptions.cpp:2419:9: warning: 'returnType' may be used uninitialized in this function [-Wmaybe-uninitialized] return returnType; ^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor 'bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)': bbEvaluateSpecificAV.h:34:27: warning: 'bbEvaluateSpecificAV::_sc' will be initialized after [-Wreorder] const sequenceContainer& _sc; ^~~ bbEvaluateSpecificAV.h:31:23: warning: 'const computePijGam& bbEvaluateSpecificAV::_bbcpij' [-Wreorder] const computePijGam& _bbcpij; ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, ^~~~~~~~~~~~~~~~~~~~ bbEvaluateSpecificAV.cpp: In member function 'double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)': bbEvaluateSpecificAV.cpp:65:12: warning: unused variable 'rate' [-Wunused-variable] MDOUBLE rate = _sp.rates(categor); // the r. ^~~~ In file included from bbEvaluateSpecificAV.h:4, from bbEvaluateSpecificAV.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ character.cpp: In member function 'int character::getLongestGapStIndex()': character.cpp:28:9: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] return longestGapStIndex; ^~~~~~~~~~~~~~~~~ character.cpp: In member function 'void character::checkForTriangleInequality(int, int)': character.cpp:6:63: warning: 'longestGapStIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ ^ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o a - indelCoderUtils.o a - character.o a - gaps.o ranlib libindelCoder.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor 'bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)': bbNodeOrderAlg.h:33:27: warning: 'bbNodeOrderAlg::_sc' will be initialized after [-Wreorder] const sequenceContainer& _sc; ^~~ bbNodeOrderAlg.h:32:23: warning: 'const computePijGam& bbNodeOrderAlg::_cpij' [-Wreorder] const computePijGam& _cpij; ^~~~~ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp In file included from bbNodeOrderAlg.h:5, from bbNodeOrderAlg.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: In constructor 'bb_options::bb_options(int&, char**)': bb_options.h:49:9: warning: 'bb_options::reportFile' will be initialized after [-Wreorder] string reportFile; ^~~~~~~~~~ bb_options.h:44:9: warning: 'std::__cxx11::string bb_options::outFile_seq_joint' [-Wreorder] string outFile_seq_joint; ^~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:45:9: warning: 'bb_options::outFile_seq_marginal' will be initialized after [-Wreorder] string outFile_seq_marginal; ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:9: warning: 'std::__cxx11::string bb_options::outFile_prob_joint' [-Wreorder] string outFile_prob_joint; ^~~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:43:9: warning: 'bb_options::outFile_prob_marginal' will be initialized after [-Wreorder] string outFile_prob_marginal; ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:9: warning: 'std::__cxx11::string bb_options::seqfile' [-Wreorder] string seqfile; ^~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:30:21: warning: 'bb_options::distributionName' will be initialized after [-Wreorder] distributionsNames distributionName; ^~~~~~~~~~~~~~~~ bb_options.h:26:16: warning: 'bb_options::SeqFileFormat bb_options::seqOutputFormat' [-Wreorder] SeqFileFormat seqOutputFormat; ^~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:41:9: warning: 'bb_options::outTreeFileAncestor' will be initialized after [-Wreorder] string outTreeFileAncestor; ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:15: warning: 'bb_options::boundMethods bb_options::boundMethod' [-Wreorder] boundMethods boundMethod; ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:47:10: warning: 'bb_options::gammaPar' will be initialized after [-Wreorder] MDOUBLE gammaPar; ^~~~~~~~ bb_options.h:28:7: warning: 'bool bb_options::userProvideAlpha' [-Wreorder] bool userProvideAlpha; ^~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:48:6: warning: 'bb_options::gammaCategies' will be initialized after [-Wreorder] int gammaCategies; ^~~~~~~~~~~~~ bb_options.h:36:19: warning: 'bb_options::modelNameOptions bb_options::modelName' [-Wreorder] modelNameOptions modelName; ^~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h:39:7: warning: 'bb_options::useChebyshev' will be initialized after [-Wreorder] bool useChebyshev; ^~~~~~~~~~~~ bb_options.h:27:9: warning: 'std::__cxx11::string bb_options::treeOutFile' [-Wreorder] string treeOutFile; ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] bb_options::bb_options(int& argc, char *argv[]): ^~~~~~~~~~ In file included from bb_options.cpp:2: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In function 'void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from bbReport.cpp:1: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void bbNodeOrderAlg::getNextNodeAndCharOrder(tree::TreeNode*&, std::vector&, std::vector&, int, bool, doubleRep&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ bbReport.h: In constructor 'BandBReport::BandBReport(const string&, int, int)': bbReport.h:53:16: warning: 'BandBReport::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:51:12: warning: 'const int BandBReport::_position' [-Wreorder] const int _position; ^~~~~~~~~ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : ^~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp computeMarginalReconstruction.cpp: In member function 'void computeMarginalReconstruction::compute(const distribution*)': computeMarginalReconstruction.cpp:67:11: warning: unused variable 'likelihoodOfPos' [-Wunused-variable] MDOUBLE likelihoodOfPos = 0; ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from bbReport.h:4, from bbReport.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from bbReport.h:4, from bbReport.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In member function 'void BandBReport::report(std::__cxx11::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:41: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h: In constructor 'gainLoss::gainLoss()': gainLoss.h:266:21: warning: 'gainLoss::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLoss.h:240:16: warning: 'distribution* gainLoss::_lossDist' [-Wreorder] distribution* _lossDist; ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h:240:16: warning: 'gainLoss::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^~~~~~~~~ gainLoss.h:239:16: warning: 'distribution* gainLoss::_gainDist' [-Wreorder] distribution* _gainDist; ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~ In file included from gainLoss.cpp:20: gainLoss.h:273:12: warning: 'gainLoss::_refSeq' will be initialized after [-Wreorder] sequence* _refSeq; // the reference sequence ^~~~~~~ gainLoss.h:267:11: warning: 'Vdouble* gainLoss::_weightsUniqPatterns' [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) ^~~~~~~~ jointNoGamma.cpp: In member function 'void jointNoGamma::compute()': jointNoGamma.cpp:23:10: warning: unused variable 'totalLikelihoodOfReconstruction' [-Wunused-variable] MDOUBLE totalLikelihoodOfReconstruction = 0; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function 'std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)': jointNoGamma.cpp:108:12: warning: unused variable 'maxL' [-Wunused-variable] MDOUBLE maxL = VERYSMALL; ^~~~ gainLoss.cpp: In member function 'void gainLoss::removePositionsWithHighPercentOfMissingData(double)': gainLoss.cpp:604:7: warning: unused variable 'missigDataChar' [-Wunused-variable] char missigDataChar = -2; ^~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1245:57: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^~ gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ ^~~~~~~~~~~~~~~~~~~ ( ) gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)': gainLoss.cpp:1868:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(sp); ^~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:1990:11: warning: unused variable 'sumPijQij' [-Wunused-variable] MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); ^~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Distance = int; _Tp = std::pair >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >*, std::vector > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceFromRootForRecent(tree&)': gainLoss.cpp:4205:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'double gainLoss::computeDistanceNearestOTUforRecent(tree&)': gainLoss.cpp:4283:7: warning: variable 'isRecentBiggerAncient' set but not used [-Wunused-but-set-variable] bool isRecentBiggerAncient = true; ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::multipleAllBranchesByFactorAtStart(double)': gainLoss.cpp:4382:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^ gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ ^~~~~~~~~~~ ( ) gainLoss.cpp: In member function 'void gainLoss::startSimultePosteriorExpectationOfChange(int, int)': gainLoss.cpp:4951:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from computeMarginalReconstruction.h:4, from computeMarginalReconstruction.cpp:1: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair, std::allocator > >}; _Tp = std::pair >; _Alloc = std::allocator > >]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector > >::iterator' {aka '__gnu_cxx::__normal_iterator >*, std::vector > > >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >*, std::vector > > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeMarginalReconstruction.h:4, from computeMarginalReconstruction.cpp:1: /usr/include/c++/8/bits/stl_vector.h: In constructor 'computeMarginalReconstruction::computeMarginalReconstruction(const tree&, std::vector&, const sequenceContainer&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ gainLoss.cpp: In function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor 'BandBReportAllPos::BandBReportAllPos(const string&, int)': bbReport.h:14:16: warning: 'BandBReportAllPos::_reportFileName' will be initialized after [-Wreorder] const string& _reportFileName; ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: 'const int BandBReportAllPos::_minNumOfNodesToVisit' [-Wreorder] const int _minNumOfNodesToVisit; ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) ^~~~~~~~~~~~~~~~~ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor 'C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)': ../../libs/phylogeny/bestGtrModelParams.h:175:21: warning: 'C_evalGTRParamProportional::_sp' will be initialized after [-Wreorder] stochasticProcess& _sp; ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:27: warning: 'const gammaDistribution* C_evalGTRParamProportional::_pProportionDist' [-Wreorder] const gammaDistribution* _pProportionDist; ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] C_evalGTRParamProportional( const GTRParam param, ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: 'const string usege_splash_screen()' defined but not used [-Wunused-function] static const string usege_splash_screen() { ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp gainLoss.cpp: In member function 'void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)': gainLoss.cpp:2035:44: warning: 'bestLossProbInvariant' may be used uninitialized in this function [-Wmaybe-uninitialized] if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp: In function 'void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)': gainLossUtils.cpp:72:5: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(probs) ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if(probs) ^ gainLossUtils.cpp: In function 'void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)': gainLossUtils.cpp:481:10: warning: variable 'normFactor' set but not used [-Wunused-but-set-variable] MDOUBLE normFactor; ^~~~~~~~~~ gainLossUtils.cpp: In function 'double sumPijQijVec(std::vector >&, distribution*, distribution*)': gainLossUtils.cpp:788:10: warning: unused variable 'scale' [-Wunused-variable] MDOUBLE scale; ^~~~~ gainLossUtils.cpp: In function 'double getRateBeta(distribution*)': gainLossUtils.cpp:312:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^~~ mainbb.cpp: In member function 'void mainbb::findAncestralSequencesGammaJoint()': mainbb.cpp:428:101: warning: 'bm' may be used uninitialized in this function [-Wmaybe-uninitialized] bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); ^ 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 gainLoss.cpp: In member function 'void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()': gainLoss.cpp:3980:52: warning: 'AlphaLoss' may be used uninitialized in this function [-Wmaybe-uninitialized] gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3980:52: warning: 'AlphaGain' may be used uninitialized in this function [-Wmaybe-uninitialized] 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 gainLoss.cpp: In member function 'void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)': gainLoss.cpp:2511:22: warning: 'countsGL' may be used uninitialized in this function [-Wmaybe-uninitialized] if(countsGL) delete countsGL; ^~~~~~~~ make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from optimizeGainLossModel.cpp:17: optimizeGainLossModel.h: In constructor 'optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModel.h:87:11: warning: 'optimizeGainLossModel::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h:86:20: warning: 'unObservableData* optimizeGainLossModel::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:85:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from optimizeGainLossModelVV.cpp:17: optimizeGainLossModelVV.h: In constructor 'optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)': optimizeGainLossModelVV.h:82:11: warning: 'optimizeGainLossModelVV::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:20: warning: 'unObservableData* optimizeGainLossModelVV::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:258:13: warning: unused variable 'currentlogL' [-Wunused-variable] MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); ^~~~~~~~~~~ optimizeGainLossModelVV.cpp:76:10: warning: variable 'sumPijQij' set but not used [-Wunused-but-set-variable] MDOUBLE sumPijQij; ^~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startStochasticProcess()': gainLoss.cpp:869:23: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted ^~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startStochasticProcessVec()': gainLoss.cpp:1127:25: warning: 'rateDist' may be used uninitialized in this function [-Wmaybe-uninitialized] if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted ^~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor 'gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)': gainLossModel.h:108:10: warning: 'gainLossModel::_gain' will be initialized after [-Wreorder] MDOUBLE _gain; // _Q[0][1] ^~~~~ gainLossModel.h:105:10: warning: 'Vdouble gainLossModel::_freq' [-Wreorder] Vdouble _freq; ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h:112:7: warning: 'gainLossModel::_isRootFreqEQstationary' will be initialized after [-Wreorder] bool _isRootFreqEQstationary; ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:111:7: warning: 'bool gainLossModel::_isReversible' [-Wreorder] bool _isReversible; ^~~~~~~~~~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ In file included from gainLossModel.cpp:17: gainLossModel.h:114:7: warning: 'gainLossModel::_isHGT_with_Q' will be initialized after [-Wreorder] bool _isHGT_with_Q; ^~~~~~~~~~~~~ gainLossModel.h:110:8: warning: 'q2pt* gainLossModel::_q2pt' [-Wreorder] q2pt *_q2pt; // dont use q2p ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): ^~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -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 siteSpecificGL.cpp:24: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function 'void gainLoss::startEvolTreeTopology(std::ostream&)': gainLoss.cpp:1195:10: warning: 'pDm' may be used uninitialized in this function [-Wmaybe-uninitialized] delete pDm; ^~~ In file included from computePosteriorExpectationOfChange.cpp:25: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from siteSpecificGL.h:22, from siteSpecificGL.cpp:18: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from siteSpecificGL.h:22, from siteSpecificGL.cpp:18: /usr/include/c++/8/bits/stl_vector.h: In function 'void computeEB_EXP_siteSpecificGL(int, const sequenceContainer&, const std::vector >&, const tree&, const distribution*, const distribution*, const distribution*, Vdouble&, double&, double&, double&, double&, double, VVVdouble&, unObservableData*)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h:35, from gainLossProject.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:35, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:134:7: warning: 'gainLossOptimizer::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ gainLossOptimizer.h:109:21: warning: 'stochasticProcess* gainLossOptimizer::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] sequenceContainer _sc; ^~~ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h: In constructor 'gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)': gainLossOptimizer.h:139:16: warning: 'gainLossOptimizer::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^~~~~~~~~ gainLossOptimizer.h:135:20: warning: 'sequenceContainer gainLossOptimizer::_sc' [-Wreorder] sequenceContainer _sc; ^~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:135:20: warning: 'gainLossOptimizer::_sc' will be initialized after [-Wreorder] sequenceContainer _sc; ^~~ gainLossOptimizer.h:93:10: warning: 'double gainLossOptimizer::_epsilonOptimization' [-Wreorder] MDOUBLE _epsilonOptimization; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:17: gainLossOptimizer.h:104:11: warning: 'gainLossOptimizer::_weightsUniqPatterns' will be initialized after [-Wreorder] Vdouble* _weightsUniqPatterns; ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: 'unObservableData* gainLossOptimizer::_unObservableData_p' [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, ^~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengths(int)': gainLossOptimizer.cpp:498:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:543:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:487:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function 'double gainLossOptimizer::optimizeBranchLengthsvv(int)': gainLossOptimizer.cpp:634:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:677:12: warning: unused variable 'oldLnoUnObservableDataCorrection' [-Wunused-variable] MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:623:10: warning: variable 'newLnoUnObservableDataCorrection' set but not used [-Wunused-but-set-variable] MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp gainLossOptimizer.cpp: In function 'gainLossOptions::distributionType getRateDistributionType(distribution*)': gainLossOptimizer.cpp:833:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized] return res; ^~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h:35, from rate4siteGL.h:24, from rate4siteGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from computeCountsGL.h:24, from computeCountsGL.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from rate4siteGL.cpp:17: rate4siteGL.h: In constructor 'rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, unObservableData*)': rate4siteGL.h:59:7: warning: 'rate4siteGL::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ rate4siteGL.h:58:21: warning: 'stochasticProcess* rate4siteGL::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): ^~~~~~~~~~~ rate4siteGL.cpp: In member function 'void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)': rate4siteGL.cpp:151:6: warning: unused variable 'precisionHigh' [-Wunused-variable] int precisionHigh = 5; ^~~~~~~~~~~~~ rate4siteGL.cpp:152:6: warning: unused variable 'precisionLow' [-Wunused-variable] int precisionLow = 3; ^~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::__cxx11::string&, VVdouble&, double, bool)': computeCountsGL.h:104:7: warning: 'computeCountsGL::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ computeCountsGL.h:102:21: warning: 'stochasticProcess* computeCountsGL::_sp' [-Wreorder] stochasticProcess *_sp; ^~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] MDOUBLE _distanceFromNearestOTUForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h: In constructor 'computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::__cxx11::string&, VVVdouble&, double, bool)': computeCountsGL.h:109:16: warning: 'computeCountsGL::_lossDist' will be initialized after [-Wreorder] distribution* _lossDist; ^~~~~~~~~ computeCountsGL.h:105:20: warning: 'sequenceContainer computeCountsGL::_sc' [-Wreorder] sequenceContainer _sc; ^~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ In file included from computeCountsGL.cpp:17: computeCountsGL.h:117:10: warning: 'computeCountsGL::_distanceFromNearestOTUForRecent' will be initialized after [-Wreorder] MDOUBLE _distanceFromNearestOTUForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: 'bool computeCountsGL::_isSilent' [-Wreorder] bool _isSilent; ^~~~~~~~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22, from rate4siteGL.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22, from rate4siteGL.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'void rate4siteGL::normalizeRates()': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp In file included from gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': computeCorrelations.cpp:130:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:408:8: warning: unused variable 'isHigherNminReducedFreqOfHighCorr' [-Wunused-variable] int isHigherNminReducedFreqOfHighCorr = false; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:7: warning: unused variable 'typeIndex' [-Wunused-variable] int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used ^~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': computeCorrelations.cpp:559:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] if(!simCorrelStream==NULL) ^~~~ computeCorrelations.cpp: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': computeCorrelations.cpp:676:9: warning: variable 'prevNumberOfSimulationsInRange' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationsInRange = 1; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:9: warning: variable 'prevNumberOfSimulationPointsMoreExtremeOrEqToCorr' set but not used [-Wunused-but-set-variable] int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:9: warning: unused variable 'numOfBinsWithLowerSignificance' [-Wunused-variable] int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:680:10: warning: unused variable 'isNextLowerBinAllowed' [-Wunused-variable] bool isNextLowerBinAllowed = true; ^~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)': computeCorrelations.cpp:894:19: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(!numOfSites_A == numOfSites_B){ ^~ computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning if(!numOfSites_A == numOfSites_B){ ^~~~~~~~~~~~~ ( ) computeCorrelations.cpp: In member function 'void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::__cxx11::string*)': computeCorrelations.cpp:1009:7: warning: unused variable 'isPearson' [-Wunused-variable] bool isPearson = false; ^~~~~~~~~ computeCorrelations.cpp:1025:6: warning: unused variable 'numOfbranches' [-Wunused-variable] int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': computeCorrelations.cpp:1347:112: warning: narrowing conversion of 'gainLossOptions::_pValueCutOffForBootStrap' from 'double' to 'float' inside { } [-Wnarrowing] float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; ^ computeCorrelations.cpp:1300:7: warning: variable 'it_siteB' set but not used [-Wunused-but-set-variable] it_B it_siteB = it_siteA->second.begin(); ^~~~~~~~ In file included from gainLoss.h:35, from gainLoss4site.h:24, from gainLoss4site.cpp:17: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss4site.cpp:17: gainLoss4site.h: In constructor 'gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::__cxx11::string&, unObservableData*, double)': gainLoss4site.h:68:7: warning: 'gainLoss4site::_tr' will be initialized after [-Wreorder] tree _tr; ^~~ gainLoss4site.h:61:38: warning: 'std::vector > gainLoss4site::_spVVec' [-Wreorder] vector > _spVVec; //save stochasticProcess for each category ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, ^~~~~~~~~~~~~ In file included from gainLoss4site.cpp:17: gainLoss4site.h:79:20: warning: 'gainLoss4site::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; // ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:10: warning: 'double gainLoss4site::_alphaConf' [-Wreorder] MDOUBLE _alphaConf; ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, ^~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'std::pair<_FIter, _FIter> std::__equal_range(_ForwardIterator, _ForwardIterator, const _Tp&, _CompareItTp, _CompareTpIt) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _CompareItTp = __gnu_cxx::__ops::_Iter_less_val; _CompareTpIt = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __equal_range(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'std::pair<_FIter, _FIter> std::__equal_range(_ForwardIterator, _ForwardIterator, const _Tp&, _CompareItTp, _CompareTpIt) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = float; _CompareItTp = __gnu_cxx::__ops::_Iter_less_val; _CompareTpIt = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In member function 'void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)': /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from simulateChangesAlongTree.cpp:20: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const extremeValDistribution&}; _Tp = extremeValDistribution; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.h:35, from simulateOnePos.cpp:32: gainLossModel.h: In constructor 'gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)': gainLossModel.h:186:10: warning: 'gainLossModelNonReversible::_loss' will be initialized after [-Wreorder] MDOUBLE _loss; // _Q[1][0] ^~~~~ gainLossModel.h:128:95: warning: base 'gainLossModel' [-Wreorder] :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor 'simulateOnePos::simulateOnePos(std::__cxx11::string, std::ostream*, std::ostream*, int, std::__cxx11::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)': simulateOnePos.h:72:7: warning: 'simulateOnePos::_simulateNullModel' will be initialized after [-Wreorder] bool _simulateNullModel; ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:6: warning: 'int simulateOnePos::_simNum' [-Wreorder] int _simNum; ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h:65:10: warning: 'simulateOnePos::_theta' will be initialized after [-Wreorder] MDOUBLE _theta; ^~~~~~ simulateOnePos.h:64:10: warning: 'double simulateOnePos::_sumGainLoss' [-Wreorder] MDOUBLE _sumGainLoss; ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h:75:11: warning: 'simulateOnePos::_freq_cpN' will be initialized after [-Wreorder] Vdouble* _freq_cpN; ^~~~~~~~~ simulateOnePos.h:69:11: warning: 'std::ostream* simulateOnePos::_simulatedEvents' [-Wreorder] ostream *_simulatedEvents; ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function 'void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::__cxx11::string)': simulateOnePos.cpp:181:9: warning: unused variable 'isRevers' [-Wunused-variable] bool isRevers = false; ^~~~~~~~ simulateOnePos.cpp:202:12: warning: variable 'sumQii' set but not used [-Wunused-but-set-variable] MDOUBLE sumQii = 1.0; ^~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::__cxx11::string, VVVVdouble&, bool, double*)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from bblLS.cpp:17: bblLS.h:50:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h:58:17: warning: converting to non-pointer type 'double' from NULL [-Wconversion-null] MDOUBLE curL =NULL); ^~~~ bblLS.h: In constructor 'evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:119:20: warning: 'evalBranchSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: 'Vdouble* evalBranchSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~ bblLS.h: In constructor 'evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)': bblLS.h:174:20: warning: 'evalBranchProportionExponentSPvv::_unObservableData_p' will be initialized after [-Wreorder] unObservableData* _unObservableData_p; ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: 'Vdouble* evalBranchProportionExponentSPvv::_weights' [-Wreorder] Vdouble* _weights; ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:36:14: warning: NULL used in arithmetic [-Wpointer-arith] if (curL == NULL) ^~~~ bblLS.cpp: In member function 'double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)': bblLS.cpp:112:14: warning: NULL used in arithmetic [-Wpointer-arith] if (curL == NULL) ^~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h: In member function 'void computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMap(VVVdouble&, VVVVdouble&, VVVdouble&)': /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:60, from ../../libs/phylogeny/njConstrain.h:6, from ../../libs/phylogeny/nj.h:11, from gainLoss.h:47, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../../libs/phylogeny/njConstrain.h:6, from ../../libs/phylogeny/nj.h:11, from gainLoss.h:47, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = double; _Compare = std::less >; _Alloc = std::allocator, double> >]': /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/map:61, from ../../libs/phylogeny/njConstrain.h:6, from ../../libs/phylogeny/nj.h:11, from gainLoss.h:47, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator, double> >'} changed in GCC 7.1 __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp computeCorrelations.cpp: In member function 'int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)': computeCorrelations.cpp:505:5: warning: 'expextedFreq' may be used uninitialized in this function [-Wmaybe-uninitialized] if(freqOfHighCorr>expextedFreq && freqOfHighCorr >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2190:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__equal_range(__first, __last, __val, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_less_val(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_less_iter()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor 'sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::__cxx11::string&, double, double)': sankoffReconstructGL.h:85:9: warning: 'sankoffReconstructGL::_outDir' will be initialized after [-Wreorder] string _outDir; ^~~~~~~ sankoffReconstructGL.h:84:10: warning: 'double sankoffReconstructGL::_costMatrixGainLossRatio' [-Wreorder] MDOUBLE _costMatrixGainLossRatio; ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^~~~~~~~~~~~~~~~~~~~ In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h:84:10: warning: 'sankoffReconstructGL::_costMatrixGainLossRatio' will be initialized after [-Wreorder] MDOUBLE _costMatrixGainLossRatio; ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:10: warning: 'double sankoffReconstructGL::_distanceFromRootForRecent' [-Wreorder] MDOUBLE _distanceFromRootForRecent; ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/tree.h:6, from sankoffReconstructGL.h:23, from sankoffReconstructGL.cpp:17: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/tree.h:6, from sankoffReconstructGL.h:23, from sankoffReconstructGL.cpp:17: /usr/include/c++/8/bits/stl_vector.h: In member function 'double sankoffReconstructGL::traverseDownMP(VVdouble&, std::vector > >&, VVint&, VVdouble&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void sankoffReconstructGL::traverseUpMP(VVdouble&, std::vector > >&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ ar rv libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o ar: creating libgainLoss.a a - gainLossOptions.o a - gainLoss.o a - gainLossUtils.o a - optimizeGainLossModel.o a - optimizeGainLossModelVV.o a - ../../libs/phylogeny/likelihoodComputationGL.o a - gainLossModel.o a - siteSpecificGL.o a - computePosteriorExpectationOfChange.o a - gainLossProject.o a - gainLossOptimizer.o a - ancestralReconstructStates.o a - rate4siteGL.o a - computeCountsGL.o a - computeCorrelations.o a - gainLoss4site.o a - simulateChangesAlongTree.o a - simulateOnePos.o a - bblLS.o a - sankoffReconstructGL.o ranlib libgainLoss.a g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny gainLoss.o libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss make[3]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[2]: Leaving directory '/build/fastml-3.1/programs' make[1]: Leaving directory '/build/fastml-3.1' dh_auto_test make -j3 test make[1]: Entering directory '/build/fastml-3.1' cd libs;make test cd programs;make test make[2]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make test make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make test cd gainLoss && make test make[3]: Entering directory '/build/fastml-3.1/programs/fastml' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' cd indelCoder && make test make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' if [ -d tests ] ; then cd tests && make -k ; fi make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[2]: Leaving directory '/build/fastml-3.1/programs' make[3]: Entering directory '/build/fastml-3.1/libs/phylogeny' cd tests; make -k test make[4]: Entering directory '/build/fastml-3.1/libs/phylogeny/tests' g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. split_test.cpp ../libEvolTree.a -lEvolTree -o split_test g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. splitMap_test.cpp ../libEvolTree.a -lEvolTree -o splitMap_test g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqTheDistBetweenThem-3.cpp ../libEvolTree.a -lEvolTree -o given2seqTheDistBetweenThem-3 g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThem.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThem g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. checkTreeLikelihoodGivenBranches.cpp ../libEvolTree.a -lEvolTree -o checkTreeLikelihoodGivenBranches g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistBetweenThemGamma.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistBetweenThemGamma g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. given2seqEstimateTheDistanceK2P.cpp ../libEvolTree.a -lEvolTree -o given2seqEstimateTheDistanceK2P g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. doubleRep.cpp ../libEvolTree.a -lEvolTree -o doubleRep g++ -g -O2 -ffile-prefix-map=/build/fastml-3.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wno-sign-compare -I.. -DLOG -O0 -L.. readTreeWithComments.cpp ../libEvolTree.a -lEvolTree -o readTreeWithComments ./split_test > split_test.out.tmp ./splitMap_test > splitMap_test.out.tmp ./given2seqTheDistBetweenThem-3 > given2seqTheDistBetweenThem-3.out.tmp ./given2seqEstimateTheDistBetweenThem > given2seqEstimateTheDistBetweenThem.out.tmp ./checkTreeLikelihoodGivenBranches > checkTreeLikelihoodGivenBranches.out.tmp ./given2seqEstimateTheDistBetweenThemGamma > given2seqEstimateTheDistBetweenThemGamma.out.tmp ./doubleRep > doubleRep.out.tmp diff split_test.out.tmp split_test.out.standard diff splitMap_test.out.tmp splitMap_test.out.standard diff given2seqTheDistBetweenThem-3.out.tmp given2seqTheDistBetweenThem-3.out.standard diff given2seqEstimateTheDistBetweenThem.out.tmp given2seqEstimateTheDistBetweenThem.out.standard diff checkTreeLikelihoodGivenBranches.out.tmp checkTreeLikelihoodGivenBranches.out.standard diff given2seqEstimateTheDistBetweenThemGamma.out.tmp given2seqEstimateTheDistBetweenThemGamma.out.standard diff doubleRep.out.tmp doubleRep.out.standard ./given2seqEstimateTheDistanceK2P > given2seqEstimateTheDistanceK2P.out.tmp diff given2seqEstimateTheDistanceK2P.out.tmp given2seqEstimateTheDistanceK2P.out.standard ./readTreeWithComments treeWithComments.tree>readTreeWithComments.out.tmp diff readTreeWithComments.out.tmp readTreeWithComments.out.standard make[4]: Leaving directory '/build/fastml-3.1/libs/phylogeny/tests' make[3]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' echo test test make[1]: Leaving directory '/build/fastml-3.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j3 install DESTDIR=/build/fastml-3.1/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/fastml-3.1' cd libs;make all make[2]: Entering directory '/build/fastml-3.1/libs' cd phylogeny && make all make[3]: Entering directory '/build/fastml-3.1/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fastml-3.1/libs/phylogeny' make[2]: Leaving directory '/build/fastml-3.1/libs' cd programs;make install make[2]: Entering directory '/build/fastml-3.1/programs' cd fastml && make install cd gainLoss && make install cd indelCoder && make install make[3]: Entering directory '/build/fastml-3.1/programs/indelCoder' mkdir -p ../../bin make[3]: Entering directory '/build/fastml-3.1/programs/fastml' mkdir -p ../../bin make[3]: Entering directory '/build/fastml-3.1/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss cp fastml ../../bin/fastml cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/build/fastml-3.1/programs/indelCoder' make[3]: Leaving directory '/build/fastml-3.1/programs/fastml' make[3]: Leaving directory '/build/fastml-3.1/programs/gainLoss' make[2]: Leaving directory '/build/fastml-3.1/programs' make[1]: Leaving directory '/build/fastml-3.1' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/fastml/usr/bin/fastml contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/gainLoss contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fastml/usr/bin/indelCoder contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fastml' in '../fastml_3.1-4_armhf.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.1-4_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../fastml_3.1-4_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1202 and its subdirectories I: Current time: Fri May 22 17:49:20 -12 2020 I: pbuilder-time-stamp: 1590212960