sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | fastml 3.11-2 (armhf) Sun, 06 Sep 2020 08:12:56 +0000 | +==============================================================================+ Package: fastml Version: 3.11-2 Source Version: 3.11-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: armhf Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-8d4737f4-ee71-4e64-968e-fbaaf93f8fd1' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-VvvTSb/resolver-K2Fshz' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://debian.oregonstate.edu/debian unstable InRelease Get:2 http://debian.oregonstate.edu/debian unstable/main armhf Packages [8112 kB] Fetched 8112 kB in 2s (4486 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'fastml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastml.git Please use: git clone https://salsa.debian.org/med-team/fastml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 861 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main fastml 3.11-2 (dsc) [1892 B] Get:2 http://debian.oregonstate.edu/debian unstable/main fastml 3.11-2 (tar) [849 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main fastml 3.11-2 (diff) [9860 B] Fetched 861 kB in 0s (16.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-VvvTSb/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-VvvTSb' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 12~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf Filtered Build-Depends: debhelper (>= 12~), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [401 B] Get:5 copy:/<>/apt_archive ./ Packages [493 B] Fetched 1851 B in 0s (73.1 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils build-essential cpp-10-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-10-arm-linux-gnueabihf gcc-10-arm-linux-gnueabihf-base gcc-10-base:armhf gcc-10-cross-base gcc-9-base:armhf gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan6-armhf-cross libatomic1:armhf libatomic1-armhf-cross libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev-armhf-cross libgcc-9-dev:armhf libgcc-s1:armhf libgcc-s1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu67 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-10-dev libstdc++-10-dev-armhf-cross libstdc++-9-dev:armhf libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db perl perl-modules-5.30 po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales cpp-doc dh-make binutils-multiarch debian-keyring g++-multilib g++-10-multilib gcc-10-doc manpages-dev flex bison gdb-arm-linux-gnueabihf gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armhf libc-l10n:armhf locales:armhf glibc-doc manpages-dev:armhf gnupg git bzr libstdc++-10-doc libstdc++-9-doc:armhf libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl Recommended packages: gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:armhf libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabihf bsdextrautils build-essential cpp-10-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dpkg-dev dwz file g++ g++-10 g++-10-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-10-arm-linux-gnueabihf gcc-10-arm-linux-gnueabihf-base gcc-10-base:armhf gcc-10-cross-base gcc-9-base:armhf gcc-arm-linux-gnueabihf gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armhf libasan6-armhf-cross libatomic1:armhf libatomic1-armhf-cross libc6:armhf libc6-armhf-cross libc6-dev libc6-dev:armhf libc6-dev-armhf-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armhf libcrypt1:armhf libdebhelper-perl libdebian-dpkgcross-perl libdpkg-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev-armhf-cross libgcc-9-dev:armhf libgcc-s1:armhf libgcc-s1-armhf-cross libglib2.0-0 libgomp1:armhf libgomp1-armhf-cross libicu67 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libperl5.30 libpipeline1 libsigsegv2 libstdc++-10-dev libstdc++-10-dev-armhf-cross libstdc++-9-dev:armhf libstdc++6:armhf libstdc++6-armhf-cross libsub-override-perl libtool libubsan1:armhf libubsan1-armhf-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armhf linux-libc-dev-armhf-cross m4 man-db perl perl-modules-5.30 po-debconf sbuild-build-depends-main-dummy:armhf sensible-utils ucf 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 94.8 MB of archives. After this operation, 386 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [912 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.36-3 [140 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main armhf gcc-10-base armhf 10.2.0-6 [199 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main armhf gcc-9-base armhf 9.3.0-17 [197 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-3 [801 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabihf amd64 2.35-2 [2766 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.17-1 [104 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.31-3 [2395 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.0-6 [1737 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10 amd64 10.2.0-6 [8663 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:10.1.0-1 [1644 B] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.5 [1473 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.5 [1909 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-arm-linux-gnueabihf-base amd64 10.2.0-3cross2 [198 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-10-arm-linux-gnueabihf amd64 10.2.0-3cross2 [7518 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabihf amd64 4:10.1.0-1 [16.8 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3.1 [39.9 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.2.0-3cross2 [195 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armhf-cross all 2.31-1cross2 [1115 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armhf-cross all 10.2.0-3cross2 [36.3 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armhf-cross all 10.2.0-3cross2 [82.9 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armhf-cross all 10.2.0-3cross2 [6644 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-armhf-cross all 10.2.0-3cross2 [303 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armhf-cross all 10.2.0-3cross2 [380 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armhf-cross all 10.2.0-3cross2 [115 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-10-dev-armhf-cross all 10.2.0-3cross2 [693 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-arm-linux-gnueabihf amd64 10.2.0-3cross2 [14.9 MB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabihf amd64 4:10.1.0-1 [1476 B] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armhf-cross all 5.7.6-1cross2 [1198 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armhf-cross all 2.31-1cross2 [1901 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev-armhf-cross all 10.2.0-3cross2 [1751 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10-arm-linux-gnueabihf amd64 10.2.0-3cross2 [8181 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabihf amd64 4:10.1.0-1 [1184 B] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3.1 [38.9 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3.1 [49.9 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armhf all 12.8 [6644 B] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.2 [187 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.180-1+b1 [165 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.4-1 [1341 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.2 [1007 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-s1 armhf 10.2.0-6 [36.1 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt1 armhf 1:4.4.17-1 [94.9 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main armhf libc6 armhf 2.31-3 [2350 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armhf libasan5 armhf 9.3.0-17 [370 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armhf libatomic1 armhf 10.2.0-6 [6888 B] Get:90 http://debian.oregonstate.edu/debian unstable/main armhf linux-libc-dev armhf 5.8.7-1 [1144 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armhf libcrypt-dev armhf 1:4.4.17-1 [113 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armhf libc6-dev armhf 2.31-3 [1924 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armhf libgomp1 armhf 10.2.0-6 [84.7 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++6 armhf 10.2.0-6 [420 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armhf libubsan1 armhf 10.2.0-6 [116 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armhf libgcc-9-dev armhf 9.3.0-17 [661 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armhf libstdc++-9-dev armhf 9.3.0-17 [1757 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.8 MB in 1s (113 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10443 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3_amd64.deb ... Unpacking bsdextrautils (2.36-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../05-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... 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Setting up perl-modules-5.30 (5.30.3-4) ... Setting up bsdextrautils (2.36-3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-4) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libglib2.0-0:amd64 (2.64.4-1) ... No schema files found: doing nothing. Setting up libmagic1:amd64 (1:5.38-5) ... Setting up linux-libc-dev:armhf (5.8.7-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-5) ... Setting up gcc-10-base:armhf (10.2.0-6) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up linux-libc-dev-armhf-cross (5.7.6-1cross2) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-10-cross-base (10.2.0-3cross2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up libc6-dev:amd64 (2.31-3) ... Setting up binutils-arm-linux-gnueabihf (2.35-2) ... Setting up libelf1:amd64 (0.180-1+b1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-10-arm-linux-gnueabihf-base:amd64 (10.2.0-3cross2) ... Setting up gcc-9-base:armhf (9.3.0-17) ... Setting up libgomp1-armhf-cross (10.2.0-3cross2) ... Setting up libstdc++-10-dev:amd64 (10.2.0-6) ... Setting up g++-10 (10.2.0-6) ... Setting up libtool (2.4.6-14) ... Setting up libgcc-s1-armhf-cross (10.2.0-3cross2) ... Setting up libc6-dev-armhf-cross (2.31-1cross2) ... Setting up m4 (1.4.18-4) ... Setting up libatomic1-armhf-cross (10.2.0-3cross2) ... Setting up perl (5.30.3-4) ... Setting up libstdc++6-armhf-cross (10.2.0-3cross2) ... Setting up libasan6-armhf-cross (10.2.0-3cross2) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up cpp-10-arm-linux-gnueabihf (10.2.0-3cross2) ... Setting up libubsan1-armhf-cross (10.2.0-3cross2) ... Setting up ucf (3.0043) ... Setting up libdpkg-perl (1.20.5) ... Setting up autoconf (2.69-11.1) ... Setting up g++ (4:10.1.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgcc-10-dev-armhf-cross (10.2.0-3cross2) ... Setting up cpp-arm-linux-gnueabihf (4:10.1.0-1) ... Setting up automake (1:1.16.2-3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-which-perl (1.23-1) ... Setting up gettext (0.19.8.1-10) ... Setting up gcc-10-arm-linux-gnueabihf (10.2.0-3cross2) ... Setting up libstdc++-10-dev-armhf-cross (10.2.0-3cross2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.2) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libyaml-perl (1.30-1) ... Setting up dpkg-dev (1.20.5) ... Setting up g++-10-arm-linux-gnueabihf (10.2.0-3cross2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up build-essential (12.8) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up gcc-arm-linux-gnueabihf (4:10.1.0-1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up g++-arm-linux-gnueabihf (4:10.1.0-1) ... Setting up po-debconf (1.0.21) ... Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0134+dfsg-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3.1) ... Setting up dpkg-cross (2.6.15-3.1) ... Setting up crossbuild-essential-armhf (12.8) ... Setting up libcrypt1:armhf (1:4.4.17-1) ... Setting up libgcc-s1:armhf (10.2.0-6) ... Setting up dh-autoreconf (19) ... Setting up libc6:armhf (2.31-3) ... Setting up libcrypt-dev:armhf (1:4.4.17-1) ... Setting up libc6-dev:armhf (2.31-3) ... Setting up libstdc++6:armhf (10.2.0-6) ... Setting up debhelper (13.2) ... Setting up libgomp1:armhf (10.2.0-6) ... Setting up libasan5:armhf (9.3.0-17) ... Setting up libatomic1:armhf (10.2.0-6) ... Setting up libubsan1:armhf (10.2.0-6) ... Setting up libgcc-9-dev:armhf (9.3.0-17) ... Setting up libstdc++-9-dev:armhf (9.3.0-17) ... Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) amd64 (x86_64) Toolchain package versions: binutils_2.35-2 dpkg-dev_1.20.5 g++-10_10.2.0-6 gcc-10_10.2.0-6 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-6 libstdc++-10-dev-armhf-cross_10.2.0-3cross2 libstdc++-9-dev_9.3.0-17 libstdc++6_10.2.0-6 libstdc++6-armhf-cross_10.2.0-3cross2 linux-libc-dev_5.8.7-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-2 binutils-arm-linux-gnueabihf_2.35-2 binutils-common_2.35-2 binutils-x86-64-linux-gnu_2.35-2 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-3 cpp_4:10.1.0-1 cpp-10_10.2.0-6 cpp-10-arm-linux-gnueabihf_10.2.0-3cross2 cpp-8_8.4.0-4 cpp-arm-linux-gnueabihf_4:10.1.0-1 cross-config_2.6.15-3.1 crossbuild-essential-armhf_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debian-archive-keyring_2019.1 debianutils_4.11.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dpkg_1.20.5 dpkg-cross_2.6.15-3.1 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1 g++-10_10.2.0-6 g++-10-arm-linux-gnueabihf_10.2.0-3cross2 g++-arm-linux-gnueabihf_4:10.1.0-1 gcc_4:10.1.0-1 gcc-10_10.2.0-6 gcc-10-arm-linux-gnueabihf_10.2.0-3cross2 gcc-10-arm-linux-gnueabihf-base_10.2.0-3cross2 gcc-10-base_10.2.0-6 gcc-10-cross-base_10.2.0-3cross2 gcc-8-base_8.4.0-4 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libxml2_2.9.10+dfsg-6 libyaml-perl_1.30-1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.7-1 linux-libc-dev-armhf-cross_5.7.6-1cross2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.3-4 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0043 util-linux_2.36-3 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper (>= 12~) Package-List: fastml deb science optional arch=any Checksums-Sha1: 2bc5d72d636c37c0890c36b7e426d24131bfac8d 849058 fastml_3.11.orig.tar.gz 536a5ece528ac397cb19cec322fd167a4d7b5b11 9860 fastml_3.11-2.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz 9fe4d255bbf723df1c08821b5cba0de5399cadffc5904a80024f76b0cab09fee 9860 fastml_3.11-2.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz 174551c75f7fb35adb706053129142cc 9860 fastml_3.11-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl1AULwRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGPmxAAleh4yCwkmApYIOJwSf2DXk/olkmmjKfD 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signature: No public key dpkg-source: warning: failed to verify signature on ./fastml_3.11-2.dsc dpkg-source: info: extracting fastml in /<> dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_5.patch dpkg-source: info: applying fix_makefile4test.patch dpkg-source: info: applying fix_intall_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch dpkg-source: info: applying skip_failing_tests.patch dpkg-source: info: applying remove-template-depth.patch dpkg-source: info: applying cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armhf DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-8d4737f4-ee71-4e64-968e-fbaaf93f8fd1 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmhf -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable 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 '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' cd libs;make clean make[3]: Entering directory '/<>/libs' cd phylogeny && make clean make[4]: Entering directory '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/<>/libs/phylogeny' make[3]: Leaving directory '/<>/libs' cd programs;make clean make[3]: Entering directory '/<>/programs' cd fastml && make clean make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/<>/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/<>/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/programs/indelCoder' make[3]: Leaving directory '/<>/programs' make[2]: Leaving directory '/<>' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabihf-pkg-config CXX=arm-linux-gnueabihf-g\+\+ CC=arm-linux-gnueabihf-gcc make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' making depend arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from allTrees.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from allTrees.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void allTrees::recursiveFind(tree, const stochasticProcess&, const sequenceContainer&, std::vector, const Vdouble*, int, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp 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] 371 | MDOUBLE oldA=0; | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from bestAlpha.h:6, from bestAlpha.cpp:6: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from bestAlpha.h:6, from bestAlpha.cpp:6: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘bestAlphasAndBBLProportional::bestAlphasAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp 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] 184 | 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] 184 | 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] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from bestHKYparam.h:6, from bestHKYparam.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘bestHkyParamAlphaAndBBLProportional::bestHkyParamAlphaAndBBLProportional(tree&, std::vector&, multipleStochasticProcess*, gammaDistribution*, Vdouble, Vdouble, double, double, double, double, int, int, bool, bool, std::string, bool, bool, const Vdouble*, double, double, double, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from bblEM.h:5, from bblEMProportionalEB.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from bblEM.h:5, from bblEMProportionalEB.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void bblEMProportionalEB::allocatePlacePropEB()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from codon.h:6, from codon.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from codon.h:6, from codon.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In static member function ‘static void codonUtility::readCodonUsage(const string&, Vdouble&, const codon&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In static member function ‘static void codonUtility::getCodonUsage(const sequenceContainer&, Vint&, Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In static member function ‘static double codonUtility::calcCodonAdaptationIndex(const sequenceContainer&, const Vdouble&, Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from computeUpAlgFactors.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from computeUpAlgFactors.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const computePijHom&, suffStatGlobalHomPos&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeUpAlg::fillComputeUpWithFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree&, const sequenceContainer&, int, const stochasticProcess&, suffStatGlobalHomPos&, double, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor ‘computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::string&, VVVdouble&, int, double, bool)’: computeSubstitutionCounts.h:57:12: warning: ‘computeSubstitutionCounts::_LpostPerSpPerCat’ will be initialized after [-Wreorder] 57 | VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] | ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:6: warning: ‘int computeSubstitutionCounts::_simulationsIterNum’ [-Wreorder] 53 | int _simulationsIterNum; | ^~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | 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] 54 | MDOUBLE _probCutOffSum; | ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:7: warning: ‘bool computeSubstitutionCounts::_isSilent’ [-Wreorder] 52 | bool _isSilent; | ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | 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/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from computeSubstitutionCounts.h:4, from computeSubstitutionCounts.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from computeSubstitutionCounts.h:4, from computeSubstitutionCounts.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeSubstitutionCounts::run()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeSubstitutionCounts::printProbExpPerPosPerBranch(int, double, double, VVVdouble&, VVVdouble&, std::ostream&, std::ostream&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int, VVVdouble&, std::ostream&, std::ostream&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from distanceTable.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from distanceTable.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void giveDistanceTable(const distanceMethod*, const sequenceContainer&, VVdouble&, std::vector >&, const std::vector*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from fastStartTree.cpp:15: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from fastStartTree.cpp:15: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘std::vector eliminateHalf(std::vector&, sequenceContainer&, stochasticProcess&, std::ostream&, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp 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] 29 | const int _nodeID; | ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:27: warning: ‘const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist’ [-Wreorder] 28 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from fromQtoPt.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from fromQtoPt.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘VVdouble get1PamFromCountMatrix(const std::vector&, const VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, from generalGammaDistributionFixedCategories.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from generalGammaDistributionFixedCategories.h:9, from generalGammaDistributionFixedCategories.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistributionFixedCategories::setDefaultBoundaries(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistributionFixedCategories::fill_mean()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from generalGammaDistribution.h:11, from generalGammaDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from generalGammaDistribution.h:11, from generalGammaDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistribution::setGammaParameters(int, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘generalGammaDistribution::generalGammaDistribution(double, double, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistribution::change_number_of_categories(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistribution::setAlpha(double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void generalGammaDistribution::setBeta(double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp goldmanYangModel.cpp: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, bool)’: goldmanYangModel.cpp:8:1: warning: ‘goldmanYangModel::_globalV’ is initialized with itself [-Winit-self] 8 | 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] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from goldmanYangModel.h:6, from goldmanYangModel.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from goldmanYangModel.h:6, from goldmanYangModel.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, bool)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from tree.h:6, from simulateWithDependence.h:29, from simulateWithDependence.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘double sim_with_dep::simulate_with_dependence(std::string, double, double, int, int, double, int, double, double, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp 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] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VVdoubleRep&, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘Vdouble likelihoodComputation::getTreeLikelihoodProportionalAllPosAlphTheSame(const tree&, const std::vector&, multipleStochasticProcess*, const gammaDistribution*, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from likelihoodComputation.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, stochasticProcess&, const suffStatGlobalGamProportional&, const gammaDistribution*, VdoubleRep&, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘double likelihoodComputation::getTreeLikelihoodFromUpSpecifcRates(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘double likelihoodComputation::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, VdoubleRep&, const Vdouble*, unObservableData*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from nj.h:8, from nj.cpp:6: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from nj.h:8, from nj.cpp:6: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void NJalg::UpdateDistanceTableAndCurrentNodes(std::vector&, VVdouble&, tree::nodeP, tree::nodeP, tree::nodeP, int, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/cassert:44, from njConstrain.cpp:4: njConstrain.cpp: In function ‘tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)’: njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;i >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from numRec.cpp:6: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double performKSTest(const uniformDistribution&, Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from numRec.h:13, from numRec.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from numRec.h:13, from numRec.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void houseHolder(VVdouble&, VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from readDatMatrix.h:6, from readDatMatrix.cpp:14: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from readDatMatrix.h:6, from readDatMatrix.cpp:14: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘VVdouble fromWagSandFreqToQ(const VVdouble&, const Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void readDatMatrixFromFile(const string&, VVdouble&, Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void readDatMatrixFromString(const string&, VVdouble&, Vdouble&, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void pupAll::fillMatrices(const string&, const Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp sequence.cpp: In constructor ‘sequence::sequence(const sequence&, const alphabet*)’: sequence.cpp:76:28: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp sequenceContainer.cpp: In member function ‘void sequenceContainer::removeGapPositions()’: sequenceContainer.cpp:187:7: warning: variable ‘gapCol’ set but not used [-Wunused-but-set-variable] 187 | 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] 199 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function ‘int sequenceContainer::getNumOfOccurancesPerPos(int, char)’: sequenceContainer.cpp:452:12: warning: unused variable ‘len’ [-Wunused-variable] 452 | 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] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from someUtil.cpp:9: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from someUtil.cpp:9: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1881 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double computeFDRthreshold(Vdouble&, double, bool)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double orderVec(const std::vector&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void orderVec(const Vdouble&, std::vector >&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void orderRankNoTies(const std::vector&, std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double computeQuantileFrac(const std::vector&, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double computeQuantile(const std::vector&, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘double computeMedian(const std::vector&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1977 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp tree.cpp: In constructor ‘tree::tree(const string&)’: tree.cpp:180:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | 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’ 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp treeUtil.cpp: In function ‘std::vector getNexusTreesFromFile(const string&)’: treeUtil.cpp:371:25: warning: variable ‘itStrStart’ set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); | ^~~~~~~~~~ treeUtil.cpp:372:25: warning: variable ‘itStrEnd’ set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from uniformDistribution.h:22, from uniformDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from uniformDistribution.h:22, from uniformDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void uniformDistribution::setUniformParameters(int, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘uniformDistribution::uniformDistribution(int, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void uniformDistribution::change_number_of_categories(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from generalGammaDistributionLaguerre.h:26, from generalGammaDistributionLaguerre.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘virtual void generalGammaDistributionLaguerre::fillRatesAndProbs(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘virtual void generalGammaDistributionLaguerre::setGammaParameters(int, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In constructor ‘generalGammaDistributionLaguerre::generalGammaDistributionLaguerre(double, double, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from GLaguer.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from GLaguer.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void GLaguer::GetPhylipLaguer(int, double, Vdouble&, Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void GLaguer::gaulag(Vdouble&, Vdouble&, double, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp 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] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:27: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from replacementModel.h:6, from replacementModelSSRV.h:6, from replacementModelSSRV.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from replacementModel.h:6, from replacementModelSSRV.h:6, from replacementModelSSRV.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void replacementModelSSRV::updateQ()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘Vdouble getSubDiagonalFromMatrix(VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void appendVectors(VVdouble&, const VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘Vdouble getDiagonalFromMatrix(VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from matrixUtils.h:4, from matrixUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘void readDoubleVecFromFile(Vdouble&, std::string)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘void readMatrixFromFile(VVdouble&, std::string)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp 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] 54 | vector _boundary; | ^~~~~~~~~ betaDistribution.h:47:10: warning: ‘double betaDistribution::_alpha’ [-Wreorder] 47 | MDOUBLE _alpha; | ^~~~~~ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from betaDistribution.h:10, from betaDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from betaDistribution.h:10, from betaDistribution.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistribution::setBetaParameters(int, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘betaDistribution::betaDistribution(double, double, int, betaDistribution::discretizationType)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistribution::change_number_of_categories(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistribution::setAlpha(double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistribution::setBeta(double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from likelihoodComputation2USSRV.h:5, from likelihoodComputation2USSRV.cpp:2: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘double likelihoodComputation2USSRV::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const sequenceContainer&, const ussrvModel&, const suffStatGlobalGam&, const suffStatGlobalHom&, VdoubleRep&, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from bestTamura92param.h:6, from bestTamura92param.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from bestTamura92param.h:6, from bestTamura92param.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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::string, bool, bool, const Vdouble*, double, double, double, double, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateCodonsJumps.h:4, from simulateCodonsJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateCodonsJumps.h:4, from simulateCodonsJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void simulateCodonsJumps::init()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateJumps.h:4, from simulateJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateJumps.h:4, from simulateJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void simulateJumps::init()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp 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] 59 | MDOUBLE _Lambda2; | ^~~~~~~~ computeJumps.h:57:11: warning: ‘double computeJumps::gFunc::_r’ [-Wreorder] 57 | MDOUBLE _r; | ^~ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp seqeuncesFilter.cpp: In static member function ‘static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)’: seqeuncesFilter.cpp:141:18: warning: unused variable ‘pAlph’ [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ 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::string)’: sequenceContainer.h:31:81: warning: ‘refID’ may be used uninitialized in this function [-Wmaybe-uninitialized] 31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} | ^ seqeuncesFilter.cpp:165:6: note: ‘refID’ was declared here 165 | int refID; | ^~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::rates(int) const’: mixtureDistribution.cpp:221:33: warning: ‘componentNum’ may be used uninitialized in this function [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; | ^ mixtureDistribution.cpp:221:41: warning: ‘categoryInComponent’ may be used uninitialized in this function [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from mixtureDistribution.cpp:1: mixtureDistribution.h: In member function ‘virtual const double mixtureDistribution::ratesProb(int) const’: mixtureDistribution.h:40:95: warning: ‘componentNum’ may be used uninitialized in this function [-Wmaybe-uninitialized] 40 | const MDOUBLE getComponentProb(int componentNum) const {return _componentsWeight[componentNum] / _totalWeight;} | ^ mixtureDistribution.cpp:228:6: note: ‘componentNum’ was declared here 228 | 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] 28 | virtual const MDOUBLE ratesProb(const int i) const {return _ratesProb[i];} | ^ mixtureDistribution.cpp:228:20: note: ‘categoryInComponent’ was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from mixtureDistribution.h:11, from mixtureDistribution.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from mixtureDistribution.h:11, from mixtureDistribution.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void mixtureDistribution::change_number_of_components(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp suffStatGammaMixture.cpp: In member function ‘void suffStatGammaMixture::computeStatistics()’: suffStatGammaMixture.cpp:123:12: warning: variable ‘Exp_Rk’ set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; | ^~~~~~ suffStatGammaMixture.cpp: In member function ‘double suffStatGammaMixture::computeQ()’: suffStatGammaMixture.cpp:224:11: warning: unused variable ‘first’ [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); | ^~~~~ suffStatGammaMixture.cpp:225:11: warning: unused variable ‘second’ [-Wunused-variable] 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); | ^~~~~~ suffStatGammaMixture.cpp:226:11: warning: unused variable ‘third’ [-Wunused-variable] 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); | ^~~~~ suffStatGammaMixture.cpp:227:11: warning: unused variable ‘fourth’ [-Wunused-variable] 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; | ^~~~~~ suffStatGammaMixture.cpp:228:11: warning: unused variable ‘fifth’ [-Wunused-variable] 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); | ^~~~~ suffStatGammaMixture.cpp:216:10: warning: variable ‘res2’ set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from suffStatGammaMixture.h:16, from suffStatGammaMixture.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from suffStatGammaMixture.h:16, from suffStatGammaMixture.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void suffStatGammaMixture::allocatePlaceForSuffStat()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp 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] 76 | 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] 87 | 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 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from GamMixtureOptimizer.cpp:7: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from GamMixtureOptimizer.cpp:7: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In member function ‘double GamMixtureOptimizer::findBestParamManyStarts(Vint, Vint, std::vector, Vdouble, const Vdouble*, std::ofstream*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp 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] 76 | 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] 87 | 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 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘double optGammaMixtureEM::findBestParamManyStarts(int, int, int, int, double, double, std::ofstream*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from optGammaMixtureEM.h:11, from optGammaMixtureEM.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from optGammaMixtureEM.cpp:7: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from replacementModel.h:6, from wYangModel.h:4, from wYangModel.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from replacementModel.h:6, from wYangModel.h:4, from wYangModel.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘wYangModel::wYangModel(double, double, bool, codon*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘wYangModel::wYangModel(double, double, const Vdouble&, bool, codon*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from codonUtils.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from codonUtils.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘Vdouble freqCodonF3x4(const sequenceContainer&, codon*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void kaks2Color(const Vdouble&, const Vdouble&, const sequence&, std::string, codon*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from nucleotide.h:7, from codonUtils.h:5, from codonUtils.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from codonUtils.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from likelihoodComputation2Codon.h:6, from likelihoodComputation2Codon.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘double likelihoodComputation2Codon::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const stochasticProcess&, const suffStatGlobalGam&, Vdouble&, const distribution*, const Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from likelihoodComputationGL.h:4, from likelihoodComputationGL.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In function ‘double likelihoodComputationGL::getTreeLikelihoodFromUp2(const tree&, const sequenceContainer&, const std::vector >&, const suffStatGlobalGam&, const distribution*, const distribution*, const Vdouble*, unObservableData*, Vdouble*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from betaDistributionFixedCategories.h:9, from betaDistributionFixedCategories.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from betaDistributionFixedCategories.h:9, from betaDistributionFixedCategories.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistributionFixedCategories::setDefaultBoundaries(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistributionFixedCategories::fill_mean()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘betaDistributionFixedCategories::betaDistributionFixedCategories()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘betaDistributionFixedCategories::betaDistributionFixedCategories(double, double, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘virtual void betaDistributionFixedCategories::change_number_of_categories(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp In file included from 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] 54 | MDOUBLE _g2t; | ^~~~ gtrModel.h:47:10: warning: ‘Vdouble gtrModel::_freq’ [-Wreorder] 47 | Vdouble _freq; | ^~~~~ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 5 | 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] 139 | 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] 153 | 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] 167 | 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] 181 | return result; | ^~~~~~ 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] 195 | 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] 209 | return result; | ^~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from replacementModel.h:6, from gtrModel.h:4, from gtrModel.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from replacementModel.h:6, from gtrModel.h:4, from gtrModel.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp 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] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:27: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from bestGtrModelParams.h:6, from bestGtrModelParams.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from bestGtrModelParams.h:6, from bestGtrModelParams.cpp:3: /usr/arm-linux-gnueabihf/include/c++/10/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::string, bool, bool, const Vdouble*, double, double, double, double, double)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from definitions.h:18, from simulateJumpsAbstract.h:4, from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void simulateRateShiftJumps::init(std::vector)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o ar: creating libEvolTree.a a - AddLog.o a - NNiProp.o a - NNiSep.o a - Nni.o a - aaJC.o a - allTrees.o a - allTreesSeparateModel.o a - alphabet.o a - amino.o a - bestAlpha.o a - bestAlphaManyTrees.o a - bestHKYparam.o a - bootstrap.o a - bblEM.o a - bblEMfixRoot.o a - bblEMProprtional.o a - bblEMProportionalEB.o a - bblLSProportionalEB.o a - bblEMSeperate.o a - chebyshevAccelerator.o a - clustalFormat.o a - codon.o a - codonJC.o a - computeCounts.o a - computeDownAlg.o a - computeMarginalAlg.o a - computePijComponent.o a - computeUpAlg.o a - computeUpAlgFactors.o a - computeSubstitutionCounts.o a - computePosteriorExpectationOfSubstitutions.o a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o a - ConversionUtils.o a - countTableComponent.o a - datMatrixHolder.o a - distanceTable.o a - distribution.o a - errorMsg.o a - evaluateCharacterFreq.o a - fastStartTree.o a - fastaFormat.o a - findRateOfGene.o a - fromCountTableComponentToDistance.o a - fromCountTableComponentToDistancefixRoot.o a - fromCountTableComponentToDistanceProp.o a - fromCountTableComponentToDistancePropEB.o a - fromQtoPt.o a - generalGammaDistributionFixedCategories.o a - gammaDistribution.o a - gammaUtilities.o a - generalGammaDistribution.o a - getRandomWeights.o a - goldmanYangModel.o a - granthamChemicalDistances.o a - hky.o a - simulateWithDependence.o a - KH_calculation.o a - likeDist.o a - likeDistfixRoot.o a - likeDistProp.o a - likeDistPropEB.o a - likelihoodComputation.o a - likelihoodComputationFactors.o a - logFile.o a - maseFormat.o a - molphyFormat.o a - nexusFormat.o a - nj.o a - njConstrain.o a - nucJC.o a - nucleotide.o a - numRec.o a - Parameters.o a - phylipFormat.o a - pijAccelerator.o a - readDatMatrix.o a - readTree.o a - recognizeFormat.o a - replacementModel.o a - searchStatus.o a - seqContainerTreeMap.o a - sequence.o a - sequenceContainer.o a - simulateTree.o a - siteSpecificRate.o a - someUtil.o a - split.o a - splitMap.o a - splitTreeUtil.o a - stochasticProcess.o a - suffStatComponent.o a - talRandom.o a - tree.o a - treeIt.o a - treeUtil.o a - uniDistribution.o a - uniformDistribution.o a - cmdline2EvolObjs.o a - generalGammaDistributionLaguerre.o a - gammaDistributionLaguerre.o a - GLaguer.o a - givenRatesMLDistance.o a - distanceBasedSeqs2Tree.o a - posteriorDistance.o a - pairwiseGammaDistance.o a - doubleRep.o a - logRep.o a - indel.o a - indelModel.o a - mulAlphabet.o a - replacementModelSSRV.o a - stochasticProcessSSRV.o a - bestAlphaAndNu.o a - C_evalParamUSSRV.o a - matrixUtils.o a - betaOmegaDistribution.o a - betaUtilities.o a - betaDistribution.o a - geneticCodeHolder.o a - samplingSequences.o a - bblEM2USSRV.o a - bestParamUSSRV.o a - likeDist2USSRV.o a - ussrvModel.o a - likelihoodComputation2USSRV.o a - fromCountTableComponentToDistance2USSRV.o a - normalDist.o a - tamura92.o a - bestTamura92param.o a - phylipSequentialFormat.o a - simulateCodonsJumps.o a - simulateJumpsAbstract.o a - ssrvDistanceSeqs2Tree.o a - multipleStochasticProcess.o a - distributionPlusInvariant.o a - extremeValDistribution.o a - gammaDistributionFixedCategories.o a - generalGammaDistributionPlusInvariant.o a - gammaDistributionPlusInvariant.o a - distributionPlusCategory.o a - simulateJumps.o a - computeJumps.o a - seqeuncesFilter.o a - optGammaMixtureLS.o a - mixtureDistribution.o a - suffStatGammaMixture.o a - GamMixtureOptimizer.o a - optGammaMixtureEM.o a - gainLossAlphabet.o a - wYangModel.o a - codonUtils.o a - likelihoodComputation2Codon.o a - likeDist2Codon.o a - unObservableData.o a - likelihoodComputationGL.o a - threeStateModel.o a - threeStateAlphabet.o a - oneTwoMoreModel.o a - betaDistributionFixedCategories.o a - betaDistributionFixedCategoriesWithOmegaUniform.o a - bblEM2codon.o a - bestAlphaAndK.o a - fromCountTableComponentToDistance2Codon.o a - gtrModel.o a - bestGtrModelParams.o a - simulateRateShiftJumps.o a - integerAlphabet.o ranlib libEvolTree.a make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make all make[2]: Entering directory '/<>/programs' cd fastml && make all make[3]: Entering directory '/<>/programs/fastml' making depend arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp 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] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp 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] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | 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] 61 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbAlg.h:60:20: warning: ‘BandBReportAllPos bbAlg::BandBReportAllPos1’ [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ In file included from bbAlg.cpp:1: bbAlg.h:60:20: warning: ‘bbAlg::BandBReportAllPos1’ will be initialized after [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:14: warning: ‘const tree& bbAlg::_et’ [-Wreorder] 29 | const tree& _et; | ^~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/computePijComponent.h:6, from bbAlg.h:4, from bbAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/computePijComponent.h:6, from bbAlg.h:4, from bbAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘double bbAlg::bbReconstructAllPositions(sequenceContainer&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp 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] 34 | const sequenceContainer& _sc; | ^~~ bbEvaluateSpecificAV.h:31:23: warning: ‘const computePijGam& bbEvaluateSpecificAV::_bbcpij’ [-Wreorder] 31 | const computePijGam& _bbcpij; | ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 3 | 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] 65 | 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: ‘const string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp 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] 33 | const sequenceContainer& _sc; | ^~~ bbNodeOrderAlg.h:32:23: warning: ‘const computePijGam& bbNodeOrderAlg::_cpij’ [-Wreorder] 32 | const computePijGam& _cpij; | ^~~~~ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, | ^~~~~~~~~~~~~~ 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void bbNodeOrderAlg::putBack(tree::TreeNode*&, const doubleRep&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void bbNodeOrderAlg::rankRemainingNodesAccordingToTheirMarginalProb(int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1662 | __heap_select(_RandomAccessIterator __first, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1937 | std::__heap_select(__first, __middle, __last, __comp); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from bbNodeOrderAlg.h:4, from bbNodeOrderAlg.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘std::vector bbNodeOrderAlg::findBestOrderInNode(tree::nodeP, int) const’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from bbNodeOrderAlg.cpp:5: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp In file included from 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] 49 | string reportFile; | ^~~~~~~~~~ bb_options.h:44:9: warning: ‘std::string bb_options::outFile_seq_joint’ [-Wreorder] 44 | string outFile_seq_joint; | ^~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 45 | string outFile_seq_marginal; | ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:9: warning: ‘std::string bb_options::outFile_prob_joint’ [-Wreorder] 42 | string outFile_prob_joint; | ^~~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 43 | string outFile_prob_marginal; | ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:9: warning: ‘std::string bb_options::seqfile’ [-Wreorder] 24 | string seqfile; | ^~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 30 | distributionsNames distributionName; | ^~~~~~~~~~~~~~~~ bb_options.h:26:16: warning: ‘bb_options::SeqFileFormat bb_options::seqOutputFormat’ [-Wreorder] 26 | SeqFileFormat seqOutputFormat; | ^~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 41 | string outTreeFileAncestor; | ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:15: warning: ‘bb_options::boundMethods bb_options::boundMethod’ [-Wreorder] 32 | boundMethods boundMethod; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 47 | MDOUBLE gammaPar; | ^~~~~~~~ bb_options.h:28:7: warning: ‘bool bb_options::userProvideAlpha’ [-Wreorder] 28 | bool userProvideAlpha; | ^~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 48 | int gammaCategies; | ^~~~~~~~~~~~~ bb_options.h:36:19: warning: ‘bb_options::modelNameOptions bb_options::modelName’ [-Wreorder] 36 | modelNameOptions modelName; | ^~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 39 | bool useChebyshev; | ^~~~~~~~~~~~ bb_options.h:27:9: warning: ‘std::string bb_options::treeOutFile’ [-Wreorder] 27 | string treeOutFile; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp 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] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ bbReport.h: In constructor ‘BandBReport::BandBReport(const string&, int, int)’: bbReport.h:53:16: warning: ‘BandBReport::_reportFileName’ will be initialized after [-Wreorder] 53 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:51:12: warning: ‘const int BandBReport::_position’ [-Wreorder] 51 | const int _position; | ^~~~~~~~~ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from bbReport.h:4, from bbReport.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from bbReport.h:4, from bbReport.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void BandBReport::report(std::string, int, int, doubleRep, doubleRep, doubleRep, doubleRep)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp computeMarginalReconstruction.cpp: In member function ‘void computeMarginalReconstruction::compute(const distribution*)’: computeMarginalReconstruction.cpp:67:11: warning: unused variable ‘likelihoodOfPos’ [-Wunused-variable] 67 | MDOUBLE likelihoodOfPos = 0; | ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:10: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1819 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeMarginalReconstruction.h:4, from computeMarginalReconstruction.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector > >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘void computeMarginalReconstruction::outputTheMarginalProbForEachCharForEachNodePos(std::ostream&, int)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from computeMarginalReconstruction.cpp:8: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeMarginalReconstruction.h:4, from computeMarginalReconstruction.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In constructor ‘computeMarginalReconstruction::computeMarginalReconstruction(const tree&, std::vector&, const sequenceContainer&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp jointNoGamma.cpp: In member function ‘void jointNoGamma::compute()’: jointNoGamma.cpp:23:10: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 23 | 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] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from jointNoGamma.h:4, from jointNoGamma.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from jointNoGamma.h:4, from jointNoGamma.cpp:1: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void jointNoGamma::compute()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp 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] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:12: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:11: warning: when initialized here [-Wreorder] 10 | 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] 175 | stochasticProcess& _sp; | ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:27: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ mainbb.cpp: In member function ‘void mainbb::findAncestralSequencesGammaJoint()’: mainbb.cpp:428:101: warning: ‘bm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); | ^ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/<>/programs/gainLoss' making depend arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp 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] 2064 | 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] 2111 | return returnType; | ^~~~~~~~~~ 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] 2419 | return returnType; | ^~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | 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] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 96 | 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] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 152 | 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] 266 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLoss.h:240:16: warning: ‘distribution* gainLoss::_lossDist’ [-Wreorder] 240 | distribution* _lossDist; | ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | 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] 240 | distribution* _lossDist; | ^~~~~~~~~ gainLoss.h:239:16: warning: ‘distribution* gainLoss::_gainDist’ [-Wreorder] 239 | distribution* _gainDist; | ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | 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] 273 | sequence* _refSeq; // the reference sequence | ^~~~~~~ gainLoss.h:267:11: warning: ‘Vdouble* gainLoss::_weightsUniqPatterns’ [-Wreorder] 267 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::removePositionsWithHighPercentOfMissingData(double)’: gainLoss.cpp:604:7: warning: unused variable ‘missigDataChar’ [-Wunused-variable] 604 | 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] 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~ gainLoss.cpp:1245:38: note: add parentheses around left hand side expression to silence this warning 1245 | 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] 1868 | 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] 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); | ^~~~~~~~~ gainLoss.cpp: In member function ‘double gainLoss::computeDistanceFromRootForRecent(tree&)’: gainLoss.cpp:4205:7: warning: variable ‘isRecentBiggerAncient’ set but not used [-Wunused-but-set-variable] 4205 | 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] 4283 | 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] 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^ gainLoss.cpp:4382:7: note: add parentheses around left hand side expression to silence this warning 4382 | 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] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ 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] 2035 | if(probInvariant) updateLossProbInvariant(bestLossProbInvariant,lossDist); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()’: gainLoss.cpp:3980:52: warning: ‘AlphaLoss’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); | ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3980:52: warning: ‘AlphaGain’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from computePosteriorExpectationOfChange.h:23, from gainLoss.cpp:19: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘Vdouble gainLoss::computeFreq()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startStochasticProcess()’: gainLoss.cpp:869:23: warning: ‘rateDist’ may be used uninitialized in this function [-Wmaybe-uninitialized] 869 | 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] 1127 | 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::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)’: gainLoss.cpp:2511:22: warning: ‘countsGL’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2511 | if(countsGL) delete countsGL; | ^~~~~~~~ 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] 1195 | delete pDm; | ^~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 72 | if(probs) | ^ gainLossUtils.cpp:88:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 88 | 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] 481 | MDOUBLE normFactor; | ^~~~~~~~~~ gainLossUtils.cpp: In function ‘double sumPijQijVec(std::vector >&, distribution*, distribution*)’: gainLossUtils.cpp:788:10: warning: unused variable ‘scale’ [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ gainLossUtils.cpp: In function ‘double getRateBeta(distribution*)’: gainLossUtils.cpp:312:9: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized] 312 | return res; | ^~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 87 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h:86:20: warning: ‘unObservableData* optimizeGainLossModel::_unObservableData_p’ [-Wreorder] 86 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] 20 | 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] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 82 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:20: warning: ‘unObservableData* optimizeGainLossModelVV::_unObservableData_p’ [-Wreorder] 81 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, | ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:258:13: warning: unused variable ‘currentlogL’ [-Wunused-variable] 258 | 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] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 108 | MDOUBLE _gain; // _Q[0][1] | ^~~~~ gainLossModel.h:105:10: warning: ‘Vdouble gainLossModel::_freq’ [-Wreorder] 105 | Vdouble _freq; | ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | 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] 112 | bool _isRootFreqEQstationary; | ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:111:7: warning: ‘bool gainLossModel::_isReversible’ [-Wreorder] 111 | bool _isReversible; | ^~~~~~~~~~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | 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] 114 | bool _isHGT_with_Q; | ^~~~~~~~~~~~~ gainLossModel.h:110:8: warning: ‘q2pt* gainLossModel::_q2pt’ [-Wreorder] 110 | q2pt *_q2pt; // dont use q2p | ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from siteSpecificGL.h:22, from siteSpecificGL.cpp:18: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from siteSpecificGL.h:22, from siteSpecificGL.cpp:18: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | 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] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 96 | 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] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 152 | 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] 134 | tree _tr; | ^~~ gainLossOptimizer.h:109:21: warning: ‘stochasticProcess* gainLossOptimizer::_sp’ [-Wreorder] 109 | stochasticProcess *_sp; | ^~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | 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] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:10: warning: ‘double gainLossOptimizer::_epsilonOptimization’ [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | 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] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: ‘unObservableData* gainLossOptimizer::_unObservableData_p’ [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | 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] 139 | distribution* _lossDist; | ^~~~~~~~~ gainLossOptimizer.h:135:20: warning: ‘sequenceContainer gainLossOptimizer::_sc’ [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | 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] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:10: warning: ‘double gainLossOptimizer::_epsilonOptimization’ [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | 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] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:21: warning: ‘unObservableData* gainLossOptimizer::_unObservableData_p’ [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | 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] 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:543:12: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:487:10: warning: variable ‘newLnoUnObservableDataCorrection’ set but not used [-Wunused-but-set-variable] 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function ‘double gainLossOptimizer::optimizeBranchLengthsvv(int)’: gainLossOptimizer.cpp:634:12: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:677:12: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 677 | 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] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In function ‘gainLossOptions::distributionType getRateDistributionType(distribution*)’: gainLossOptimizer.cpp:833:9: warning: ‘res’ may be used uninitialized in this function [-Wmaybe-uninitialized] 833 | return res; | ^~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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::string&, unObservableData*)’: rate4siteGL.h:59:7: warning: ‘rate4siteGL::_tr’ will be initialized after [-Wreorder] 59 | tree _tr; | ^~~ rate4siteGL.h:58:21: warning: ‘stochasticProcess* rate4siteGL::_sp’ [-Wreorder] 58 | stochasticProcess *_sp; | ^~~ rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] 24 | 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] 151 | int precisionHigh = 5; | ^~~~~~~~~~~~~ rate4siteGL.cpp:152:6: warning: unused variable ‘precisionLow’ [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22, from rate4siteGL.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from rate4siteGL.h:22, from rate4siteGL.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void rate4siteGL::normalizeRates()’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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 computeCountsGL.cpp:17: computeCountsGL.h: In constructor ‘computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)’: computeCountsGL.h:104:7: warning: ‘computeCountsGL::_tr’ will be initialized after [-Wreorder] 104 | tree _tr; | ^~~ computeCountsGL.h:102:21: warning: ‘stochasticProcess* computeCountsGL::_sp’ [-Wreorder] 102 | stochasticProcess *_sp; | ^~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | 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] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: ‘bool computeCountsGL::_isSilent’ [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | 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::string&, VVVdouble&, double, bool)’: computeCountsGL.h:109:16: warning: ‘computeCountsGL::_lossDist’ will be initialized after [-Wreorder] 109 | distribution* _lossDist; | ^~~~~~~~~ computeCountsGL.h:105:20: warning: ‘sequenceContainer computeCountsGL::_sc’ [-Wreorder] 105 | sequenceContainer _sc; | ^~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | 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] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:7: warning: ‘bool computeCountsGL::_isSilent’ [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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] 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)’: computeCorrelations.cpp:408:8: warning: unused variable ‘isHigherNminReducedFreqOfHighCorr’ [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:7: warning: unused variable ‘typeIndex’ [-Wunused-variable] 348 | 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] 559 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:569:24: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:579:24: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:23: warning: NULL used in arithmetic [-Wpointer-arith] 584 | 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] 676 | int prevNumberOfSimulationsInRange = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:9: warning: variable ‘prevNumberOfSimulationPointsMoreExtremeOrEqToCorr’ set but not used [-Wunused-but-set-variable] 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:9: warning: unused variable ‘numOfBinsWithLowerSignificance’ [-Wunused-variable] 679 | 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] 680 | 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] 894 | if(!numOfSites_A == numOfSites_B){ | ^~ computeCorrelations.cpp:894:5: note: add parentheses around left hand side expression to silence this warning 894 | if(!numOfSites_A == numOfSites_B){ | ^~~~~~~~~~~~~ | ( ) computeCorrelations.cpp: In member function ‘void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)’: computeCorrelations.cpp:1009:7: warning: unused variable ‘isPearson’ [-Wunused-variable] 1009 | bool isPearson = false; | ^~~~~~~~~ computeCorrelations.cpp:1025:6: warning: unused variable ‘numOfbranches’ [-Wunused-variable] 1025 | 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:1347:53: warning: narrowing conversion of ‘gainLossOptions::_pValueCutOffForBootStrap’ from ‘double’ to ‘float’ [-Wnarrowing] 1347 | 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] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2136:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2136 | __equal_range(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2136:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2136:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2136:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:61, from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1945 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In function ‘void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In member function ‘void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void computeCorrelations::produceSortedVectorsOfAllCorrelations(Vdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In function ‘void computeCorrelations::fillMapValPerPosPerBranch(VVdouble&, std::string, VVVVdouble&, bool, double*)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc: In member function ‘void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h: In member function ‘void computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMap(VVVdouble&, VVVVdouble&, VVVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h: In member function ‘VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/stl_map.h:520:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ 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] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:2203:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2203 | return std::__equal_range(__first, __last, __val, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2204 | __gnu_cxx::__ops::__iter_less_val(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2205 | __gnu_cxx::__ops::__val_less_iter()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/algorithm:62, from gainLoss.h:75, from computeCorrelations.h:25, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1974 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1975 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1976 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1891 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from computeCorrelations.h:22, from computeCorrelations.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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::string&, unObservableData*, double)’: gainLoss4site.h:68:7: warning: ‘gainLoss4site::_tr’ will be initialized after [-Wreorder] 68 | tree _tr; | ^~~ gainLoss4site.h:61:38: warning: ‘std::vector > gainLoss4site::_spVVec’ [-Wreorder] 61 | vector > _spVVec; //save stochasticProcess for each category | ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | 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] 79 | unObservableData* _unObservableData_p; // | ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:10: warning: ‘double gainLoss4site::_alphaConf’ [-Wreorder] 78 | MDOUBLE _alphaConf; | ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp 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] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:95: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:11: warning: when initialized here [-Wreorder] 127 | 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::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)’: simulateOnePos.h:72:7: warning: ‘simulateOnePos::_simulateNullModel’ will be initialized after [-Wreorder] 72 | bool _simulateNullModel; | ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:6: warning: ‘int simulateOnePos::_simNum’ [-Wreorder] 63 | int _simNum; | ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | 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] 65 | MDOUBLE _theta; | ^~~~~~ simulateOnePos.h:64:10: warning: ‘double simulateOnePos::_sumGainLoss’ [-Wreorder] 64 | MDOUBLE _sumGainLoss; | ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | 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] 75 | Vdouble* _freq_cpN; | ^~~~~~~~~ simulateOnePos.h:69:11: warning: ‘std::ostream* simulateOnePos::_simulatedEvents’ [-Wreorder] 69 | ostream *_simulatedEvents; | ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function ‘void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)’: simulateOnePos.cpp:181:9: warning: unused variable ‘isRevers’ [-Wunused-variable] 181 | bool isRevers = false; | ^~~~~~~~ simulateOnePos.cpp:202:12: warning: variable ‘sumQii’ set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from bblLS.cpp:17: bblLS.h:50:17: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:17: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | 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] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:11: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:11: warning: when initialized here [-Wreorder] 96 | 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] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:11: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:11: warning: when initialized here [-Wreorder] 152 | 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] 36 | 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] 112 | if (curL == NULL) | ^~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor ‘sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)’: sankoffReconstructGL.h:85:9: warning: ‘sankoffReconstructGL::_outDir’ will be initialized after [-Wreorder] 85 | string _outDir; | ^~~~~~~ sankoffReconstructGL.h:84:10: warning: ‘double sankoffReconstructGL::_costMatrixGainLossRatio’ [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | 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] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:10: warning: ‘double sankoffReconstructGL::_distanceFromRootForRecent’ [-Wreorder] 83 | MDOUBLE _distanceFromRootForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:72, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/tree.h:6, from sankoffReconstructGL.h:23, from sankoffReconstructGL.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/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/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabihf/include/c++/10/vector:67, from ../../libs/phylogeny/definitions.h:18, from ../../libs/phylogeny/tree.h:6, from sankoffReconstructGL.h:23, from sankoffReconstructGL.cpp:17: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘double sankoffReconstructGL::traverseDownMP(VVdouble&, std::vector > >&, VVint&, VVdouble&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h: In member function ‘void sankoffReconstructGL::traverseUpMP(VVdouble&, std::vector > >&)’: /usr/arm-linux-gnueabihf/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _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 arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make all make[3]: Entering directory '/<>/programs/indelCoder' making depend arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp indelCoder.cpp: In member function ‘void indelCoder::printGapsInfo()’: indelCoder.cpp:422:6: warning: unused variable ‘gapNum’ [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ indelCoder.cpp: In member function ‘void indelCoder::printIndelSummary()’: indelCoder.cpp:587:7: warning: unused variable ‘isSIC’ [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; | ^~~~~ indelCoder.cpp:597:6: warning: unused variable ‘seqLeng’ [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ 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] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp character.cpp: In member function ‘int character::getLongestGapStIndex()’: character.cpp:28:9: warning: ‘longestGapStIndex’ may be used uninitialized in this function [-Wmaybe-uninitialized] 28 | 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] 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ | ^ arm-linux-gnueabihf-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp 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 arm-linux-gnueabihf-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make install make[2]: Entering directory '/<>/programs' cd fastml && make install make[3]: Entering directory '/<>/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make install make[3]: Entering directory '/<>/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make install make[3]: Entering directory '/<>/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a 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 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 dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'fastml' in '../fastml_3.11-2_armhf.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-2_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../fastml_3.11-2_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-09-06T08:20:28Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.11-2_armhf.changes: ---------------------------- Format: 1.8 Date: Tue, 30 Jul 2019 16:01:25 +0200 Source: fastml Binary: fastml fastml-dbgsym Built-For-Profiles: cross nocheck Architecture: armhf Version: 3.11-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Closes: 933405 Changes: fastml (3.11-2) unstable; urgency=medium . * Description: Enable cross building Closes: #933405 Checksums-Sha1: 55a6c707d351b953e58b396f1b609fc8b0137ec0 16562280 fastml-dbgsym_3.11-2_armhf.deb 0918c1681c47d55e4b819d5356f636ebf9501e91 4465 fastml_3.11-2_armhf.buildinfo 1212b4cb3fdd05cceb19eba746729c8789872946 762772 fastml_3.11-2_armhf.deb Checksums-Sha256: 30b5d2c4c48a78bcc81b496c0560635d563afb1bb3bf913ee63476b81bb903c2 16562280 fastml-dbgsym_3.11-2_armhf.deb 14555b0640ca9621a12566ab51e6e446a941495c1210f8c45fb8c63b20a0aa53 4465 fastml_3.11-2_armhf.buildinfo be5ef7ffe57302d1e97ac9b4622497ba338c7af2ff9f692d3d13ff0d0656e081 762772 fastml_3.11-2_armhf.deb Files: 424b1fe87bf9df0bd4faefa0d6239cc0 16562280 debug optional fastml-dbgsym_3.11-2_armhf.deb 56c3a60445b7ee2de2250d850959053f 4465 science optional fastml_3.11-2_armhf.buildinfo da0269917df8622a6d7d1b86565db667 762772 science optional fastml_3.11-2_armhf.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: fastml Binary: fastml fastml-dbgsym Architecture: armhf Version: 3.11-2 Checksums-Md5: 424b1fe87bf9df0bd4faefa0d6239cc0 16562280 fastml-dbgsym_3.11-2_armhf.deb da0269917df8622a6d7d1b86565db667 762772 fastml_3.11-2_armhf.deb Checksums-Sha1: 55a6c707d351b953e58b396f1b609fc8b0137ec0 16562280 fastml-dbgsym_3.11-2_armhf.deb 1212b4cb3fdd05cceb19eba746729c8789872946 762772 fastml_3.11-2_armhf.deb Checksums-Sha256: 30b5d2c4c48a78bcc81b496c0560635d563afb1bb3bf913ee63476b81bb903c2 16562280 fastml-dbgsym_3.11-2_armhf.deb be5ef7ffe57302d1e97ac9b4622497ba338c7af2ff9f692d3d13ff0d0656e081 762772 fastml_3.11-2_armhf.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 06 Sep 2020 08:20:28 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-3), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-7), binutils (= 2.35-2), binutils-common (= 2.35-2), binutils-x86-64-linux-gnu (= 2.35-2), bsdextrautils (= 2.36-3), bsdutils (= 1:2.36-3), build-essential (= 12.8), bzip2 (= 1.0.8-4), coreutils (= 8.32-3), cpp (= 4:10.1.0-1), cpp-10 (= 10.2.0-6), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13.2), debianutils (= 4.11.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3), dpkg (= 1.20.5), dpkg-dev (= 1.20.5), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1), g++ (= 4:10.1.0-1), g++-10 (= 10.2.0-6), gcc (= 4:10.1.0-1), gcc-10 (= 10.2.0-6), gcc-10-base (= 10.2.0-6), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), hostname (= 3.23), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan6 (= 10.2.0-6), libatomic1 (= 10.2.0-6), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbinutils (= 2.35-2), libblkid1 (= 2.36-3), libbz2-1.0 (= 1.0.8-4), libc-bin (= 2.31-3), libc-dev-bin (= 2.31-3), libc6 (= 2.31-3), libc6-dev (= 2.31-3), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.2.0-6), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1), libcrypt1 (= 1:4.4.17-1), libctf-nobfd0 (= 2.35-2), libctf0 (= 2.35-2), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.253), libdebhelper-perl (= 13.2), libdpkg-perl (= 1.20.5), libelf1 (= 0.180-1+b1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-6), libgcc-s1 (= 10.2.0-6), libgcrypt20 (= 1.8.6-2), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libglib2.0-0 (= 2.64.4-1), libgmp10 (= 2:6.2.0+dfsg-6), libgomp1 (= 10.2.0-6), libgpg-error0 (= 1.38-2), libicu67 (= 67.1-4), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-6), liblsan0 (= 10.2.0-6), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36-3), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.30 (= 5.30.3-4), libpipeline1 (= 1.5.3-1), libquadmath0 (= 10.2.0-6), libseccomp2 (= 2.4.3-1+b1), libselinux1 (= 3.1-2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.36-3), libstdc++-10-dev (= 10.2.0-6), libstdc++6 (= 10.2.0-6), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.4-1), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-6), libubsan1 (= 10.2.0-6), libuchardet0 (= 0.0.7-1), libudev1 (= 246.4-1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3), libxml2 (= 2.9.10+dfsg-6), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.7-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.3-4), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.3-4), perl-base (= 5.30.3-4), perl-modules-5.30 (= 5.30.3-4), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-4), tar (= 1.30+dfsg-7), util-linux (= 2.36-3), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1564495285" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml-dbgsym_3.11-2_armhf.deb ------------------------------ new Debian package, version 2.0. size 16562280 bytes: control archive=696 bytes. 448 bytes, 12 lines control 404 bytes, 4 lines md5sums Package: fastml-dbgsym Source: fastml Version: 3.11-2 Auto-Built-Package: debug-symbols Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 16785 Depends: fastml (= 3.11-2) Section: debug Priority: optional Description: debug symbols for fastml Build-Ids: 30972ac19693aac7ddd08d09c1720e2f3665d461 3762581af439e899d1cfd16629bcebbdd3cac193 95fbb58903d2dd05d2d1ab65dfa9adb6b9aaed4e drwxr-xr-x root/root 0 2019-07-30 14:01 ./ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.build-id/30/ -rw-r--r-- root/root 1189760 2019-07-30 14:01 ./usr/lib/debug/.build-id/30/972ac19693aac7ddd08d09c1720e2f3665d461.debug drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.build-id/37/ -rw-r--r-- root/root 5782828 2019-07-30 14:01 ./usr/lib/debug/.build-id/37/62581af439e899d1cfd16629bcebbdd3cac193.debug drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.build-id/95/ -rw-r--r-- root/root 9158644 2019-07-30 14:01 ./usr/lib/debug/.build-id/95/fbb58903d2dd05d2d1ab65dfa9adb6b9aaed4e.debug drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/ -rw-r--r-- root/root 1040556 2019-07-30 14:01 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/fastml.debug drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/doc/ lrwxrwxrwx root/root 0 2019-07-30 14:01 ./usr/share/doc/fastml-dbgsym -> fastml fastml_3.11-2_armhf.deb ----------------------- new Debian package, version 2.0. size 762772 bytes: control archive=1236 bytes. 1433 bytes, 26 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.11-2 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 2107 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://fastml.tau.ac.il/ Description: maximum likelihood ancestral amino-acid sequence reconstruction FastML is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. FastML runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters. For character reconstruction the previously described FastML algorithms are used to efficiently infer the most likely ancestral sequences for each internal node of the tree. Both joint and the marginal reconstructions are provided. For indels reconstruction the sequences are first coded according to the indel events detected within the multiple sequence alignment (MSA) and then a state-of-the-art likelihood model is used to reconstruct ancestral indels states. The results are the most probable sequences, together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. FastML is generic and is applicable for any type of molecular sequences (nucleotide, protein, or codon sequences). drwxr-xr-x root/root 0 2019-07-30 14:01 ./ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/bin/ -rwxr-xr-x root/root 734872 2019-07-30 14:01 ./usr/bin/fastml -rwxr-xr-x root/root 1230488 2019-07-30 14:01 ./usr/bin/gainLoss -rwxr-xr-x root/root 173720 2019-07-30 14:01 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/doc/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/doc/fastml/ -rw-r--r-- root/root 685 2019-07-30 14:01 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2937 2019-07-30 14:01 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/man/ drwxr-xr-x root/root 0 2019-07-30 14:01 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2019-07-30 14:01 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2019-07-30 14:01 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2019-07-30 14:01 ./usr/share/man/man1/indelCoder.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [530 B] Get:5 copy:/<>/apt_archive ./ Packages [618 B] Fetched 2111 B in 0s (82.4 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common t1utils unzip Suggested packages: libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl The following NEW packages will be installed: diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libproc-processtable-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian lzip lzop patchutils readline-common sbuild-build-depends-lintian-dummy:armhf t1utils unzip 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 7530 kB of archives. After this operation, 22.1 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7.1 [50.5 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.33.0-1 [790 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libaliased-perl all 0.34-1 [13.8 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB] Get:11 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[12.0 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.114-1 [53.6 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b6 [17.4 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.59-2 [45.7 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1 [98.9 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1 [103 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b7 [8696 B] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.12-1 [12.7 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.8-1 [198 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b2 [75.1 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-1 [39.2 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010005-1 [340 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.21-8 [84.3 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-1 [83.4 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-25 [172 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.93.0 [1281 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7530 kB in 0s (27.4 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20818 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package diffstat. Preparing to unpack .../02-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../03-libassuan0_2.5.3-7.1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7.1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../04-gpgconf_2.2.20-1_amd64.deb ... Unpacking gpgconf (2.2.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../05-libsqlite3-0_3.33.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.33.0-1) ... Selecting previously unselected package gpg. 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Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up libtype-tiny-perl (1.010005-1) ... Setting up libtext-markdown-discount-perl:amd64 (0.12-1) ... Setting up libexception-class-perl (1.44-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libdata-optlist-perl (0.110-1) ... Setting up gpgconf (2.2.20-1) ... Setting up gpg (2.2.20-1) ... Setting up libsub-exporter-perl (0.987-1) ... Setting up libiterator-perl (0.03+ds1-1) ... Setting up libiterator-util-perl (0.02+ds1-1) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004000-1) ... Setting up libmoox-aliases-perl (0.001006-1) ... Setting up libb-hooks-endofscope-perl (0.24-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.93.0) ... Setting up sbuild-build-depends-lintian-dummy:armhf (0.invalid.0) ... Processing triggers for man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.31-3) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 431692 Build-Time: 423 Distribution: unstable Foreign Architectures: armhf Host Architecture: armhf Install-Time: 19 Job: fastml_3.11-2 Lintian: pass Machine Architecture: amd64 Package: fastml Package-Time: 452 Source-Version: 3.11-2 Space: 431692 Status: successful Version: 3.11-2 -------------------------------------------------------------------------------- Finished at 2020-09-06T08:20:28Z Build needed 00:07:32, 431692k disk space