DC-Build-Header: libbpp-phyl 2.1.0-1 / 2014-09-04 15:45:23 +0000 DC-Task: source:libbpp-phyl version:2.1.0-1 architecture:any chroot:unstable esttime:1765 logfile:/tmp/libbpp-phyl_2.1.0-1_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " libbpp-phyl_2.1.0-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-9-31.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ libbpp-phyl 2.1.0-1clang1 (amd64) 04 Sep 2014 15:45 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: libbpp-phyl Version: 2.1.0-1clang1 Source Version: 2.1.0-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/libbpp-phyl-f0iNAN/libbpp-phyl-2.1.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/libbpp-phyl-f0iNAN' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-df67c1fc-f8e2-4c96-9f7b-dadeee99b29e' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [233 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2014-09-03-1436.55.pdiff [24.7 kB] Get:6 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [10.5 kB] Get:7 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [7545 B] Get:8 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:9 http://localhost:9999 unstable/main amd64 2014-09-03-1436.55.pdiff [26.7 kB] Get:10 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [14.0 kB] Get:11 http://localhost:9999 unstable/main amd64 2014-09-03-2030.01.pdiff [12.4 kB] Get:12 http://localhost:9999 unstable/main amd64 2014-09-04-0229.22.pdiff [5892 B] Get:13 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:14 http://localhost:9999 unstable/main 2014-09-03-1436.55.pdiff [3960 B] Get:15 http://localhost:9999 unstable/main 2014-09-03-2030.01.pdiff [1010 B] Get:16 http://localhost:9999 unstable/main 2014-09-04-0229.22.pdiff [648 B] Get:17 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Get:18 http://localhost:9999 unstable/main amd64 2014-09-04-0831.05.pdiff [18.1 kB] Get:19 http://localhost:9999 unstable/main 2014-09-04-0831.05.pdiff [61 B] Fetched 382 kB in 5s (72.9 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: binutils 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3310 kB of archives. After this operation, 50.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main binutils amd64 2.24.51.20140903-1 [3310 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3310 kB in 0s (31.7 MB/s) (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../binutils_2.24.51.20140903-1_amd64.deb ... Unpacking binutils (2.24.51.20140903-1) over (2.24.51.20140818-1) ... Setting up binutils (2.24.51.20140903-1) ... Processing triggers for libc-bin (2.19-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... Need to get 574 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main libbpp-phyl 2.1.0-1 (dsc) [1117 B] Get:2 http://localhost:9999/debian/ unstable/main libbpp-phyl 2.1.0-1 (tar) [568 kB] Get:3 http://localhost:9999/debian/ unstable/main libbpp-phyl 2.1.0-1 (diff) [4697 B] Fetched 574 kB in 1s (382 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.5 + echo 'Install of clang-3.5' Install of clang-3.5 + apt-get update Hit http://localhost:9999 unstable InRelease Get:1 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:2 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Fetched 23.6 kB in 1s (12.9 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.5 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel clang-3.5-doc Recommended packages: llvm-3.5-dev python The following NEW packages will be installed: clang-3.5 libbsd0 libclang-common-3.5-dev libclang1-3.5 libedit2 libffi6 libllvm3.5 libobjc-4.9-dev libobjc4 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 33.3 MB of archives. After this operation, 132 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libbsd0 amd64 0.7.0-2 [67.9 kB] Get:2 http://localhost:9999/debian/ unstable/main libedit2 amd64 3.1-20140620-2 [85.1 kB] Get:3 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:4 http://localhost:9999/debian/ unstable/main libllvm3.5 amd64 1:3.5-1 [7609 kB] Get:5 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.1-12 [112 kB] Get:6 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.1-12 [372 kB] Get:7 http://localhost:9999/debian/ unstable/main libclang1-3.5 amd64 1:3.5-1 [3628 kB] Get:8 http://localhost:9999/debian/ unstable/main libclang-common-3.5-dev amd64 1:3.5-1 [677 kB] Get:9 http://localhost:9999/debian/ unstable/main clang-3.5 amd64 1:3.5-1 [20.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.3 MB in 1s (32.3 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 15135 files and directories currently installed.) Preparing to unpack .../libbsd0_0.7.0-2_amd64.deb ... Unpacking libbsd0:amd64 (0.7.0-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../libedit2_3.1-20140620-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20140620-2) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.5:amd64. Preparing to unpack .../libllvm3.5_1%3a3.5-1_amd64.deb ... Unpacking libllvm3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.1-12_amd64.deb ... Unpacking libobjc4:amd64 (4.9.1-12) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.1-12_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.1-12) ... Selecting previously unselected package libclang1-3.5:amd64. Preparing to unpack .../libclang1-3.5_1%3a3.5-1_amd64.deb ... Unpacking libclang1-3.5:amd64 (1:3.5-1) ... Selecting previously unselected package libclang-common-3.5-dev. Preparing to unpack .../libclang-common-3.5-dev_1%3a3.5-1_amd64.deb ... Unpacking libclang-common-3.5-dev (1:3.5-1) ... Selecting previously unselected package clang-3.5. Preparing to unpack .../clang-3.5_1%3a3.5-1_amd64.deb ... Unpacking clang-3.5 (1:3.5-1) ... Setting up libbsd0:amd64 (0.7.0-2) ... Setting up libedit2:amd64 (3.1-20140620-2) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.5:amd64 (1:3.5-1) ... Setting up libobjc4:amd64 (4.9.1-12) ... Setting up libobjc-4.9-dev:amd64 (4.9.1-12) ... Setting up libclang1-3.5:amd64 (1:3.5-1) ... Setting up libclang-common-3.5-dev (1:3.5-1) ... Setting up clang-3.5 (1:3.5-1) ... Processing triggers for libc-bin (2.19-10) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-3.5 g++-4.6 + ln -s clang-3.5 gcc-4.6 + ln -s clang-3.5 cpp-4.6 + ln -s clang-3.5 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-3.5 g++-4.7 + ln -s clang-3.5 gcc-4.7 + ln -s clang-3.5 cpp-4.7 + ln -s clang-3.5 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-3.5 g++-4.8 + ln -s clang-3.5 gcc-4.8 + ln -s clang-3.5 cpp-4.8 + ln -s clang-3.5 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-3.5 g++-4.9 + ln -s clang-3.5 gcc-4.9 + ln -s clang-3.5 cpp-4.9 + ln -s clang-3.5 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-ImVbjl/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/818 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 15338 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.1.0) Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.1.0) dpkg-deb: building package `sbuild-build-depends-libbpp-phyl-dummy' in `/«BUILDDIR»/resolver-I6G8Q2/apt_archive/sbuild-build-depends-libbpp-phyl-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install libbpp-phyl build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils cmake cmake-data debhelper file gettext gettext-base groff-base intltool-debian libarchive13 libasprintf0c2 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libglib2.0-0 libgnutls-deb0-28 libgnutls26 libgssapi-krb5-2 libhogweed2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation codeblocks eclipse ninja-build dh-make gettext-doc groff lrzip gnutls-bin krb5-doc krb5-user less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev ca-certificates libglib2.0-data shared-mime-info krb5-locales libsasl2-modules xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils cmake cmake-data debhelper file gettext gettext-base groff-base intltool-debian libarchive13 libasprintf0c2 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libglib2.0-0 libgnutls-deb0-28 libgnutls26 libgssapi-krb5-2 libhogweed2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libp11-kit0 libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl1.0.0 libtasn1-6 libunistring0 libxml2 man-db po-debconf sbuild-build-depends-libbpp-phyl-dummy 0 upgraded, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 21.3 MB/21.3 MB of archives. After this operation, 74.5 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.3.0-1 [25.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libssl1.0.0 amd64 1.0.1i-2 [1026 kB] Get:3 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-7 [1142 kB] Get:4 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:5 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.7.1-1 [990 kB] Get:6 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.19.2-2 [30.8 kB] Get:7 http://localhost:9999/debian/ unstable/main libnettle4 amd64 2.7.1-3 [175 kB] Get:8 http://localhost:9999/debian/ unstable/main libhogweed2 amd64 2.7.1-3 [125 kB] Get:9 http://localhost:9999/debian/ unstable/main libp11-kit0 amd64 0.20.3-2 [153 kB] Get:10 http://localhost:9999/debian/ unstable/main libtasn1-6 amd64 4.1-1 [48.2 kB] Get:11 http://localhost:9999/debian/ unstable/main libgnutls-deb0-28 amd64 3.3.7-2 [685 kB] Get:12 http://localhost:9999/debian/ unstable/main libgnutls26 amd64 2.12.23-17 [531 kB] Get:13 http://localhost:9999/debian/ unstable/main libkeyutils1 amd64 1.5.9-5 [11.7 kB] Get:14 http://localhost:9999/debian/ unstable/main libkrb5support0 amd64 1.12.1+dfsg-9 [57.8 kB] Get:15 http://localhost:9999/debian/ unstable/main libk5crypto3 amd64 1.12.1+dfsg-9 [113 kB] Get:16 http://localhost:9999/debian/ unstable/main libkrb5-3 amd64 1.12.1+dfsg-9 [302 kB] Get:17 http://localhost:9999/debian/ unstable/main libgssapi-krb5-2 amd64 1.12.1+dfsg-9 [150 kB] Get:18 http://localhost:9999/debian/ unstable/main libidn11 amd64 1.29-1 [135 kB] Get:19 http://localhost:9999/debian/ unstable/main libsasl2-modules-db amd64 2.1.26.dfsg1-11 [66.8 kB] Get:20 http://localhost:9999/debian/ unstable/main libsasl2-2 amd64 2.1.26.dfsg1-11 [104 kB] Get:21 http://localhost:9999/debian/ unstable/main libldap-2.4-2 amd64 2.4.39-1.1+b1 [214 kB] Get:22 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.19-1 [237 kB] Get:23 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-4 [797 kB] Get:24 http://localhost:9999/debian/ unstable/main liblzo2-2 amd64 2.08-1 [54.9 kB] Get:25 http://localhost:9999/debian/ unstable/main libarchive13 amd64 3.1.2-9 [269 kB] Get:26 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.40.0-5 [2421 kB] Get:27 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-3 [135 kB] Get:28 http://localhost:9999/debian/ unstable/main librtmp1 amd64 2.4+20131018.git79459a2-4 [59.4 kB] Get:29 http://localhost:9999/debian/ unstable/main libssh2-1 amd64 1.4.3-4 [125 kB] Get:30 http://localhost:9999/debian/ unstable/main libcurl3 amd64 7.37.1-1 [254 kB] Get:31 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5.2 [283 kB] Get:32 http://localhost:9999/debian/ unstable/main file amd64 1:5.19-1 [58.0 kB] Get:33 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.19.2-2 [120 kB] Get:34 http://localhost:9999/debian/ unstable/main cmake-data all 2.8.12.2-1 [1285 kB] Get:35 http://localhost:9999/debian/ unstable/main cmake amd64 2.8.12.2-1 [2650 kB] Get:36 http://localhost:9999/debian/ unstable/main gettext amd64 0.19.2-2 [1237 kB] Get:37 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:38 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB] Get:39 http://localhost:9999/debian/ unstable/main debhelper all 9.20140817 [814 kB] Get:40 http://localhost:9999/debian/ unstable/main libbpp-core2 amd64 2.1.0-1 [613 kB] Get:41 http://localhost:9999/debian/ unstable/main libbpp-core-dev amd64 2.1.0-1 [1476 kB] Get:42 http://localhost:9999/debian/ unstable/main libbpp-seq9 amd64 2.1.0-1 [515 kB] Get:43 http://localhost:9999/debian/ unstable/main libbpp-seq-dev amd64 2.1.0-1 [1310 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.3 MB in 5s (4095 kB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 15338 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package libssl1.0.0:amd64. Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ... Unpacking libssl1.0.0:amd64 (1.0.1i-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-7_amd64.deb ... Unpacking groff-base (1.22.2-7) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ... Unpacking bsdmainutils (9.0.5) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.7.1-1_amd64.deb ... Unpacking man-db (2.6.7.1-1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.2-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.2-2) ... Selecting previously unselected package libnettle4:amd64. Preparing to unpack .../libnettle4_2.7.1-3_amd64.deb ... Unpacking libnettle4:amd64 (2.7.1-3) ... Selecting previously unselected package libhogweed2:amd64. Preparing to unpack .../libhogweed2_2.7.1-3_amd64.deb ... Unpacking libhogweed2:amd64 (2.7.1-3) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../libp11-kit0_0.20.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.20.3-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../libtasn1-6_4.1-1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.1-1) ... Selecting previously unselected package libgnutls-deb0-28:amd64. Preparing to unpack .../libgnutls-deb0-28_3.3.7-2_amd64.deb ... Unpacking libgnutls-deb0-28:amd64 (3.3.7-2) ... Selecting previously unselected package libgnutls26:amd64. Preparing to unpack .../libgnutls26_2.12.23-17_amd64.deb ... Unpacking libgnutls26:amd64 (2.12.23-17) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../libkeyutils1_1.5.9-5_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-5) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../libkrb5support0_1.12.1+dfsg-9_amd64.deb ... Unpacking libkrb5support0:amd64 (1.12.1+dfsg-9) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../libk5crypto3_1.12.1+dfsg-9_amd64.deb ... Unpacking libk5crypto3:amd64 (1.12.1+dfsg-9) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../libkrb5-3_1.12.1+dfsg-9_amd64.deb ... Unpacking libkrb5-3:amd64 (1.12.1+dfsg-9) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-9_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.12.1+dfsg-9) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../libidn11_1.29-1_amd64.deb ... Unpacking libidn11:amd64 (1.29-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-11_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-11) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-11_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-11) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../libldap-2.4-2_2.4.39-1.1+b1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.39-1.1+b1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.19-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.19-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.1+dfsg1-4_amd64.deb ... Unpacking libxml2:amd64 (2.9.1+dfsg1-4) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../liblzo2-2_2.08-1_amd64.deb ... 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Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ... Unpacking po-debconf (1.0.16+nmu3) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20140817_all.deb ... Unpacking debhelper (9.20140817) ... Selecting previously unselected package libbpp-core2. Preparing to unpack .../libbpp-core2_2.1.0-1_amd64.deb ... Unpacking libbpp-core2 (2.1.0-1) ... Selecting previously unselected package libbpp-core-dev. Preparing to unpack .../libbpp-core-dev_2.1.0-1_amd64.deb ... Unpacking libbpp-core-dev (2.1.0-1) ... Selecting previously unselected package libbpp-seq9. Preparing to unpack .../libbpp-seq9_2.1.0-1_amd64.deb ... Unpacking libbpp-seq9 (2.1.0-1) ... Selecting previously unselected package libbpp-seq-dev. Preparing to unpack .../libbpp-seq-dev_2.1.0-1_amd64.deb ... Unpacking libbpp-seq-dev (2.1.0-1) ... Selecting previously unselected package sbuild-build-depends-libbpp-phyl-dummy. Preparing to unpack .../sbuild-build-depends-libbpp-phyl-dummy.deb ... Unpacking sbuild-build-depends-libbpp-phyl-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up libssl1.0.0:amd64 (1.0.1i-2) ... Setting up groff-base (1.22.2-7) ... Setting up bsdmainutils (9.0.5) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.19.2-2) ... Setting up libnettle4:amd64 (2.7.1-3) ... Setting up libhogweed2:amd64 (2.7.1-3) ... Setting up libp11-kit0:amd64 (0.20.3-2) ... Setting up libtasn1-6:amd64 (4.1-1) ... Setting up libgnutls-deb0-28:amd64 (3.3.7-2) ... Setting up libgnutls26:amd64 (2.12.23-17) ... Setting up libkeyutils1:amd64 (1.5.9-5) ... Setting up libkrb5support0:amd64 (1.12.1+dfsg-9) ... Setting up libk5crypto3:amd64 (1.12.1+dfsg-9) ... Setting up libkrb5-3:amd64 (1.12.1+dfsg-9) ... Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-9) ... Setting up libidn11:amd64 (1.29-1) ... Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-11) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-11) ... Setting up libldap-2.4-2:amd64 (2.4.39-1.1+b1) ... Setting up libmagic1:amd64 (1:5.19-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-4) ... Setting up liblzo2-2:amd64 (2.08-1) ... Setting up libarchive13:amd64 (3.1.2-9) ... Setting up libglib2.0-0:amd64 (2.40.0-5) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-3) ... Setting up librtmp1:amd64 (2.4+20131018.git79459a2-4) ... Setting up libssh2-1:amd64 (1.4.3-4) ... Setting up libcurl3:amd64 (7.37.1-1) ... Setting up libunistring0:amd64 (0.9.3-5.2) ... Setting up file (1:5.19-1) ... Setting up gettext-base (0.19.2-2) ... Setting up cmake-data (2.8.12.2-1) ... Setting up cmake (2.8.12.2-1) ... Setting up gettext (0.19.2-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up debhelper (9.20140817) ... Setting up libbpp-core2 (2.1.0-1) ... Setting up libbpp-core-dev (2.1.0-1) ... -- Creating generic include file: /usr/include/Bpp.all -- Creating generic include file: /usr/include/Bpp/App.all -- Creating generic include file: /usr/include/Bpp/Graph.all -- Creating generic include file: /usr/include/Bpp/Graphics.all -- Creating generic include file: /usr/include/Bpp/Graphics/Fig.all -- Creating generic include file: /usr/include/Bpp/Graphics/Font.all -- Creating generic include file: /usr/include/Bpp/Graphics/Latex.all -- Creating generic include file: /usr/include/Bpp/Graphics/Molscript.all -- Creating generic include file: /usr/include/Bpp/Graphics/R.all -- Creating generic include file: /usr/include/Bpp/Graphics/Svg.all -- Creating generic include file: /usr/include/Bpp/Io.all -- Creating generic include file: /usr/include/Bpp/Numeric.all -- Creating generic include file: /usr/include/Bpp/Numeric/Function.all -- Creating generic include file: /usr/include/Bpp/Numeric/Hmm.all -- Creating generic include file: /usr/include/Bpp/Numeric/Matrix.all -- Creating generic include file: /usr/include/Bpp/Numeric/Prob.all -- Creating generic include file: /usr/include/Bpp/Numeric/Random.all -- Creating generic include file: /usr/include/Bpp/Numeric/Stat.all -- Creating generic include file: /usr/include/Bpp/Numeric/Stat/Mva.all -- Creating generic include file: /usr/include/Bpp/Seq.all -- Creating generic include file: /usr/include/Bpp/Seq/Alphabet.all -- Creating generic include file: /usr/include/Bpp/Seq/AlphabetIndex.all -- Creating generic include file: /usr/include/Bpp/Seq/App.all -- Creating generic include file: /usr/include/Bpp/Seq/Container.all -- Creating generic include file: /usr/include/Bpp/Seq/GeneticCode.all -- Creating generic include file: /usr/include/Bpp/Seq/Io.all -- Creating generic include file: /usr/include/Bpp/Text.all -- Creating generic include file: /usr/include/Bpp/Utils.all Setting up libbpp-seq9 (2.1.0-1) ... Setting up libbpp-seq-dev (2.1.0-1) ... -- Creating generic include file: /usr/include/Bpp.all -- Creating generic include file: /usr/include/Bpp/App.all -- Creating generic include file: /usr/include/Bpp/Graph.all -- Creating generic include file: /usr/include/Bpp/Graphics.all -- Creating generic include file: /usr/include/Bpp/Graphics/Fig.all -- Creating generic include file: /usr/include/Bpp/Graphics/Font.all -- Creating generic include file: /usr/include/Bpp/Graphics/Latex.all -- Creating generic include file: /usr/include/Bpp/Graphics/Molscript.all -- Creating generic include file: /usr/include/Bpp/Graphics/R.all -- Creating generic include file: /usr/include/Bpp/Graphics/Svg.all -- Creating generic include file: /usr/include/Bpp/Io.all -- Creating generic include file: /usr/include/Bpp/Numeric.all -- Creating generic include file: /usr/include/Bpp/Numeric/Function.all -- Creating generic include file: /usr/include/Bpp/Numeric/Hmm.all -- Creating generic include file: /usr/include/Bpp/Numeric/Matrix.all -- Creating generic include file: /usr/include/Bpp/Numeric/Prob.all -- Creating generic include file: /usr/include/Bpp/Numeric/Random.all -- Creating generic include file: /usr/include/Bpp/Numeric/Stat.all -- Creating generic include file: /usr/include/Bpp/Numeric/Stat/Mva.all -- Creating generic include file: /usr/include/Bpp/Seq.all -- Creating generic include file: /usr/include/Bpp/Seq/Alphabet.all -- Creating generic include file: /usr/include/Bpp/Seq/AlphabetIndex.all -- Creating generic include file: /usr/include/Bpp/Seq/App.all -- Creating generic include file: /usr/include/Bpp/Seq/Container.all -- Creating generic include file: /usr/include/Bpp/Seq/GeneticCode.all -- Creating generic include file: /usr/include/Bpp/Seq/Io.all -- Creating generic include file: /usr/include/Bpp/Text.all -- Creating generic include file: /usr/include/Bpp/Utils.all Setting up sbuild-build-depends-libbpp-phyl-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-10) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-3 gcc-4.9_4.9.1-12 libc6-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.15-2 Package versions: acl_2.2.52-1.1 adduser_3.113+nmu3 apt_1.0.7 base-files_7.5 base-passwd_3.5.35 bash_4.3-9 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 clang-3.5_1:3.5-1 cmake_2.8.12.2-1 cmake-data_2.8.12.2-1 coreutils_8.23-2 cpp_4:4.9.1-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-3 cpp-4.9_4.9.1-12 dash_0.5.7-4 dbus_1.8.6-2 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.88-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-1 findutils_4.4.2-9 g++_4:4.9.1-3 g++-4.6_4.6.4-7 g++-4.9_4.9.1-12 gcc_4:4.9.1-3 gcc-4.4-base_4.4.7-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-7 gcc-4.6-base_4.6.4-7 gcc-4.7_4.7.4-3 gcc-4.7-base_4.7.4-3 gcc-4.8-base_4.8.3-10 gcc-4.9_4.9.1-12 gcc-4.9-base_4.9.1-12 gettext_0.19.2-2 gettext-base_0.19.2-2 gnupg_1.4.18-3 gpgv_1.4.18-3 grep_2.20-2 groff-base_1.22.2-7 gzip_1.6-3 hostname_3.15 init_1.21 initscripts_2.88dsf-53.4 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1.1 libalgorithm-c3-perl_0.09-1 libapt-pkg4.12_1.0.7 libarchive-extract-perl_0.72-1 libarchive13_3.1.2-9 libasan1_4.9.1-12 libasprintf0c2_0.19.2-2 libatomic1_4.9.1-12 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblkid1_2.20.1-5.8 libbpp-core-dev_2.1.0-1 libbpp-core2_2.1.0-1 libbpp-seq-dev_2.1.0-1 libbpp-seq9_2.1.0-1 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-7 libc-bin_2.19-10 libc-dev-bin_2.19-10 libc6_2.19-10 libc6-dev_2.19-10 libcap-ng0_0.7.4-2 libcap2_1:2.24-4 libcap2-bin_1:2.24-4 libcgi-fast-perl_1:2.02-1 libcgi-pm-perl_4.03-1 libcilkrts5_4.9.1-12 libclang-common-3.5-dev_1:3.5-1 libclang1-3.5_1:3.5-1 libclass-c3-perl_0.26-1 libclass-c3-xs-perl_0.13-2+b1 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.12-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-1 libcurl3_7.37.1-1 libdata-optlist-perl_0.109-1 libdata-section-perl_0.200006-1 libdb5.1_5.1.29-5 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.191 libdevmapper1.02.1_2:1.02.88-1 libdpkg-perl_1.17.13 libedit2_3.1-20140620-2 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libfcgi-perl_0.77-1+b1 libffi6_3.1-2 libfile-fcntllock-perl_0.22-1+b1 libgc1c2_1:7.2d-6.3 libgcc-4.7-dev_4.7.4-3 libgcc-4.9-dev_4.9.1-12 libgcc1_1:4.9.1-12 libgcrypt11_1.5.4-3 libgcrypt20_1.6.2-3 libgdbm3_1.8.3-13 libglib2.0-0_2.40.0-5 libgmp10_2:6.0.0+dfsg-6 libgmpxx4ldbl_2:6.0.0+dfsg-6 libgnutls-deb0-28_3.3.7-2 libgnutls26_2.12.23-17 libgomp1_4.9.1-12 libgpg-error0_1.13-4 libgpm2_1.20.4-6.1 libgssapi-krb5-2_1.12.1+dfsg-9 libhogweed2_2.7.1-3 libidn11_1.29-1 libisl10_0.12.2-2 libitm1_4.9.1-12 libk5crypto3_1.12.1+dfsg-9 libkeyutils1_1.5.9-5 libkmod2_18-1 libkrb5-3_1.12.1+dfsg-9 libkrb5support0_1.12.1+dfsg-9 libldap-2.4-2_2.4.39-1.1+b1 libllvm3.5_1:3.5-1 liblocale-gettext-perl_1.05-8+b1 liblog-message-perl_0.8-1 liblog-message-simple-perl_0.10-2 liblsan0_4.9.1-12 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.08-1 libmagic1_1:5.19-1 libmodule-build-perl_0.420800-1 libmodule-pluggable-perl_5.1-1 libmodule-signature-perl_0.73-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libmro-compat-perl_0.12-1 libncurses5_5.9+20140712-2 libncursesw5_5.9+20140712-2 libnettle4_2.7.1-3 libobjc-4.9-dev_4.9.1-12 libobjc4_4.9.1-12 libp11-kit0_0.20.3-2 libpackage-constants-perl_0.04-1 libpam-cap_1:2.24-4 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam-systemd_208-8 libpam0g_1.1.8-3.1 libparams-util-perl_1.07-2+b1 libpcre3_1:8.35-3 libpipeline1_1.3.0-1 libpod-latex-perl_0.61-1 libpod-readme-perl_0.11-1 libppl-c4_1:1.1-3 libppl13_1:1.1-3 libprocps3_1:3.3.9-7 libquadmath0_4.9.1-12 libreadline6_6.3-8 libregexp-common-perl_2013031301-1 librtmp1_2.4+20131018.git79459a2-4 libsasl2-2_2.1.26.dfsg1-11 libsasl2-modules-db_2.1.26.dfsg1-11 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.2.4-17 libsoftware-license-perl_0.103010-1 libss2_1.42.12-1 libssh2-1_1.4.3-4 libssl1.0.0_1.0.1i-2 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12 libstdc++6-4.6-dev_4.6.4-7 libsub-exporter-perl_0.986-1 libsub-install-perl_0.928-1 libswitch-perl_2.17-1 libsystemd-daemon0_208-8 libsystemd-journal0_208-8 libsystemd-login0_208-8 libtasn1-6_4.1-1 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b2 libtext-soundex-perl_3.4-1+b2 libtext-template-perl_1.46-1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140712-2 libtsan0_4.9.1-12 libubsan0_4.9.1-12 libudev1_208-8 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libwrap0_7.6.q-25 libxml2_2.9.1+dfsg1-4 linux-libc-dev_3.14.15-2 login_1:4.2-2+b1 lsb-base_4.1+Debian13 make_4.0-8 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-10 ncurses-base_5.9+20140712-2 ncurses-bin_5.9+20140712-2 passwd_1:4.2-2+b1 patch_2.7.1-6 perl_5.20.0-6 perl-base_5.20.0-6 perl-modules_5.20.0-6 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 psmisc_22.21-2 readline-common_6.3-8 rename_0.20-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbpp-phyl-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.9p5-1 systemd_208-8 systemd-sysv_208-8 sysv-rc_2.88dsf-53.4 sysvinit_2.88dsf-53.4 sysvinit-utils_2.88dsf-53.4 tar_1.27.1-2 tcpd_7.6.q-25 tzdata_2014g-1 ucf_3.0030 udev_208-8 util-linux_2.20.1-5.8 vim_2:7.4.430-1 vim-common_2:7.4.430-1 vim-runtime_2:7.4.430-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Sun May 26 15:22:05 2013 UTC using DSA key ID 497A176D gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./libbpp-phyl_2.1.0-1.dsc dpkg-source: info: extracting libbpp-phyl in libbpp-phyl-2.1.0 dpkg-source: info: unpacking libbpp-phyl_2.1.0.orig.tar.gz dpkg-source: info: unpacking libbpp-phyl_2.1.0-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 2.1.0-1clang1 User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user 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=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-df67c1fc-f8e2-4c96-9f7b-dadeee99b29e SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package libbpp-phyl dpkg-buildpackage: source version 2.1.0-1clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build libbpp-phyl-2.1.0 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh_testdir dh_testroot # Add here commands to clean up after the build process. [ ! -f Makefile ] || /usr/bin/make clean; [ ! -f Makefile ] || rm Makefile; [ ! -f src/Makefile ] || rm src/Makefile; [ ! -f test/Makefile ] || rm test/Makefile; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f src/*.cmake rm -f test/*.cmake rm -rf CMakeFiles rm -rf src/CMakeFiles rm -rf test/CMakeFiles rm -rf _CPack_Packages rm -rf Testing rm -f DartConfiguration.tcl dh_clean dpkg-buildpackage: warning: debian/rules must be updated to support the 'build-arch' and 'build-indep' targets (at least 'build-arch' seems to be missing) debian/rules build cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . -- The CXX compiler identification is Clang 3.5.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Library bpp-seq found here: includes : /usr/include libraries: /usr/lib/libbpp-seq.so -- Library bpp-core found here: includes : /usr/include libraries: /usr/lib/libbpp-core.so -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done -- Generating done -- Build files have been written to: /«PKGBUILDDIR» dh_testdir dh_testdir # Add here commands to compile the package. /usr/bin/make make[1]: Entering directory '/«PKGBUILDDIR»' make[2]: Entering directory '/«PKGBUILDDIR»' make[3]: Entering directory '/«PKGBUILDDIR»' Scanning dependencies of target bppphyl-shared make[3]: Leaving directory '/«PKGBUILDDIR»' make[3]: Entering directory '/«PKGBUILDDIR»' [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:51: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:43: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Model/Protein/Coala.h:104:8: warning: 'bpp::Coala::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data, bool param = true); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:49: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:140:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:140:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:151:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[0] = label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/NaiveSubstitutionCount.h:151:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[0] = label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:50: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/OneJumpSubstitutionCount.h:91:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Mapping/OneJumpSubstitutionCount.h:91:52: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../OptimizationTools.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../OptimizationTools.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../OptimizationTools.h:47: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Parsimony/DRTreeParsimonyScore.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Parsimony/AbstractTreeParsimonyScore.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Parsimony/../Model/StateMap.h:139:129: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] catch (ElementNotFoundException& ex) { throw Exception("AbstractStateMap::whichState. Unsupported alphabet char: " + code); } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Parsimony/../Model/StateMap.h:139:129: note: use array indexing to silence this warning catch (ElementNotFoundException& ex) { throw Exception("AbstractStateMap::whichState. Unsupported alphabet char: " + code); } ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:51: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/App/../OptimizationTools.h:49: /«PKGBUILDDIR»/src/Bpp/Phyl/App/../Distance/DistanceEstimation.h:392:55: warning: field 'defaultOptimizer_' is uninitialized when used here [-Wuninitialized] defaultOptimizer_(dynamic_cast(defaultOptimizer_->clone())), ^ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:570:114: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] const MixedSubstitutionModel* pSM = dynamic_cast(mixedModelSet.getModel(num - 1)); ~~~~~~~~~~~~~ ~~~~^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:575:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] mixedModelSet.addToHyperNode(num - 1, submodnb); ~~~~~~~~~~~~~ ~~~~^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:638:25: warning: implicit conversion changes signedness: 'int' to 'const value_type' (aka 'const unsigned long') [-Wsign-conversion] classes.push_back(TextTools::toInt(strtok2.nextToken())); ~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:951:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] optNumFirst, tolBefore, tolDuring, nbEvalMax, topoNbStep, messageHandler, profiler, ^~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:974:44: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion] optNumFirst, tolBefore, tolDuring, nbEvalMax, topoNbStep, messageHandler, profiler, ^~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1471:25: warning: 'reinterpret_cast' from class 'bpp::LabelSubstitutionCount *' to its virtual base 'bpp::SubstitutionCount *' behaves differently from 'static_cast' [-Wreinterpret-base-class] substitutionCount = reinterpret_cast(new LabelSubstitutionCount(alphabet)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1471:25: note: use 'static_cast' to adjust the pointer correctly while upcasting substitutionCount = reinterpret_cast(new LabelSubstitutionCount(alphabet)); ^~~~~~~~~~~~~~~~ static_cast /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1475:25: warning: 'reinterpret_cast' from class 'bpp::OneJumpSubstitutionCount *' to its virtual base 'bpp::SubstitutionCount *' behaves differently from 'static_cast' [-Wreinterpret-base-class] substitutionCount = reinterpret_cast(new OneJumpSubstitutionCount(model)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:1475:25: note: use 'static_cast' to adjust the pointer correctly while upcasting substitutionCount = reinterpret_cast(new OneJumpSubstitutionCount(model)); ^~~~~~~~~~~~~~~~ static_cast 29 warnings generated. [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionList.cpp:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionList.cpp:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionList.cpp:43: /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionList.cpp:326:59: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] bitBipartitionList_.erase(bitBipartitionList_.begin() + i); ~~~~~~~~~~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionList.cpp:522:88: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] bitBipartitionList_.erase(bitBipartitionList_.begin(), bitBipartitionList_.begin() + nbbip); ~~~~~~~~~~~~~~~~~~~ ^~~~~ 12 warnings generated. [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:42: /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:73:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] plist += (num / LWORD); ^~~ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:74:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] *plist |= (1 << (num % LWORD)); ^~~ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:82:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] plist += (num / LWORD); ^~~ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:83:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] *plist &= ~(1 << (num % LWORD)); ^~~ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:120:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] plist += (num / LWORD); ^~~ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/BipartitionTools.cpp:121:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] return (*plist) & (1 << (num % LWORD)); ^~~ ~ 16 warnings generated. [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/BioNJ.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.h:392:55: warning: field 'defaultOptimizer_' is uninitialized when used here [-Wuninitialized] defaultOptimizer_(dynamic_cast(defaultOptimizer_->clone())), ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:143:49: warning: field 'brLenConstraint_' is uninitialized when used here [-Wuninitialized] brLenConstraint_ (dynamic_cast(brLenConstraint_->clone())), ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:267:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return rootLikelihoods_[rootPatternLinks_[site]][rateClass][state]; ~~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:274:67: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return log(rootLikelihoods_[rootPatternLinks_[site]][rateClass][state]); ~~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:658:26: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32] optimizer_->setVerbose(static_cast(max(static_cast(verbose_) - 2, 0))); ~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 17 warnings generated. [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/NeighborJoining.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/PGMA.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/HierarchicalClustering.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h:46: /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Distance/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/CladogramPlot.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/PhylogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:167:46: warning: 'reinterpret_cast' from class 'bpp::NodesIdTreeDrawingListener *' to its virtual base 'bpp::TreeDrawingListener *' behaves differently from 'static_cast' [-Wreinterpret-base-class] addListener(PROPERTY_NODE_IDS , reinterpret_cast(new NodesIdTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:167:46: note: use 'static_cast' to adjust the pointer correctly while upcasting addListener(PROPERTY_NODE_IDS , reinterpret_cast(new NodesIdTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~ static_cast /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:168:46: warning: 'reinterpret_cast' from class 'bpp::LeafNamesTreeDrawingListener *' to its virtual base 'bpp::TreeDrawingListener *' behaves differently from 'static_cast' [-Wreinterpret-base-class] addListener(PROPERTY_LEAF_NAMES , reinterpret_cast(new LeafNamesTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:168:46: note: use 'static_cast' to adjust the pointer correctly while upcasting addListener(PROPERTY_LEAF_NAMES , reinterpret_cast(new LeafNamesTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~ static_cast /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:169:46: warning: 'reinterpret_cast' from class 'bpp::BranchLengthsTreeDrawingListener *' to its virtual base 'bpp::TreeDrawingListener *' behaves differently from 'static_cast' [-Wreinterpret-base-class] addListener(PROPERTY_BRANCH_LENGTHS , reinterpret_cast(new BranchLengthsTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:169:46: note: use 'static_cast' to adjust the pointer correctly while upcasting addListener(PROPERTY_BRANCH_LENGTHS , reinterpret_cast(new BranchLengthsTreeDrawingListener (settings_, true))); ^~~~~~~~~~~~~~~~ static_cast /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:170:46: warning: 'reinterpret_cast' from class 'bpp::BootstrapValuesTreeDrawingListener *' to its virtual base 'bpp::TreeDrawingListener *' behaves differently from 'static_cast' [-Wreinterpret-base-class] addListener(PROPERTY_BOOTSTRAP_VALUES, reinterpret_cast(new BootstrapValuesTreeDrawingListener(settings_, true))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h:170:46: note: use 'static_cast' to adjust the pointer correctly while upcasting addListener(PROPERTY_BOOTSTRAP_VALUES, reinterpret_cast(new BootstrapValuesTreeDrawingListener(settings_, true))); ^~~~~~~~~~~~~~~~ static_cast 4 warnings generated. [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Graphics/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:392:55: warning: field 'defaultOptimizer_' is uninitialized when used here [-Wuninitialized] defaultOptimizer_(dynamic_cast(defaultOptimizer_->clone())), ^ 13 warnings generated. [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoTreeFactory.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Newick.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/NexusIoTree.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/Nhx.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:143:7: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses] if (!psl.getLikelihoods().size() > 0) ^ ~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:143:7: note: add parentheses after the '!' to evaluate the comparison first if (!psl.getLikelihoods().size() > 0) ^ ( ) /«PKGBUILDDIR»/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp:143:7: note: add parentheses around left hand side expression to silence this warning if (!psl.getLikelihoods().size() > 0) ^ ( ) 11 warnings generated. [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:63: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/RE08.h:173:10: warning: 'bpp::RE08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:66: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/F84.h:207:12: warning: 'bpp::F84::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:66: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/F84.h:208:12: warning: 'bpp::F84::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:66: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/F84.h:209:12: warning: 'bpp::F84::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:69: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95.h:166:10: warning: 'bpp::RN95::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:69: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95.h:167:10: warning: 'bpp::RN95::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:69: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95.h:168:10: warning: 'bpp::RN95::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:71: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95s.h:141:10: warning: 'bpp::RN95s::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:71: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95s.h:142:10: warning: 'bpp::RN95s::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:71: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/RN95s.h:143:10: warning: 'bpp::RN95s::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:72: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/HKY85.h:207:10: warning: 'bpp::HKY85::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:72: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/HKY85.h:208:10: warning: 'bpp::HKY85::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:72: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/HKY85.h:209:10: warning: 'bpp::HKY85::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:74: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/JCnuc.h:166:8: warning: 'bpp::JCnuc::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:75: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/T92.h:181:10: warning: 'bpp::T92::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:75: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/T92.h:182:10: warning: 'bpp::T92::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:75: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/T92.h:183:10: warning: 'bpp::T92::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:76: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/K80.h:172:12: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:76: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/K80.h:173:12: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:76: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/K80.h:174:12: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:76: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:77: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/TN93.h:160:10: warning: 'bpp::TN93::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:77: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/TN93.h:161:10: warning: 'bpp::TN93::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:77: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Nucleotide/TN93.h:162:10: warning: 'bpp::TN93::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:82: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/Coala.h:104:8: warning: 'bpp::Coala::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data, bool param = true); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:84: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/DSO78.h:143:10: warning: 'bpp::DSO78::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:86: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/JCprot.h:192:12: warning: 'bpp::JCprot::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:278:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t (size_t i, size_t j, double t) const { return getPij_t(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:257:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double Pij_t(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:86: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/JCprot.h:193:12: warning: 'bpp::JCprot::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:279:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt (size_t i, size_t j, double t) const { return getdPij_dt(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:264:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double dPij_dt(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:86: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/JCprot.h:194:12: warning: 'bpp::JCprot::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:280:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:271:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'int') virtual double d2Pij_dt2(size_t i, size_t j, double t) const = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:86: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/JCprot.h:224:10: warning: 'bpp::JCprot::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:88: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/JTT92.h:143:10: warning: 'bpp::JTT92::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:90: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/LG08.h:141:10: warning: 'bpp::LG08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:91: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/UserProteinSubstitutionModel.h:151:10: warning: 'bpp::UserProteinSubstitutionModel::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:93: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/Protein/WAG01.h:148:10: warning: 'bpp::WAG01::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: different number of parameters (2 vs 1) virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:97: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:97: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:97: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:49: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/HomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:97: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/PhylogeneticsApplicationTools.h:51: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../App/../Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:569:30: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion] unsigned int nbCat = TextTools::toInt(args["nbCat"]); ~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:590:38: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion] model.reset(new Coala(alpha, TextTools::toInt(nbrOfParametersPerBranch), exchangeability, file)); ~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp:1295:22: warning: implicit conversion changes signedness: 'unsigned int' to 'const key_type' (aka 'const int') [-Wsign-conversion] frequencies[i++] = TextTools::toDouble(strtok.nextToken()); ~~~~~~~~~~~ ~^~ 48 warnings generated. [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/FrequenciesSet/MvaFrequenciesSet.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/Coala.h:104:8: warning: 'bpp::Coala::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data, bool param = true); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/FrequenciesSet/../Protein/../AbstractSubstitutionModel.h:284:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0); ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/../Model/SubstitutionModel.h:448:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here: type mismatch at 2nd parameter ('double' vs 'bool') virtual void setFreqFromData(const SequenceContainer& data, double pseudoCount = 0) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp:552:15: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion] psc = TextTools::toInt(unparsedArguments_["observedPseudoCount"]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ 12 warnings generated. [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:146:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLikelihoodForASite' hides overloaded virtual function [-Woverloaded-virtual] double getLikelihoodForASite (unsigned int site) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:150:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASite' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLikelihoodForASite (size_t site) const; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:147:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASite' hides overloaded virtual function [-Woverloaded-virtual] double getLogLikelihoodForASite(unsigned int site) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:151:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASite' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLogLikelihoodForASite(size_t site) const; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:156:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClass' hides overloaded virtual function [-Woverloaded-virtual] double getLikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:163:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:157:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClass' hides overloaded virtual function [-Woverloaded-virtual] double getLogLikelihoodForASiteForARateClass(unsigned int site, unsigned int rateClass) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:164:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:158:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClassForAState' hides overloaded virtual function [-Woverloaded-virtual] double getLikelihoodForASiteForARateClassForAState(unsigned int site, unsigned int rateClass, int state) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:165:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:159:10: warning: 'bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState' hides overloaded virtual function [-Woverloaded-virtual] double getLogLikelihoodForASiteForARateClassForAState(unsigned int site, unsigned int rateClass, int state) const; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:166:12: note: hidden overloaded virtual function 'bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState' declared here: type mismatch at 1st parameter ('size_t' (aka 'unsigned long') vs 'unsigned int') double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const; ^ 18 warnings generated. [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:221:108: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return likelihoodData_->getRootLikelihoodArray()[likelihoodData_->getRootArrayPosition(site)][rateClass][state]; ~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:228:112: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return log(likelihoodData_->getRootLikelihoodArray()[likelihoodData_->getRootArrayPosition(site)][rateClass][state]); ~~~~~~~~~~~~~~~ ^~~~~ 14 warnings generated. [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:225:108: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return likelihoodData_->getRootLikelihoodArray()[likelihoodData_->getRootArrayPosition(site)][rateClass][state]; ~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp:232:112: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return log(likelihoodData_->getRootLikelihoodArray()[likelihoodData_->getRootArrayPosition(site)][rateClass][state]); ~~~~~~~~~~~~~~~ ^~~~~ 12 warnings generated. [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:61:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] ancestors[i] = (int)j; ~ ^~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp:92:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion] ancestors[i] = (int)j; ~ ^~~~~~ 12 warnings generated. [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ 12 warnings generated. [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:42: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ 12 warnings generated. [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RASTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ 12 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ 12 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:199:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:201:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual const SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) const throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here: different number of parameters (2 vs 0) virtual SubstitutionModel* getSubstitutionModel(int nodeId, size_t siteIndex) throw (NodeNotFoundException) = 0; ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:238:133: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return likelihoodData_->getLikelihoodArray(tree_->getRootNode()->getId())[likelihoodData_->getRootArrayPosition(site)][rateClass][state]; ~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:245:137: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return log(likelihoodData_->getLikelihoodArray(tree_->getRootNode()->getId())[likelihoodData_->getRootArrayPosition(site)][rateClass][state]); ~~~~~~~~~~~~~~~ ^~~~~ 14 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:216:62: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] mapmodels[*it] = static_cast(hyperNode_.getNode(*it).size()); ~~~~~~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:217:21: warning: implicit conversion changes signedness: 'mapped_type' (aka 'int') to 'unsigned long' [-Wsign-conversion] ttmodels *= mapmodels[*it]; ~~ ^~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:229:60: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] hn.setModel(j, Vint(1, hyperNode_.getNode(j)[s % mapmodels[static_cast(j)]])); ~~~~~~~~~~ ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:738:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] vModel.push_back(mmodel->getNModel(nd[i])); ~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:739:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] vProba.push_back(mmodel->getNProbability(nd[i])); ~~~~~~ ^~~~~ 15 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:41: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:242:133: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return likelihoodData_->getLikelihoodArray(tree_->getRootNode()->getId())[likelihoodData_->getRootArrayPosition(site)][rateClass][state]; ~~~~~~~~~~~~~~~ ^~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp:249:137: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] return log(likelihoodData_->getLikelihoodArray(tree_->getRootNode()->getId())[likelihoodData_->getRootArrayPosition(site)][rateClass][state]); ~~~~~~~~~~~~~~~ ^~~~~ 12 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h:48: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp:184:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] ++v.at(RandomTools::giveIntRandomNumberBetweenZeroAndEntry(static_cast(length))); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 11 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:46: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Likelihood/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] 10 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:72:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] MatrixTools::pow(Q, p, M3); // Q^p -> M5 ~~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:74:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] MatrixTools::pow(Q, n - p - 1, M3); // Q^(n-p-1) -> M3 ~~~~~~~~~~~ ~~~~~~^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:98:15: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return m_(initialState, finalState); ~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:98:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return m_(initialState, finalState); ~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:105:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return m_(initialState, finalState); ~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp:105:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return m_(initialState, finalState); ~~ ^~~~~~~~~~ 7 warnings generated. [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:91:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:91:52: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~ 3 warnings generated. [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ 11 warnings generated. [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:140:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:140:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:151:21: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[0] = label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h:151:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[0] = label_(initialState, finalState); ~~~~~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:47:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] RowMatrix* mat = new RowMatrix(n, n); ~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:47:53: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] RowMatrix* mat = new RowMatrix(n, n); ~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:52:14: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] (*mat)(i, j) = (register_->getType(i, j) == type ? (weights_ ? weights_->getIndex(i, j) : 1.) : 0.); ~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:52:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] (*mat)(i, j) = (register_->getType(i, j) == type ? (weights_ ? weights_->getIndex(i, j) : 1.) : 0.); ~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:65:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] if (i == j) label_(i, j) = 0; ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:65:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] if (i == j) label_(i, j) = 0; ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:66:19: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else label_(i, j) = ++count; ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp:66:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else label_(i, j) = ++count; ~~~~~~ ^ 13 warnings generated. [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:85:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:85:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:85:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:85:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:215:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return counts_[type - 1](initialState, finalState); ~~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:215:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return counts_[type - 1](initialState, finalState); ~~~~~~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:231:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[t] = counts_[t](initialState, finalState); ~~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp:231:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[t] = counts_[t](initialState, finalState); ~~~~~~~ ^~~~~~~~~~ 9 warnings generated. [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:106:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:106:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:106:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:106:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] bMatrices_[i - 1](j, k) = model_->Qij(j, k) * (weights_ ? weights_->getIndex(j, k) : 1); ~~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:192:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return counts_[type - 1](initialState, finalState); ~~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:192:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] return counts_[type - 1](initialState, finalState); ~~~~~~~ ^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:208:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[t] = counts_[t](initialState, finalState); ~~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp:208:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] v[t] = counts_[t](initialState, finalState); ~~~~~~~ ^~~~~~~~~~ 9 warnings generated. [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h:43: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ 1 warning generated. [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:45: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTools.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:411:36: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.insert(sons_.begin() + pos, node); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:436:60: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] if (search == sons_.end() || search == sons_.begin() + pos) ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:448:33: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + pos); ~~~~~ ^~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:461:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] sons_.erase(sons_.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:497:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] Node* operator[](int i) { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../Node.h:499:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] const Node* operator[](int i) const { return (i < 0) ? father_ : sons_[i]; } ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:325:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:327:37: warning: implicit conversion changes signedness: 'size_t' (aka 'unsigned long') to 'difference_type' (aka 'long') [-Wsign-conversion] names.erase(names.begin() + i); ~~~~~ ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplateTools.h:325:72: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] size_t i = RandomTools::giveIntRandomNumberBetweenZeroAndEntry(n); ~~~~~~~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMapping.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:391:112: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ~~~^~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/../TreeTemplate.h:391:112: note: use array indexing to silence this warning if (nodes.size() == 0) throw NodeNotFoundException("TreeTemplate:swapNodes(): Node with id not found.", "" + parentId); ^ & [ ] In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h:44: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionCount.h:178:53: warning: field 'register_' is uninitialized when used here [-Wuninitialized] register_(dynamic_cast(register_->clone())) ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h:45: /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:91:38: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h:91:52: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion] else return 1. - model_->Pij_t(initialState, finalState, length); ~~~~~~ ^~~~~~~~~~ 13 warnings generated. [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Model/StateMap.cpp:40: /«PKGBUILDDIR»/src/Bpp/Phyl/Model/StateMap.h:139:129: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int] catch (ElementNotFoundException& ex) { throw Exception("AbstractStateMap::whichState. Unsupported alphabet char: " + code); } ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /«PKGBUILDDIR»/src/Bpp/Phyl/Model/StateMap.h:139:129: note: use array indexing to silence this warning catch (ElementNotFoundException& ex) { throw Exception("AbstractStateMap::whichState. Unsupported alphabet char: " + code); } ^ & [ ] /«PKGBUILDDIR»/src/Bpp/Phyl/Model/StateMap.cpp:48:23: warning: implicit conversion changes signedness: 'unsigned int' to 'const value_type' (aka 'const int') [-Wsign-conversion] states_.push_back(i); ~~~~~~~ ^ 2 warnings generated. [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o /«PKGBUILDDIR»/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:393:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion] freq_[i] = freqs[i]; ~~~~~ ^ In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43: In file included from /«PKGBUILDDIR»/src/Bpp/Phyl/Model/SubstitutionModel.h:51: In file included from /usr/include/Bpp/Numeric/VectorTools.h:44: /usr/include/Bpp/Numeric/NumTools.h:116:50: error: call to function 'operator*' that is neither visible in the template definition nor found by argument-dependent lookup template static T sqr(T a) { return a * a; } ^ /«PKGBUILDDIR»/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:281:55: note: in instantiation of function template specialization 'bpp::NumTools::sqr > >' requested here MatrixTools::mult(rightEigenVectors_, NumTools::sqr(rate_ * eigenValues_) * VectorTools::exp(eigenValues_ * (rate_ * t)), leftEigenVectors_, d2pijt_); ^ /usr/include/Bpp/Numeric/VectorTools.h:128:16: note: 'operator*' should be declared prior to the call site std::vector operator*(const std::vector& v1, const std::vector& v2) throw (DimensionException) ^ 1 warning and 1 error generated. make[3]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o] Error 1 src/CMakeFiles/bppphyl-shared.dir/build.make:1411: recipe for target 'src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o' failed make[3]: Leaving directory '/«PKGBUILDDIR»' make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2 make[1]: *** [all] Error 2 CMakeFiles/Makefile2:232: recipe for target 'src/CMakeFiles/bppphyl-shared.dir/all' failed make[2]: Leaving directory '/«PKGBUILDDIR»' Makefile:143: recipe for target 'all' failed make: *** [build-stamp] Error 2 make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules:43: recipe for target 'build-stamp' failed dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140904-1549 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 77992 Build-Time: 181 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: libbpp-phyl_2.1.0-1 Machine Architecture: amd64 Package: libbpp-phyl Package-Time: 233 Source-Version: 2.1.0-1 Space: 77992 Status: attempted Version: 2.1.0-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140904-1549 Build needed 00:03:53, 77992k disc space DC-Status: Failed 234.390492583s DC-Time-Estimation: 234.390492583 versus expected 1765 (r/m: 6.530168909794821 ; m: 234.390492583)