DC-Build-Header: libbpp-phyl 2.0.2-1 / Thu Jan 12 22:43:09 +0100 2012 sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-19.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ libbpp-phyl 2.0.2-1 (amd64) 12 Jan 2012 22:43 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: libbpp-phyl Version: 2.0.2-1 Source Version: 2.0.2-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 3s (5314 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 477 kB of source archives. Get:1 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (dsc) [1117 B] Get:2 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (tar) [472 kB] Get:3 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (diff) [3751 B] Fetched 477 kB in 0s (21.1 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/libbpp-phyl-KVFifU/resolver-fYc93P/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 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64b-e280c6e8-e7a3-4295-bf0d-c597aa1bf165/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.0.1) Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.0.1) dpkg-deb: building package `sbuild-build-depends-libbpp-phyl-dummy' in `/build/libbpp-phyl-KVFifU/resolver-UMoI7b/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 emacsen-common file gettext gettext-base groff-base html2text intltool-debian libarchive1 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libcurl3-gnutls libexpat1 libgcrypt11 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libp11-kit0 libpcre3 libpipeline1 libprocps0 librtmp0 libsasl2-2 libssh2-1 libssl1.0.0 libtasn1-3 libunistring0 libxml2 libxmlrpc-core-c3 man-db po-debconf procps Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff rng-tools krb5-doc krb5-user www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint ca-certificates libglib2.0-data shared-mime-info krb5-locales libsasl2-modules xml-core libmail-sendmail-perl psmisc The following NEW packages will be installed: bsdmainutils cmake cmake-data debhelper emacsen-common file gettext gettext-base groff-base html2text intltool-debian libarchive1 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libcurl3-gnutls libexpat1 libgcrypt11 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libp11-kit0 libpcre3 libpipeline1 libprocps0 librtmp0 libsasl2-2 libssh2-1 libssl1.0.0 libtasn1-3 libunistring0 libxml2 libxmlrpc-core-c3 man-db po-debconf procps sbuild-build-depends-libbpp-phyl-dummy 0 upgraded, 48 newly installed, 0 to remove and 10 not upgraded. Need to get 23.7 MB/23.7 MB of archives. After this operation, 68.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libprocps0 libssl1.0.0 libgpg-error0 libgcrypt11 libp11-kit0 libtasn1-3 libgnutls26 libkeyutils1 libkrb5support0 libk5crypto3 libkrb5-3 libgssapi-krb5-2 libidn11 libsasl2-2 libldap-2.4-2 libpcre3 libxml2 libarchive1 libglib2.0-0 libcroco3 librtmp0 libssh2-1 libcurl3 libcurl3-gnutls libexpat1 libunistring0 bsdmainutils groff-base man-db procps libmagic1 file gettext-base libxmlrpc-core-c3 emacsen-common cmake-data cmake html2text gettext intltool-debian po-debconf debhelper libbpp-core2 libbpp-core-dev libbpp-seq9 libbpp-seq-dev sbuild-build-depends-libbpp-phyl-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libprocps0 amd64 1:3.3.2-1 [56.5 kB] Get:3 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-3 [1143 kB] Get:4 http://localhost/debian/ sid/main libgpg-error0 amd64 1.10-2 [66.8 kB] Get:5 http://localhost/debian/ sid/main libgcrypt11 amd64 1.5.0-3 [298 kB] Get:6 http://localhost/debian/ sid/main libp11-kit0 amd64 0.10-1 [51.4 kB] Get:7 http://localhost/debian/ sid/main libtasn1-3 amd64 2.11-1 [65.9 kB] Get:8 http://localhost/debian/ sid/main libgnutls26 amd64 2.12.16-1 [614 kB] Get:9 http://localhost/debian/ sid/main libkeyutils1 amd64 1.5.2-2 [8860 B] Get:10 http://localhost/debian/ sid/main libkrb5support0 amd64 1.10+dfsg~alpha2-1 [48.5 kB] Get:11 http://localhost/debian/ sid/main libk5crypto3 amd64 1.10+dfsg~alpha2-1 [108 kB] Get:12 http://localhost/debian/ sid/main libkrb5-3 amd64 1.10+dfsg~alpha2-1 [388 kB] Get:13 http://localhost/debian/ sid/main libgssapi-krb5-2 amd64 1.10+dfsg~alpha2-1 [147 kB] Get:14 http://localhost/debian/ sid/main libidn11 amd64 1.23-2 [170 kB] Get:15 http://localhost/debian/ sid/main libsasl2-2 amd64 2.1.25.dfsg1-2 [120 kB] Get:16 http://localhost/debian/ sid/main libldap-2.4-2 amd64 2.4.28-1 [240 kB] Get:17 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:18 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:19 http://localhost/debian/ sid/main libarchive1 amd64 2.8.5-5 [122 kB] Get:20 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:21 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:22 http://localhost/debian/ sid/main librtmp0 amd64 2.4+20111222.git4e06e21-1 [62.3 kB] Get:23 http://localhost/debian/ sid/main libssh2-1 amd64 1.2.8-2 [123 kB] Get:24 http://localhost/debian/ sid/main libcurl3 amd64 7.23.1-3 [325 kB] Get:25 http://localhost/debian/ sid/main libcurl3-gnutls amd64 7.23.1-3 [304 kB] Get:26 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7.2 [139 kB] Get:27 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:28 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:29 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:30 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:31 http://localhost/debian/ sid/main procps amd64 1:3.3.2-1 [243 kB] Get:32 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:33 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:34 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:35 http://localhost/debian/ sid/main libxmlrpc-core-c3 amd64 1.16.33-3.1 [181 kB] Get:36 http://localhost/debian/ sid/main emacsen-common all 1.4.22 [18.8 kB] Get:37 http://localhost/debian/ sid/main cmake-data all 2.8.5-1 [1273 kB] Get:38 http://localhost/debian/ sid/main cmake amd64 2.8.5-1 [4214 kB] Get:39 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:40 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:41 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:42 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:43 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:44 http://localhost/debian/ sid/main libbpp-core2 amd64 2.0.2-1 [578 kB] Get:45 http://localhost/debian/ sid/main libbpp-core-dev amd64 2.0.2-1 [1361 kB] Get:46 http://localhost/debian/ sid/main libbpp-seq9 amd64 2.0.2-1 [493 kB] Get:47 http://localhost/debian/ sid/main libbpp-seq-dev amd64 2.0.2-1 [1188 kB] Extracting templates from packages: 62% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 23.7 MB in 1s (15.1 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libprocps0. Unpacking libprocps0 (from .../libprocps0_1%3a3.3.2-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ... Selecting previously unselected package libgpg-error0. Unpacking libgpg-error0 (from .../libgpg-error0_1.10-2_amd64.deb) ... Selecting previously unselected package libgcrypt11. Unpacking libgcrypt11 (from .../libgcrypt11_1.5.0-3_amd64.deb) ... Selecting previously unselected package libp11-kit0. Unpacking libp11-kit0 (from .../libp11-kit0_0.10-1_amd64.deb) ... Selecting previously unselected package libtasn1-3. Unpacking libtasn1-3 (from .../libtasn1-3_2.11-1_amd64.deb) ... Selecting previously unselected package libgnutls26. Unpacking libgnutls26 (from .../libgnutls26_2.12.16-1_amd64.deb) ... Selecting previously unselected package libkeyutils1. Unpacking libkeyutils1 (from .../libkeyutils1_1.5.2-2_amd64.deb) ... Selecting previously unselected package libkrb5support0. Unpacking libkrb5support0 (from .../libkrb5support0_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libk5crypto3. Unpacking libk5crypto3 (from .../libk5crypto3_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libkrb5-3. Unpacking libkrb5-3 (from .../libkrb5-3_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libgssapi-krb5-2. Unpacking libgssapi-krb5-2 (from .../libgssapi-krb5-2_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libidn11. Unpacking libidn11 (from .../libidn11_1.23-2_amd64.deb) ... Selecting previously unselected package libsasl2-2. 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Unpacking procps (from .../procps_1%3a3.3.2-1_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package libxmlrpc-core-c3. Unpacking libxmlrpc-core-c3 (from .../libxmlrpc-core-c3_1.16.33-3.1_amd64.deb) ... Selecting previously unselected package emacsen-common. Unpacking emacsen-common (from .../emacsen-common_1.4.22_all.deb) ... Selecting previously unselected package cmake-data. Unpacking cmake-data (from .../cmake-data_2.8.5-1_all.deb) ... Selecting previously unselected package cmake. Unpacking cmake (from .../cmake_2.8.5-1_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ... Selecting previously unselected package libbpp-core2. Unpacking libbpp-core2 (from .../libbpp-core2_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-core-dev. Unpacking libbpp-core-dev (from .../libbpp-core-dev_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-seq9. Unpacking libbpp-seq9 (from .../libbpp-seq9_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-seq-dev. Unpacking libbpp-seq-dev (from .../libbpp-seq-dev_2.0.2-1_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-libbpp-phyl-dummy. Unpacking sbuild-build-depends-libbpp-phyl-dummy (from .../sbuild-build-depends-libbpp-phyl-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libprocps0 (1:3.3.2-1) ... Setting up libssl1.0.0 (1.0.0e-3) ... Setting up libgpg-error0 (1.10-2) ... Setting up libgcrypt11 (1.5.0-3) ... Setting up libp11-kit0 (0.10-1) ... Setting up libtasn1-3 (2.11-1) ... Setting up libgnutls26 (2.12.16-1) ... Setting up libkeyutils1 (1.5.2-2) ... Setting up libkrb5support0 (1.10+dfsg~alpha2-1) ... Setting up libk5crypto3 (1.10+dfsg~alpha2-1) ... Setting up libkrb5-3 (1.10+dfsg~alpha2-1) ... Setting up libgssapi-krb5-2 (1.10+dfsg~alpha2-1) ... Setting up libidn11 (1.23-2) ... Setting up libsasl2-2 (2.1.25.dfsg1-2) ... Setting up libldap-2.4-2 (2.4.28-1) ... Setting up libpcre3 (8.12-4) ... Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libarchive1 (2.8.5-5) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-2) ... Setting up librtmp0 (2.4+20111222.git4e06e21-1) ... Setting up libssh2-1 (1.2.8-2) ... Setting up libcurl3 (7.23.1-3) ... Setting up libcurl3-gnutls (7.23.1-3) ... Setting up libexpat1 (2.0.1-7.2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... 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 groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up procps (1:3.3.2-1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up libxmlrpc-core-c3 (1.16.33-3.1) ... Setting up emacsen-common (1.4.22) ... emacsen-common: Handling install of emacsen flavor emacs Setting up cmake-data (2.8.5-1) ... emacsen-common: Handling install of emacsen flavor emacs Setting up cmake (2.8.5-1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up libbpp-core2 (2.0.2-1) ... Setting up libbpp-core-dev (2.0.2-1) ... Setting up libbpp-seq9 (2.0.2-1) ... Setting up libbpp-seq-dev (2.0.2-1) ... Setting up sbuild-build-depends-libbpp-phyl-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 clang_3.0-5 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 emacsen-common_1.4.22 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libarchive1_2.8.5-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbpp-core-dev_2.0.2-1 libbpp-core2_2.0.2-1 libbpp-seq-dev_2.0.2-1 libbpp-seq9_2.0.2-1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libcurl3_7.23.1-3 libcurl3-gnutls_7.23.1-3 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.16-1 libgomp1_4.6.2-9 libgpg-error0_1.10-2 libgssapi-krb5-2_1.10+dfsg~alpha2-1 libidn11_1.23-2 libk5crypto3_1.10+dfsg~alpha2-1 libkeyutils1_1.5.2-2 libkrb5-3_1.10+dfsg~alpha2-1 libkrb5support0_1.10+dfsg~alpha2-1 libldap-2.4-2_2.4.28-1 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.10-1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libprocps0_1:3.3.2-1 libquadmath0_4.6.2-9 libreadline6_6.2-8 librtmp0_2.4+20111222.git4e06e21-1 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libssh2-1_1.2.8-2 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtasn1-3_2.11-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 libxmlrpc-core-c3_1.16.33-3.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.3.2-1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbpp-phyl-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jun 17 15:35:14 2011 CEST using DSA key ID 497A176D gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./libbpp-phyl_2.0.2-1.dsc dpkg-source: info: extracting libbpp-phyl in libbpp-phyl-2.0.2 dpkg-source: info: unpacking libbpp-phyl_2.0.2.orig.tar.gz dpkg-source: info: unpacking libbpp-phyl_2.0.2-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package libbpp-phyl dpkg-buildpackage: source version 2.0.2-1 dpkg-source --before-build libbpp-phyl-2.0.2 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 Makefile ] || rm src/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-source -b libbpp-phyl-2.0.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building libbpp-phyl using existing ./libbpp-phyl_2.0.2.orig.tar.gz dpkg-source: info: building libbpp-phyl in libbpp-phyl_2.0.2-1.debian.tar.gz dpkg-source: info: building libbpp-phyl in libbpp-phyl_2.0.2-1.dsc debian/rules build cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . -- The CXX compiler identification is Clang -- 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: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2 dh_testdir dh_testdir # Add here commands to compile the package. /usr/bin/make make[1]: Entering directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' make[2]: Entering directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' make[3]: Entering directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' Scanning dependencies of target bppphyl-shared make[3]: Leaving directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' make[3]: Entering directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:47: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/MarkovModulatedSubstitutionModel.h:249:18: warning: 'bpp::MarkovModulatedSubstitutionModel::getRate' hides overloaded virtual function [-Woverloaded-virtual] unsigned int getRate(unsigned int i) const ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:326:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::getRate' declared here virtual double getRate() const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:10: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/DSO78.h:139:10: warning: 'bpp::DSO78::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:17: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCnuc.h:166:8: warning: 'bpp::JCnuc::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:188:10: warning: 'bpp::JCprot::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:189:10: warning: 'bpp::JCprot::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:190:10: warning: 'bpp::JCprot::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:220:10: warning: 'bpp::JCprot::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:19: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JTT92.h:139:10: warning: 'bpp::JTT92::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:22: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/LG08.h:137:10: warning: 'bpp::LG08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:35: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RE08.h:169:10: warning: 'bpp::RE08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:167:12: warning: 'bpp::RN95::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:168:12: warning: 'bpp::RN95::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:169:12: warning: 'bpp::RN95::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:143:12: warning: 'bpp::RN95s::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:144:12: warning: 'bpp::RN95s::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:145:12: warning: 'bpp::RN95s::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:48: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/UserProteinSubstitutionModel.h:147:10: warning: 'bpp::UserProteinSubstitutionModel::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:49: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/WAG01.h:144:10: warning: 'bpp::WAG01::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood.all:2: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood.all:2: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 36 warnings generated. [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io.all:2: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io.all:2: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:10: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/DSO78.h:139:10: warning: 'bpp::DSO78::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:13: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/G2001.h:43: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/MarkovModulatedSubstitutionModel.h:249:18: warning: 'bpp::MarkovModulatedSubstitutionModel::getRate' hides overloaded virtual function [-Woverloaded-virtual] unsigned int getRate(unsigned int i) const ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:326:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::getRate' declared here virtual double getRate() const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:17: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCnuc.h:166:8: warning: 'bpp::JCnuc::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:188:10: warning: 'bpp::JCprot::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:189:10: warning: 'bpp::JCprot::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:190:10: warning: 'bpp::JCprot::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:220:10: warning: 'bpp::JCprot::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:19: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JTT92.h:139:10: warning: 'bpp::JTT92::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:22: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/LG08.h:137:10: warning: 'bpp::LG08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:35: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RE08.h:169:10: warning: 'bpp::RE08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:167:12: warning: 'bpp::RN95::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:168:12: warning: 'bpp::RN95::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:169:12: warning: 'bpp::RN95::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:143:12: warning: 'bpp::RN95s::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:144:12: warning: 'bpp::RN95s::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:145:12: warning: 'bpp::RN95s::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:48: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/UserProteinSubstitutionModel.h:147:10: warning: 'bpp::UserProteinSubstitutionModel::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:49: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/WAG01.h:144:10: warning: 'bpp::WAG01::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ 34 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.cpp.o [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/SimpleSubstitutionCount.cpp.o [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/IndexToCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o [ 22%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ 4 warnings generated. [ 22%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.cpp.o [ 23%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43: In file included from /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/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; } ^ /build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:113:41: note: in instantiation of function template specialization 'bpp::NumTools::sqr > >' requested here MatrixTools::mult(rightEigenVectors_, NumTools::sqr(rate_ * eigenValues_) * VectorTools::exp(rate_ * eigenValues_ * t), leftEigenVectors_, d2pijt_); ^ /usr/include/Bpp/Numeric/VectorTools.h:112:16: note: 'operator*' should be declared prior to the call site or in namespace '__gnu_cxx' std::vector operator* (const std::vector & v1, const std::vector & v2) throw (DimensionException) ^ 1 error generated. make[3]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o] Error 1 make[3]: Leaving directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2 make[2]: Leaving directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' make[1]: *** [all] Error 2 make: *** [build-stamp] Error 2 make[1]: Leaving directory `/build/libbpp-phyl-KVFifU/libbpp-phyl-2.0.2' dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120112-2246 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-e280c6e8-e7a3-4295-bf0d-c597aa1bf165/build/libbpp-phyl-KVFifU Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 62196 Build-Time: 162 Distribution: lsid64b Fail-Stage: build Install-Time: 10 Job: libbpp-phyl_2.0.2-1 Package: libbpp-phyl Package-Time: 186 Source-Version: 2.0.2-1 Space: 62196 Status: attempted Version: 2.0.2-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120112-2246 Build needed 00:03:06, 62196k disc space DC-Message: Failed, but took only 188.271952. Retrying, you never know. Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Another build requested exclusive access to the build node Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. Requested exclusive mode, but other builds running. sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on stremi-19.reims.grid5000.fr ╔══════════════════════════════════════════════════════════════════════════════╗ ║ libbpp-phyl 2.0.2-1 (amd64) 12 Jan 2012 23:03 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: libbpp-phyl Version: 2.0.2-1 Source Version: 2.0.2-1 Distribution: lsid64b Architecture: amd64 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost sid InRelease Get:1 http://localhost sid Release.gpg [836 B] Get:2 http://localhost sid Release [188 kB] Ign http://localhost sid/main Sources/DiffIndex Ign http://localhost sid/main amd64 Packages/DiffIndex Ign http://localhost sid/main TranslationIndex Get:3 http://localhost sid/main Sources [7544 kB] Get:4 http://localhost sid/main amd64 Packages [10.4 MB] Ign http://localhost sid/main Translation-en Fetched 18.2 MB in 3s (5360 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages have been kept back: clang cpp-4.6 g++-4.6 gcc-4.6 gcc-4.6-base libgcc1 libgomp1 libquadmath0 libstdc++6 libstdc++6-4.6-dev 0 upgraded, 0 newly installed, 0 to remove and 10 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ 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 477 kB of source archives. Get:1 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (dsc) [1117 B] Get:2 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (tar) [472 kB] Get:3 http://localhost/debian/ sid/main libbpp-phyl 2.0.2-1 (diff) [3751 B] Fetched 477 kB in 0s (22.1 MB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/build/libbpp-phyl-Wo1LvW/resolver-OVXlK1/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 0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded. Need to get 0 B/706 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10821 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Cannot open /var/lib/schroot/mount/lsid64b-d94e2f61-0649-41a4-89c7-4f2eb5c87acf/etc/lsb-release: No such file or directory Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.0.1) Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 5), cmake (>= 2.6), libbpp-seq-dev (>= 2.0.1) dpkg-deb: building package `sbuild-build-depends-libbpp-phyl-dummy' in `/build/libbpp-phyl-Wo1LvW/resolver-smiH3g/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 emacsen-common file gettext gettext-base groff-base html2text intltool-debian libarchive1 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libcurl3-gnutls libexpat1 libgcrypt11 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libp11-kit0 libpcre3 libpipeline1 libprocps0 librtmp0 libsasl2-2 libssh2-1 libssl1.0.0 libtasn1-3 libunistring0 libxml2 libxmlrpc-core-c3 man-db po-debconf procps Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff rng-tools krb5-doc krb5-user www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint ca-certificates libglib2.0-data shared-mime-info krb5-locales libsasl2-modules xml-core libmail-sendmail-perl psmisc The following NEW packages will be installed: bsdmainutils cmake cmake-data debhelper emacsen-common file gettext gettext-base groff-base html2text intltool-debian libarchive1 libbpp-core-dev libbpp-core2 libbpp-seq-dev libbpp-seq9 libcroco3 libcurl3 libcurl3-gnutls libexpat1 libgcrypt11 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libp11-kit0 libpcre3 libpipeline1 libprocps0 librtmp0 libsasl2-2 libssh2-1 libssl1.0.0 libtasn1-3 libunistring0 libxml2 libxmlrpc-core-c3 man-db po-debconf procps sbuild-build-depends-libbpp-phyl-dummy 0 upgraded, 48 newly installed, 0 to remove and 10 not upgraded. Need to get 23.7 MB/23.7 MB of archives. After this operation, 68.1 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libpipeline1 libprocps0 libssl1.0.0 libgpg-error0 libgcrypt11 libp11-kit0 libtasn1-3 libgnutls26 libkeyutils1 libkrb5support0 libk5crypto3 libkrb5-3 libgssapi-krb5-2 libidn11 libsasl2-2 libldap-2.4-2 libpcre3 libxml2 libarchive1 libglib2.0-0 libcroco3 librtmp0 libssh2-1 libcurl3 libcurl3-gnutls libexpat1 libunistring0 bsdmainutils groff-base man-db procps libmagic1 file gettext-base libxmlrpc-core-c3 emacsen-common cmake-data cmake html2text gettext intltool-debian po-debconf debhelper libbpp-core2 libbpp-core-dev libbpp-seq9 libbpp-seq-dev sbuild-build-depends-libbpp-phyl-dummy Authentication warning overridden. Get:1 http://localhost/debian/ sid/main libpipeline1 amd64 1.2.0-5 [38.2 kB] Get:2 http://localhost/debian/ sid/main libprocps0 amd64 1:3.3.2-1 [56.5 kB] Get:3 http://localhost/debian/ sid/main libssl1.0.0 amd64 1.0.0e-3 [1143 kB] Get:4 http://localhost/debian/ sid/main libgpg-error0 amd64 1.10-2 [66.8 kB] Get:5 http://localhost/debian/ sid/main libgcrypt11 amd64 1.5.0-3 [298 kB] Get:6 http://localhost/debian/ sid/main libp11-kit0 amd64 0.10-1 [51.4 kB] Get:7 http://localhost/debian/ sid/main libtasn1-3 amd64 2.11-1 [65.9 kB] Get:8 http://localhost/debian/ sid/main libgnutls26 amd64 2.12.16-1 [614 kB] Get:9 http://localhost/debian/ sid/main libkeyutils1 amd64 1.5.2-2 [8860 B] Get:10 http://localhost/debian/ sid/main libkrb5support0 amd64 1.10+dfsg~alpha2-1 [48.5 kB] Get:11 http://localhost/debian/ sid/main libk5crypto3 amd64 1.10+dfsg~alpha2-1 [108 kB] Get:12 http://localhost/debian/ sid/main libkrb5-3 amd64 1.10+dfsg~alpha2-1 [388 kB] Get:13 http://localhost/debian/ sid/main libgssapi-krb5-2 amd64 1.10+dfsg~alpha2-1 [147 kB] Get:14 http://localhost/debian/ sid/main libidn11 amd64 1.23-2 [170 kB] Get:15 http://localhost/debian/ sid/main libsasl2-2 amd64 2.1.25.dfsg1-2 [120 kB] Get:16 http://localhost/debian/ sid/main libldap-2.4-2 amd64 2.4.28-1 [240 kB] Get:17 http://localhost/debian/ sid/main libpcre3 amd64 8.12-4 [225 kB] Get:18 http://localhost/debian/ sid/main libxml2 amd64 2.7.8.dfsg-5.1 [891 kB] Get:19 http://localhost/debian/ sid/main libarchive1 amd64 2.8.5-5 [122 kB] Get:20 http://localhost/debian/ sid/main libglib2.0-0 amd64 2.30.2-4 [1844 kB] Get:21 http://localhost/debian/ sid/main libcroco3 amd64 0.6.2-2 [122 kB] Get:22 http://localhost/debian/ sid/main librtmp0 amd64 2.4+20111222.git4e06e21-1 [62.3 kB] Get:23 http://localhost/debian/ sid/main libssh2-1 amd64 1.2.8-2 [123 kB] Get:24 http://localhost/debian/ sid/main libcurl3 amd64 7.23.1-3 [325 kB] Get:25 http://localhost/debian/ sid/main libcurl3-gnutls amd64 7.23.1-3 [304 kB] Get:26 http://localhost/debian/ sid/main libexpat1 amd64 2.0.1-7.2 [139 kB] Get:27 http://localhost/debian/ sid/main libunistring0 amd64 0.9.3-5 [434 kB] Get:28 http://localhost/debian/ sid/main bsdmainutils amd64 8.2.3 [208 kB] Get:29 http://localhost/debian/ sid/main groff-base amd64 1.21-6 [1150 kB] Get:30 http://localhost/debian/ sid/main man-db amd64 2.6.0.2-3 [1015 kB] Get:31 http://localhost/debian/ sid/main procps amd64 1:3.3.2-1 [243 kB] Get:32 http://localhost/debian/ sid/main libmagic1 amd64 5.09-2 [246 kB] Get:33 http://localhost/debian/ sid/main file amd64 5.09-2 [52.0 kB] Get:34 http://localhost/debian/ sid/main gettext-base amd64 0.18.1.1-5 [154 kB] Get:35 http://localhost/debian/ sid/main libxmlrpc-core-c3 amd64 1.16.33-3.1 [181 kB] Get:36 http://localhost/debian/ sid/main emacsen-common all 1.4.22 [18.8 kB] Get:37 http://localhost/debian/ sid/main cmake-data all 2.8.5-1 [1273 kB] Get:38 http://localhost/debian/ sid/main cmake amd64 2.8.5-1 [4214 kB] Get:39 http://localhost/debian/ sid/main html2text amd64 1.3.2a-15 [103 kB] Get:40 http://localhost/debian/ sid/main gettext amd64 0.18.1.1-5 [2080 kB] Get:41 http://localhost/debian/ sid/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:42 http://localhost/debian/ sid/main po-debconf all 1.0.16+nmu2 [224 kB] Get:43 http://localhost/debian/ sid/main debhelper all 8.9.14 [693 kB] Get:44 http://localhost/debian/ sid/main libbpp-core2 amd64 2.0.2-1 [578 kB] Get:45 http://localhost/debian/ sid/main libbpp-core-dev amd64 2.0.2-1 [1361 kB] Get:46 http://localhost/debian/ sid/main libbpp-seq9 amd64 2.0.2-1 [493 kB] Get:47 http://localhost/debian/ sid/main libbpp-seq-dev amd64 2.0.2-1 [1188 kB] Extracting templates from packages: 62% Extracting templates from packages: 100% Preconfiguring packages ... Fetched 23.7 MB in 0s (42.5 MB/s) Selecting previously unselected package libpipeline1. (Reading database ... 10821 files and directories currently installed.) Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ... Selecting previously unselected package libprocps0. Unpacking libprocps0 (from .../libprocps0_1%3a3.3.2-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0. Unpacking libssl1.0.0 (from .../libssl1.0.0_1.0.0e-3_amd64.deb) ... Selecting previously unselected package libgpg-error0. Unpacking libgpg-error0 (from .../libgpg-error0_1.10-2_amd64.deb) ... Selecting previously unselected package libgcrypt11. Unpacking libgcrypt11 (from .../libgcrypt11_1.5.0-3_amd64.deb) ... Selecting previously unselected package libp11-kit0. Unpacking libp11-kit0 (from .../libp11-kit0_0.10-1_amd64.deb) ... Selecting previously unselected package libtasn1-3. Unpacking libtasn1-3 (from .../libtasn1-3_2.11-1_amd64.deb) ... Selecting previously unselected package libgnutls26. Unpacking libgnutls26 (from .../libgnutls26_2.12.16-1_amd64.deb) ... Selecting previously unselected package libkeyutils1. Unpacking libkeyutils1 (from .../libkeyutils1_1.5.2-2_amd64.deb) ... Selecting previously unselected package libkrb5support0. Unpacking libkrb5support0 (from .../libkrb5support0_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libk5crypto3. Unpacking libk5crypto3 (from .../libk5crypto3_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libkrb5-3. Unpacking libkrb5-3 (from .../libkrb5-3_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libgssapi-krb5-2. Unpacking libgssapi-krb5-2 (from .../libgssapi-krb5-2_1.10+dfsg~alpha2-1_amd64.deb) ... Selecting previously unselected package libidn11. Unpacking libidn11 (from .../libidn11_1.23-2_amd64.deb) ... Selecting previously unselected package libsasl2-2. Unpacking libsasl2-2 (from .../libsasl2-2_2.1.25.dfsg1-2_amd64.deb) ... Selecting previously unselected package libldap-2.4-2. Unpacking libldap-2.4-2 (from .../libldap-2.4-2_2.4.28-1_amd64.deb) ... Selecting previously unselected package libpcre3. Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ... Selecting previously unselected package libxml2. Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5.1_amd64.deb) ... Selecting previously unselected package libarchive1. Unpacking libarchive1 (from .../libarchive1_2.8.5-5_amd64.deb) ... Selecting previously unselected package libglib2.0-0. Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ... Selecting previously unselected package libcroco3. Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ... Selecting previously unselected package librtmp0. Unpacking librtmp0 (from .../librtmp0_2.4+20111222.git4e06e21-1_amd64.deb) ... Selecting previously unselected package libssh2-1. Unpacking libssh2-1 (from .../libssh2-1_1.2.8-2_amd64.deb) ... Selecting previously unselected package libcurl3. Unpacking libcurl3 (from .../libcurl3_7.23.1-3_amd64.deb) ... Selecting previously unselected package libcurl3-gnutls. Unpacking libcurl3-gnutls (from .../libcurl3-gnutls_7.23.1-3_amd64.deb) ... Selecting previously unselected package libexpat1. Unpacking libexpat1 (from .../libexpat1_2.0.1-7.2_amd64.deb) ... Selecting previously unselected package libunistring0. Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_8.2.3_amd64.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.0.2-3_amd64.deb) ... Selecting previously unselected package procps. Unpacking procps (from .../procps_1%3a3.3.2-1_amd64.deb) ... Selecting previously unselected package libmagic1. Unpacking libmagic1 (from .../libmagic1_5.09-2_amd64.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.09-2_amd64.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package libxmlrpc-core-c3. Unpacking libxmlrpc-core-c3 (from .../libxmlrpc-core-c3_1.16.33-3.1_amd64.deb) ... Selecting previously unselected package emacsen-common. Unpacking emacsen-common (from .../emacsen-common_1.4.22_all.deb) ... Selecting previously unselected package cmake-data. Unpacking cmake-data (from .../cmake-data_2.8.5-1_all.deb) ... Selecting previously unselected package cmake. Unpacking cmake (from .../cmake_2.8.5-1_amd64.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_8.9.14_all.deb) ... Selecting previously unselected package libbpp-core2. Unpacking libbpp-core2 (from .../libbpp-core2_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-core-dev. Unpacking libbpp-core-dev (from .../libbpp-core-dev_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-seq9. Unpacking libbpp-seq9 (from .../libbpp-seq9_2.0.2-1_amd64.deb) ... Selecting previously unselected package libbpp-seq-dev. Unpacking libbpp-seq-dev (from .../libbpp-seq-dev_2.0.2-1_amd64.deb) ... Selecting previously unselected package sbuild-build-depends-libbpp-phyl-dummy. Unpacking sbuild-build-depends-libbpp-phyl-dummy (from .../sbuild-build-depends-libbpp-phyl-dummy.deb) ... Processing triggers for install-info ... Setting up libpipeline1 (1.2.0-5) ... Setting up libprocps0 (1:3.3.2-1) ... Setting up libssl1.0.0 (1.0.0e-3) ... Setting up libgpg-error0 (1.10-2) ... Setting up libgcrypt11 (1.5.0-3) ... Setting up libp11-kit0 (0.10-1) ... Setting up libtasn1-3 (2.11-1) ... Setting up libgnutls26 (2.12.16-1) ... Setting up libkeyutils1 (1.5.2-2) ... Setting up libkrb5support0 (1.10+dfsg~alpha2-1) ... Setting up libk5crypto3 (1.10+dfsg~alpha2-1) ... Setting up libkrb5-3 (1.10+dfsg~alpha2-1) ... Setting up libgssapi-krb5-2 (1.10+dfsg~alpha2-1) ... Setting up libidn11 (1.23-2) ... Setting up libsasl2-2 (2.1.25.dfsg1-2) ... Setting up libldap-2.4-2 (2.4.28-1) ... Setting up libpcre3 (8.12-4) ... Setting up libxml2 (2.7.8.dfsg-5.1) ... Setting up libarchive1 (2.8.5-5) ... Setting up libglib2.0-0 (2.30.2-4) ... No schema files found: doing nothing. Setting up libcroco3 (0.6.2-2) ... Setting up librtmp0 (2.4+20111222.git4e06e21-1) ... Setting up libssh2-1 (1.2.8-2) ... Setting up libcurl3 (7.23.1-3) ... Setting up libcurl3-gnutls (7.23.1-3) ... Setting up libexpat1 (2.0.1-7.2) ... Setting up libunistring0 (0.9.3-5) ... Setting up bsdmainutils (8.2.3) ... 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 groff-base (1.21-6) ... Setting up man-db (2.6.0.2-3) ... Building database of manual pages ... Setting up procps (1:3.3.2-1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode. invoke-rc.d: policy-rc.d denied execution of start. Setting up libmagic1 (5.09-2) ... Setting up file (5.09-2) ... Setting up gettext-base (0.18.1.1-5) ... Setting up libxmlrpc-core-c3 (1.16.33-3.1) ... Setting up emacsen-common (1.4.22) ... emacsen-common: Handling install of emacsen flavor emacs Setting up cmake-data (2.8.5-1) ... emacsen-common: Handling install of emacsen flavor emacs Setting up cmake (2.8.5-1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (8.9.14) ... Setting up libbpp-core2 (2.0.2-1) ... Setting up libbpp-core-dev (2.0.2-1) ... Setting up libbpp-seq9 (2.0.2-1) ... Setting up libbpp-seq-dev (2.0.2-1) ... Setting up sbuild-build-depends-libbpp-phyl-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-4 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-9 gcc-4.6_4.6.2-9 libc6-dev_2.13-24 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 linux-libc-dev_3.1.8-2 Package versions: apt_0.8.15.9 apt-utils_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-4 bsdmainutils_8.2.3 bsdutils_1:2.20.1-1.1 build-essential_11.5 bzip2_1.0.6-1 clang_3.0-5 cmake_2.8.5-1 cmake-data_2.8.5-1 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-9 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.14 debian-archive-keyring_2010.08.28 debianutils_4.1 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 emacsen-common_1.4.22 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-9 gcc_4:4.6.2-4 gcc-4.6_4.6.2-9 gcc-4.6-base_4.6.2-9 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.09 html2text_1.3.2a-15 initscripts_2.88dsf-18 insserv_1.14.0-2.1 install-info_4.13a.dfsg.1-8 intltool-debian_0.35.0+20060710.1 less_444-1 libacl1_2.2.51-5 libarchive1_2.8.5-5 libattr1_1:2.4.46-5 libblkid1_2.20.1-1.1 libbpp-core-dev_2.0.2-1 libbpp-core2_2.0.2-1 libbpp-seq-dev_2.0.2-1 libbpp-seq9_2.0.2-1 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclang-common-dev_3.0-5 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libcurl3_7.23.1-3 libcurl3-gnutls_7.23.1-3 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libexpat1_2.0.1-7.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-9 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgnutls26_2.12.16-1 libgomp1_4.6.2-9 libgpg-error0_1.10-2 libgssapi-krb5-2_1.10+dfsg~alpha2-1 libidn11_1.23-2 libk5crypto3_1.10+dfsg~alpha2-1 libkeyutils1_1.5.2-2 libkrb5-3_1.10+dfsg~alpha2-1 libkrb5support0_1.10+dfsg~alpha2-1 libldap-2.4-2_2.4.28-1 libllvm3.0_3.0-5 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.1 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libncursesw5_5.9-4 libp11-kit0_0.10-1 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libprocps0_1:3.3.2-1 libquadmath0_4.6.2-9 libreadline6_6.2-8 librtmp0_2.4+20111222.git4e06e21-1 libsasl2-2_2.1.25.dfsg1-2 libselinux1_2.1.0-4 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libssh2-1_1.2.8-2 libssl1.0.0_1.0.0e-3 libstdc++6_4.6.2-9 libstdc++6-4.6-dev_4.6.2-9 libswitch-perl_2.16-2 libtasn1-3_2.11-1 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.1 libxml2_2.7.8.dfsg-5.1 libxmlrpc-core-c3_1.16.33-3.1 linux-libc-dev_3.1.8-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.1 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 nvi_1.81.6-8.2 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 procps_1:3.3.2-1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbpp-phyl-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-18 sysvinit_2.88dsf-18 sysvinit-utils_2.88dsf-18 tar_1.26-4 tzdata_2011n-2 util-linux_2.20.1-1.1 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Jun 17 15:35:14 2011 CEST using DSA key ID 497A176D gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./libbpp-phyl_2.0.2-1.dsc dpkg-source: info: extracting libbpp-phyl in libbpp-phyl-2.0.2 dpkg-source: info: unpacking libbpp-phyl_2.0.2.orig.tar.gz dpkg-source: info: unpacking libbpp-phyl_2.0.2-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build dpkg-buildpackage ───────────────── dpkg-buildpackage: source package libbpp-phyl dpkg-buildpackage: source version 2.0.2-1 dpkg-source --before-build libbpp-phyl-2.0.2 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 Makefile ] || rm src/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-source -b libbpp-phyl-2.0.2 dpkg-source: info: using source format `3.0 (quilt)' dpkg-source: info: building libbpp-phyl using existing ./libbpp-phyl_2.0.2.orig.tar.gz dpkg-source: info: building libbpp-phyl in libbpp-phyl_2.0.2-1.debian.tar.gz dpkg-source: info: building libbpp-phyl in libbpp-phyl_2.0.2-1.dsc debian/rules build cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . -- The CXX compiler identification is Clang -- 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: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2 dh_testdir dh_testdir # Add here commands to compile the package. /usr/bin/make make[1]: Entering directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make[2]: Entering directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make[3]: Entering directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' Scanning dependencies of target bppphyl-shared make[3]: Leaving directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make[3]: Entering directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h:47: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/MarkovModulatedSubstitutionModel.h:249:18: warning: 'bpp::MarkovModulatedSubstitutionModel::getRate' hides overloaded virtual function [-Woverloaded-virtual] unsigned int getRate(unsigned int i) const ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:326:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::getRate' declared here virtual double getRate() const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:10: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/DSO78.h:139:10: warning: 'bpp::DSO78::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:17: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCnuc.h:166:8: warning: 'bpp::JCnuc::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:188:10: warning: 'bpp::JCprot::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:189:10: warning: 'bpp::JCprot::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:190:10: warning: 'bpp::JCprot::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JCprot.h:220:10: warning: 'bpp::JCprot::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:19: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/JTT92.h:139:10: warning: 'bpp::JTT92::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:22: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/LG08.h:137:10: warning: 'bpp::LG08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:35: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RE08.h:169:10: warning: 'bpp::RE08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:167:12: warning: 'bpp::RN95::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:168:12: warning: 'bpp::RN95::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95.h:169:12: warning: 'bpp::RN95::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:143:12: warning: 'bpp::RN95s::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:144:12: warning: 'bpp::RN95s::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/RN95s.h:145:12: warning: 'bpp::RN95s::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:48: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/UserProteinSubstitutionModel.h:147:10: warning: 'bpp::UserProteinSubstitutionModel::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model.all:49: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/WAG01.h:144:10: warning: 'bpp::WAG01::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood.all:2: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood.all:2: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/App/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 36 warnings generated. [ 0%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o [ 1%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o [ 2%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.cpp:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o [ 3%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o [ 4%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o [ 5%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o [ 6%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io.all:2: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/IoTreeFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io.all:2: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Io/IoDistanceMatrixFactory.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance.all:4: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/DistanceEstimation.h:46: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Io/../Distance/../Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 7%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o [ 8%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o [ 9%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 10%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o [ 11%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 12%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o [ 13%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o [ 14%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o [ 15%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp:39: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 16%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:195:28: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] const SubstitutionModel* getSubstitutionModel() const { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h:197:22: warning: 'bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel' hides overloaded virtual functions [-Woverloaded-virtual] SubstitutionModel* getSubstitutionModel() { return model_; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:344:38: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual const SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) const throw (NodeNotFoundException) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/TreeLikelihood.h:355:32: note: hidden overloaded virtual function 'bpp::TreeLikelihood::getSubstitutionModel' declared here virtual SubstitutionModel* getSubstitutionModel(int nodeId, unsigned int siteIndex) throw (NodeNotFoundException) = 0; ^ 2 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:10: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/DSO78.h:139:10: warning: 'bpp::DSO78::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:11: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:13: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/G2001.h:43: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/MarkovModulatedSubstitutionModel.h:249:18: warning: 'bpp::MarkovModulatedSubstitutionModel::getRate' hides overloaded virtual function [-Woverloaded-virtual] unsigned int getRate(unsigned int i) const ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:326:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::getRate' declared here virtual double getRate() const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:16: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:17: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCnuc.h:166:8: warning: 'bpp::JCnuc::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:188:10: warning: 'bpp::JCprot::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:189:10: warning: 'bpp::JCprot::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:190:10: warning: 'bpp::JCprot::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:18: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JCprot.h:220:10: warning: 'bpp::JCprot::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:19: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/JTT92.h:139:10: warning: 'bpp::JTT92::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:20: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:22: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/LG08.h:137:10: warning: 'bpp::LG08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:35: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RE08.h:169:10: warning: 'bpp::RE08::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:167:12: warning: 'bpp::RN95::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:168:12: warning: 'bpp::RN95::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:36: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95.h:169:12: warning: 'bpp::RN95::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:143:12: warning: 'bpp::RN95s::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:144:12: warning: 'bpp::RN95s::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:37: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/RN95s.h:145:12: warning: 'bpp::RN95s::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:44: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:45: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/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; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:48: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/UserProteinSubstitutionModel.h:147:10: warning: 'bpp::UserProteinSubstitutionModel::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp:42: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:41: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModelFactory.h:44: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model.all:49: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/WAG01.h:144:10: warning: 'bpp::WAG01::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer& data); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Likelihood/../Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ 34 warnings generated. [ 17%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o [ 18%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/AnalyticalSubstitutionCount.cpp.o [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o [ 19%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/SimpleSubstitutionCount.cpp.o [ 20%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/IndexToCount.cpp.o [ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o [ 22%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:172:10: warning: 'bpp::K80::Pij_t' hides overloaded virtual functions [-Woverloaded-virtual] double Pij_t (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:210:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::Pij_t' declared here virtual double Pij_t (unsigned int i, unsigned int j, double t) const { return getPij_t(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:208:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::Pij_t' declared here virtual double Pij_t(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:173:10: warning: 'bpp::K80::dPij_dt' hides overloaded virtual functions [-Woverloaded-virtual] double dPij_dt (int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:211:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::dPij_dt' declared here virtual double dPij_dt (unsigned int i, unsigned int j, double t) const { return getdPij_dt(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:215:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::dPij_dt' declared here virtual double dPij_dt(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:174:10: warning: 'bpp::K80::d2Pij_dt2' hides overloaded virtual functions [-Woverloaded-virtual] double d2Pij_dt2(int i, int j, double d) const; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:212:18: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const { return getd2Pij_dt2(t) (i, j); } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:222:18: note: hidden overloaded virtual function 'bpp::SubstitutionModel::d2Pij_dt2' declared here virtual double d2Pij_dt2(unsigned int i, unsigned int j, double t) const = 0; ^ In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp:40: /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/K80.h:188:10: warning: 'bpp::K80::setFreqFromData' hides overloaded virtual functions [-Woverloaded-virtual] void setFreqFromData(const SequenceContainer & data) {} ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:216:8: note: hidden overloaded virtual function 'bpp::AbstractSubstitutionModel::setFreqFromData' declared here void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0); ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/SubstitutionModel.h:349:16: note: hidden overloaded virtual function 'bpp::SubstitutionModel::setFreqFromData' declared here virtual void setFreqFromData(const SequenceContainer& data, unsigned int pseudoCount = 0) = 0; ^ 4 warnings generated. [ 22%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.cpp.o [ 23%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43: In file included from /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/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; } ^ /build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:113:41: note: in instantiation of function template specialization 'bpp::NumTools::sqr > >' requested here MatrixTools::mult(rightEigenVectors_, NumTools::sqr(rate_ * eigenValues_) * VectorTools::exp(rate_ * eigenValues_ * t), leftEigenVectors_, d2pijt_); ^ /usr/include/Bpp/Numeric/VectorTools.h:112:16: note: 'operator*' should be declared prior to the call site or in namespace '__gnu_cxx' std::vector operator* (const std::vector & v1, const std::vector & v2) throw (DimensionException) ^ 1 error generated. make[3]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o] Error 1 make[3]: Leaving directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2 make[2]: Leaving directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make[1]: *** [all] Error 2 make[1]: Leaving directory `/build/libbpp-phyl-Wo1LvW/libbpp-phyl-2.0.2' make: *** [build-stamp] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120112-2306 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /var/lib/schroot/mount/lsid64b-d94e2f61-0649-41a4-89c7-4f2eb5c87acf/build/libbpp-phyl-Wo1LvW Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 62196 Build-Time: 151 Distribution: lsid64b Fail-Stage: build Install-Time: 8 Job: libbpp-phyl_2.0.2-1 Package: libbpp-phyl Package-Time: 171 Source-Version: 2.0.2-1 Space: 62196 Status: attempted Version: 2.0.2-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120112-2306 Build needed 00:02:51, 62196k disc space DC-Build-Status: Failed 1382.328859s ### Content of /var/log/daemon.log ### Jan 12 21:03:54 stremi-19 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:05 stremi-19 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:21 stremi-19 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:04:51 stremi-19 approx: Concurrent download of debian/dists/sid/Release.gpg is taking too long Jan 12 21:05:08 stremi-19 approx: Concurrent download of debian/dists/sid/Release is taking too long Jan 12 21:05:30 stremi-19 approx: Concurrent download of debian/dists/sid/main/binary-amd64/Packages.xz is taking too long ### End of content of /var/log/daemon.log ### DC-Time-Estimation: 1382.328859 versus expected 838 (r/m: 0.64955711097852 ; m: 838.0) DC-Build-Network: USED. See /tmp/rulesafter.KvQu7K ! ************************************************************ # Generated by iptables-save v1.4.8 on Thu Jan 12 23:06:11 2012 *filter :INPUT ACCEPT [1628418:9926914689] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] [666363:7610225126] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.159.0/24 -j ACCEPT [0:0] -A OUTPUT -d 192.168.160.0/24 -j ACCEPT [0:0] -A OUTPUT -d 10.69.0.0/17 -j ACCEPT [0:0] -A OUTPUT -d 172.28.52.0/22 -j ACCEPT [0:0] -A OUTPUT -d 172.24.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT [232047:43559777] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT [15272:2037296] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [5:300] -A OUTPUT -j LD [5:300] -A LD -j LOG [5:300] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT # Completed on Thu Jan 12 23:06:11 2012 ************************************************************ --- /tmp/rulesbefore.rFfNbj 2012-01-12 22:43:09.625279709 +0100 +++ /tmp/rulesafter.KvQu7K 2012-01-12 23:06:11.962271370 +0100 @@ -1,10 +1,10 @@ -# Generated by iptables-save v1.4.8 on Thu Jan 12 22:43:09 2012 +# Generated by iptables-save v1.4.8 on Thu Jan 12 23:06:11 2012 *filter -:INPUT ACCEPT [1343631:8091258205] +:INPUT ACCEPT [1628418:9926914689] :FORWARD ACCEPT [0:0] :OUTPUT DROP [0:0] :LD - [0:0] -[554331:6243698964] -A OUTPUT -o lo -j ACCEPT +[666363:7610225126] -A OUTPUT -o lo -j ACCEPT [0:0] -A OUTPUT -d 129.88.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 10.0.0.0/8 -j ACCEPT [0:0] -A OUTPUT -d 192.168.133.0/24 -j ACCEPT @@ -16,11 +16,11 @@ [0:0] -A OUTPUT -d 131.254.202.0/23 -j ACCEPT [0:0] -A OUTPUT -d 138.96.20.0/22 -j ACCEPT [0:0] -A OUTPUT -d 192.168.22.0/24 -j ACCEPT -[199296:30431751] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT +[232047:43559777] -A OUTPUT -d 172.16.0.0/16 -j ACCEPT [0:0] -A OUTPUT -d 192.168.67.0/24 -j ACCEPT -[12511:1673628] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT +[15272:2037296] -A OUTPUT -d 224.0.0.0/4 -p udp -j ACCEPT [5:300] -A OUTPUT -j LD [5:300] -A LD -j LOG [5:300] -A LD -j REJECT --reject-with icmp-port-unreachable COMMIT -# Completed on Thu Jan 12 22:43:09 2012 +# Completed on Thu Jan 12 23:06:11 2012 ************************************************************ [ 8.133243] ohci_hcd 0000:00:14.5: OHCI Host Controller [ 8.139187] ohci_hcd 0000:00:14.5: new USB bus registered, assigned bus number 7 [ 8.147593] ohci_hcd 0000:00:14.5: irq 18, io mem 0xfe9ff000 [ 8.216034] usb usb7: New USB device found, idVendor=1d6b, idProduct=0001 [ 8.223720] usb usb7: New USB device strings: Mfr=3, Product=2, SerialNumber=1 [ 8.231912] usb usb7: Product: OHCI Host Controller [ 8.237457] usb usb7: Manufacturer: Linux 2.6.32-5-amd64 ohci_hcd [ 8.244360] usb usb7: SerialNumber: 0000:00:14.5 [ 8.249705] usb usb7: configuration #1 chosen from 1 choice [ 8.256066] hub 7-0:1.0: USB hub found [ 8.260358] hub 7-0:1.0: 2 ports detected [ 9.916070] Adding 3911788k swap on /dev/sda1. Priority:-1 extents:1 across:3911788k [ 9.934040] EXT3 FS on sda3, internal journal [ 10.232288] kjournald starting. Commit interval 5 seconds [ 10.242480] EXT3 FS on sda5, internal journal [ 10.247522] EXT3-fs: mounted filesystem with ordered data mode. [ 10.637266] ADDRCONF(NETDEV_UP): eth0: link is not ready [ 12.852556] igb: eth0 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX [ 12.863868] ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready [ 15.209967] fuse init (API version 7.13) [ 23.372010] eth0: no IPv6 routers present [ 214.861788] RPC: Registered udp transport module. [ 214.867177] RPC: Registered tcp transport module. [ 214.872529] RPC: Registered tcp NFSv4.1 backchannel transport module. [ 214.916207] Slow work thread pool: Starting up [ 214.921386] Slow work thread pool: Ready [ 214.925929] FS-Cache: Loaded [ 214.949862] FS-Cache: Netfs 'nfs' registered for caching [ 215.053882] svc: failed to register lockdv1 RPC service (errno 97). [ 295.427930] Adding 228556712k swap on /dev/sda5. Priority:-2 extents:1 across:228556712k [ 343.382424] ip_tables: (C) 2000-2006 Netfilter Core Team [ 2047.669425] IN= OUT=eth0 SRC=172.16.160.19 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37914 DF PROTO=TCP SPT=49067 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2050.685283] IN= OUT=eth0 SRC=172.16.160.19 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=37915 DF PROTO=TCP SPT=49067 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 2738.992355] IN= OUT=eth0 SRC=172.16.160.19 DST=1.2.3.4 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=11288 DF PROTO=TCP SPT=42514 DPT=7777 WINDOW=5840 RES=0x00 SYN URGP=0 [ 3395.252208] IN= OUT=eth0 SRC=172.16.160.19 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=18914 DF PROTO=TCP SPT=49975 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 3398.272866] IN= OUT=eth0 SRC=172.16.160.19 DST=192.9.162.55 LEN=60 TOS=0x00 PREC=0x00 TTL=64 ID=18915 DF PROTO=TCP SPT=49975 DPT=80 WINDOW=5840 RES=0x00 SYN URGP=0 [ 3725.534803] err_bad_typedef[27692]: segfault at 0 ip 00002b5429d6caad sp 00007fffc2c1acb0 error 4 in libffi.so.4.0.1[2b5429d6b000+7000] [ 3743.533878] err_bad_typedef[5749]: segfault at 0 ip 00002b58eadacaad sp 00007fff068ef1a0 error 4 in libffi.so.4.0.1[2b58eadab000+7000] [ 3763.873884] err_bad_typedef[17640]: segfault at 0 ip 00002b370ae87aad sp 00007fff9e0739b0 error 4 in libffi.so.4.0.1[2b370ae86000+7000] [ 3783.482253] err_bad_typedef[28871]: segfault at 0 ip 00002ae65a9edaad sp 00007fffd9e1c500 error 4 in libffi.so.4.0.1[2ae65a9ec000+7000] [ 3802.971814] err_bad_typedef[7106]: segfault at 0 ip 00002b4ac1ec2aad sp 00007fffae2c2170 error 4 in libffi.so.4.0.1[2b4ac1ec1000+7000] [ 3822.140371] err_bad_typedef[27392]: segfault at 0 ip 0000000055577268 sp 00000000ff8f89a0 error 4 in libffi.so.4.0.1[55576000+5000] [ 3839.884562] err_bad_typedef[26038]: segfault at 0 ip 0000000055577268 sp 00000000ffaf00c0 error 4 in libffi.so.4.0.1[55576000+5000] [ 3860.181558] err_bad_typedef[5086]: segfault at 0 ip 0000000055577268 sp 00000000ff90ffb0 error 4 in libffi.so.4.0.1[55576000+5000] [ 3879.996966] err_bad_typedef[17143]: segfault at 0 ip 0000000055577268 sp 00000000ffb20290 error 4 in libffi.so.4.0.1[55576000+5000] [ 3899.625478] err_bad_typedef[27781]: segfault at 0 ip 0000000055577268 sp 00000000ffc77e50 error 4 in libffi.so.4.0.1[55576000+5000] [ 6219.819691] try-catch-2.exe[31664]: segfault at 626f7266 ip 00002ab0f481f552 sp 00007fff0086b310 error 4 in libstdc++.so.6.0.17[2ab0f476b000+e2000] [ 6220.381788] try-catch-9.exe[31978] general protection ip:2b2e06ed2552 sp:7fff3cb772a0 error:0 in libstdc++.so.6.0.17[2b2e06e1e000+e2000] [ 6268.291819] try-catch-2.exe[22847]: segfault at 626f7256 ip 000000005563733d sp 00000000ffcabd60 error 4 in libstdc++.so.6.0.17[5558d000+d9000] [ 6268.811132] try-catch-9.exe[23016]: segfault at 74736564 ip 000000005563733d sp 00000000ffc61f50 error 4 in libstdc++.so.6.0.17[5558d000+d9000] ************************************************************