sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build01.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ libhmsbeagle 1.0-6 (armhf) 05 Jun 2012 10:56 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: libhmsbeagle Version: 1.0-6 Source Version: 1.0-6 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/libhmsbeagle-zT70kM/libhmsbeagle-1.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/libhmsbeagle-zT70kM' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-1bc90566-2fb5-47cb-bd14-7d708bcffab1' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'libhmsbeagle' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/libhmsbeagle/trunk Need to get 237 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libhmsbeagle 1.0-6 (dsc) [1578 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libhmsbeagle 1.0-6 (tar) [228 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main libhmsbeagle 1.0-6 (diff) [7131 B] Fetched 237 kB in 0s (2378 kB/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 `/«BUILDDIR»/resolver-izuAEj/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10659 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) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), autotools-dev, dh-autoreconf, doxygen, javahelper (>= 0.25), openjdk-6-jdk, ant Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), autotools-dev, dh-autoreconf, doxygen, javahelper (>= 0.25), openjdk-6-jdk, ant dpkg-deb: building package `sbuild-build-depends-libhmsbeagle-dummy' in `/«BUILDDIR»/resolver-EkgY0h/apt_archive/sbuild-build-depends-libhmsbeagle-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install libhmsbeagle build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: ant autoconf automake autotools-dev bsdmainutils ca-certificates ca-certificates-java dctrl-tools debhelper devscripts dh-autoreconf doxygen file fontconfig fontconfig-config gconf-service gconf2-common gettext gettext-base groff-base html2text intltool-debian java-common javahelper libarchive-zip-perl libasound2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcap2 libcroco3 libcups2 libdatrie1 libdbus-1-3 libdbus-glib-1-2 libexpat1 libffi5 libflac8 libfontconfig1 libfreetype6 libgconf-2-4 libgcrypt11 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgif4 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libice6 libjasper1 libjbig0 libjpeg8 libjson0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libnspr4 libnss3 libnss3-1d libogg0 libp11-kit0 libpango1.0-0 libpcre3 libpcsclite1 libpipeline1 libpixman-1-0 libpng12-0 libpulse0 libsasl2-2 libsm6 libsndfile1 libsqlite3-0 libssl1.0.0 libtasn1-3 libthai-data libthai0 libtiff4 libtool libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxtst6 m4 man-db mime-support openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openssl po-debconf python python-minimal python2.7 python2.7-minimal shared-mime-info ttf-dejavu-core tzdata-java x11-common Suggested packages: default-jdk java-compiler java-sdk ant-gcj ant-doc autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation debtags dh-make bsd-mailx mailx cvs-buildpackage devscripts-el gnuplot libauthen-sasl-perl libfile-desktopentry-perl libnet-smtp-ssl-perl libterm-size-perl libyaml-syck-perl mutt ssh-client svn-buildpackage w3m doxygen-doc doxygen-gui graphviz gettext-doc groff default-jre cvs gawk tofrodos libasound2-plugins cups-common rng-tools krb5-doc krb5-user librsvg2-common gvfs libjasper-runtime ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp pcscd pulseaudio libtool-doc automaken gfortran fortran95-compiler libxerces2-java-doc libxerces2-java-gcj libxml-commons-resolver1.1-java-doc less www-browser openjdk-6-demo openjdk-6-source visualvm icedtea-plugin libnss-mdns sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: ant-optional at curl wget debian-keyring dput dupload equivs libcrypt-ssleay-perl libjson-perl libparse-debcontrol-perl libsoap-lite-perl liburi-perl libwww-perl lintian patchutils python-debian python-magic strace unzip wdiff autopoint doxygen-latex dbus libglib2.0-data hicolor-icon-theme libgtk2.0-bin krb5-locales libsasl2-modules libltdl-dev tcpd xml-core libxt-dev ttf-dejavu-extra icedtea-netx icedtea-6-jre-cacao icedtea-6-jre-jamvm libmail-sendmail-perl The following NEW packages will be installed: ant autoconf automake autotools-dev bsdmainutils ca-certificates ca-certificates-java dctrl-tools debhelper devscripts dh-autoreconf doxygen file fontconfig fontconfig-config gconf-service gconf2-common gettext gettext-base groff-base html2text intltool-debian java-common javahelper libarchive-zip-perl libasound2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcap2 libcroco3 libcups2 libdatrie1 libdbus-1-3 libdbus-glib-1-2 libexpat1 libffi5 libflac8 libfontconfig1 libfreetype6 libgconf-2-4 libgcrypt11 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgif4 libglib2.0-0 libgnutls26 libgpg-error0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libice6 libjasper1 libjbig0 libjpeg8 libjson0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libnspr4 libnss3 libnss3-1d libogg0 libp11-kit0 libpango1.0-0 libpcre3 libpcsclite1 libpipeline1 libpixman-1-0 libpng12-0 libpulse0 libsasl2-2 libsm6 libsndfile1 libsqlite3-0 libssl1.0.0 libtasn1-3 libthai-data libthai0 libtiff4 libtool libunistring0 libvorbis0a libvorbisenc2 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxtst6 m4 man-db mime-support openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openssl po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-libhmsbeagle-dummy shared-mime-info ttf-dejavu-core tzdata-java x11-common 0 upgraded, 135 newly installed, 0 to remove and 2 not upgraded. Need to get 3970 kB/92.0 MB of archives. After this operation, 248 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main libxml-commons-resolver1.1-java all 1.2-7 [91.9 kB] Get:2 http://repo.raspbian.lan/raspbian/ testing/main libxml-commons-external-java all 1.4.01-2 [245 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main libxerces2-java all 2.11.0-5 [1448 kB] Get:4 http://repo.raspbian.lan/raspbian/ testing/main ant all 1.8.2-4 [1841 kB] Get:5 http://repo.raspbian.lan/raspbian/ testing/main dctrl-tools armhf 2.22 [159 kB] Get:6 http://repo.raspbian.lan/raspbian/ testing/main libarchive-zip-perl all 1.30-6 [97.6 kB] Get:7 http://repo.raspbian.lan/raspbian/ testing/main javahelper all 0.41 [87.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3970 kB in 1s (3542 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10659 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1c-1_armhf.deb) ... Selecting previously unselected package libgpg-error0:armhf. Unpacking libgpg-error0:armhf (from .../libgpg-error0_1.10-3_armhf.deb) ... Selecting previously unselected package libgcrypt11:armhf. Unpacking libgcrypt11:armhf (from .../libgcrypt11_1.5.0-3_armhf.deb) ... Selecting previously unselected package libp11-kit0:armhf. Unpacking libp11-kit0:armhf (from .../libp11-kit0_0.12-3_armhf.deb) ... Selecting previously unselected package libtasn1-3:armhf. Unpacking libtasn1-3:armhf (from .../libtasn1-3_2.12-1_armhf.deb) ... Selecting previously unselected package libgnutls26:armhf. Unpacking libgnutls26:armhf (from .../libgnutls26_2.12.19-1_armhf.deb) ... 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Selecting previously unselected package libatk-wrapper-java-jni:armhf. Unpacking libatk-wrapper-java-jni:armhf (from .../libatk-wrapper-java-jni_0.30.4-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libogg0. Unpacking libogg0 (from .../libogg0_1.3.0-2_armhf.deb) ... Selecting previously unselected package libflac8:armhf. Unpacking libflac8:armhf (from .../libflac8_1.2.1-6_armhf.deb) ... Selecting previously unselected package x11-common. Unpacking x11-common (from .../x11-common_1%3a7.6+13_all.deb) ... Selecting previously unselected package libice6:armhf. Unpacking libice6:armhf (from .../libice6_2%3a1.0.8-2_armhf.deb) ... Selecting previously unselected package libnspr4:armhf. Unpacking libnspr4:armhf (from .../libnspr4_2%3a4.9-3_armhf.deb) ... Selecting previously unselected package libnss3:armhf. Unpacking libnss3:armhf (from .../libnss3_2%3a3.13.4-3_armhf.deb) ... Selecting previously unselected package libpcsclite1:armhf. Unpacking libpcsclite1:armhf (from .../libpcsclite1_1.8.3-3_armhf.deb) ... Selecting previously unselected package libcap2. Unpacking libcap2 (from .../libcap2_1%3a2.22-1_armhf.deb) ... Selecting previously unselected package libjson0:armhf. Unpacking libjson0:armhf (from .../libjson0_0.9-1.1_armhf.deb) ... Selecting previously unselected package libsm6:armhf. Unpacking libsm6:armhf (from .../libsm6_2%3a1.2.1-2_armhf.deb) ... Selecting previously unselected package libvorbis0a:armhf. Unpacking libvorbis0a:armhf (from .../libvorbis0a_1.3.2-1.3_armhf.deb) ... Selecting previously unselected package libvorbisenc2:armhf. Unpacking libvorbisenc2:armhf (from .../libvorbisenc2_1.3.2-1.3_armhf.deb) ... Selecting previously unselected package libsndfile1:armhf. Unpacking libsndfile1:armhf (from .../libsndfile1_1.0.25-4_armhf.deb) ... Selecting previously unselected package libx11-xcb1:armhf. Unpacking libx11-xcb1:armhf (from .../libx11-xcb1_2%3a1.4.99.901-2_armhf.deb) ... Selecting previously unselected package libxtst6:armhf. Unpacking libxtst6:armhf (from .../libxtst6_2%3a1.2.1-1_armhf.deb) ... Selecting previously unselected package libpulse0:armhf. Unpacking libpulse0:armhf (from .../libpulse0_2.0-3_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package openjdk-6-jre-lib. Unpacking openjdk-6-jre-lib (from .../openjdk-6-jre-lib_6b24-1.11.1-6+rpi1_all.deb) ... Selecting previously unselected package openssl. Unpacking openssl (from .../openssl_1.0.1c-1_armhf.deb) ... Selecting previously unselected package ca-certificates. Unpacking ca-certificates (from .../ca-certificates_20120212_all.deb) ... Selecting previously unselected package libnss3-1d:armhf. Unpacking libnss3-1d:armhf (from .../libnss3-1d_2%3a3.13.4-3_armhf.deb) ... Selecting previously unselected package ca-certificates-java. Unpacking ca-certificates-java (from .../ca-certificates-java_20120225_all.deb) ... Selecting previously unselected package tzdata-java. Unpacking tzdata-java (from .../tzdata-java_2012c-1_all.deb) ... Selecting previously unselected package java-common. Unpacking java-common (from .../java-common_0.47_all.deb) ... Selecting previously unselected package openjdk-6-jre-headless:armhf. Unpacking openjdk-6-jre-headless:armhf (from .../openjdk-6-jre-headless_6b24-1.11.1-6+rpi1_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.2_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package m4. Unpacking m4 (from .../archives/m4_1.4.16-3_armhf.deb) ... Selecting previously unselected package mime-support. Unpacking mime-support (from .../mime-support_3.52-1_all.deb) ... Selecting previously unselected package python2.7-minimal. Unpacking python2.7-minimal (from .../python2.7-minimal_2.7.3~rc2-2.1_armhf.deb) ... Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.3~rc2-2.1_armhf.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.2-10_all.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.2-10_all.deb) ... Selecting previously unselected package libxml-commons-resolver1.1-java. Unpacking libxml-commons-resolver1.1-java (from .../libxml-commons-resolver1.1-java_1.2-7_all.deb) ... Selecting previously unselected package libxml-commons-external-java. Unpacking libxml-commons-external-java (from .../libxml-commons-external-java_1.4.01-2_all.deb) ... Selecting previously unselected package libxerces2-java. Unpacking libxerces2-java (from .../libxerces2-java_2.11.0-5_all.deb) ... Selecting previously unselected package ant. Unpacking ant (from .../archives/ant_1.8.2-4_all.deb) ... Selecting previously unselected package autoconf. Unpacking autoconf (from .../autoconf_2.69-1_all.deb) ... Selecting previously unselected package autotools-dev. Unpacking autotools-dev (from .../autotools-dev_20120210.1_all.deb) ... Selecting previously unselected package automake. Unpacking automake (from .../automake_1%3a1.11.5-1_all.deb) ... Selecting previously unselected package dctrl-tools. Unpacking dctrl-tools (from .../dctrl-tools_2.22_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.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_9.20120419_all.deb) ... Selecting previously unselected package devscripts. Unpacking devscripts (from .../devscripts_2.11.7_armhf.deb) ... Selecting previously unselected package libtool. Unpacking libtool (from .../libtool_2.4.2-1+b2_armhf.deb) ... Selecting previously unselected package dh-autoreconf. Unpacking dh-autoreconf (from .../dh-autoreconf_6_all.deb) ... Selecting previously unselected package doxygen. Unpacking doxygen (from .../doxygen_1.8.1-1_armhf.deb) ... Selecting previously unselected package libarchive-zip-perl. Unpacking libarchive-zip-perl (from .../libarchive-zip-perl_1.30-6_all.deb) ... Selecting previously unselected package javahelper. Unpacking javahelper (from .../javahelper_0.41_all.deb) ... Selecting previously unselected package libgif4. Unpacking libgif4 (from .../libgif4_4.1.6-9.1_armhf.deb) ... Selecting previously unselected package openjdk-6-jre:armhf. Unpacking openjdk-6-jre:armhf (from .../openjdk-6-jre_6b24-1.11.1-6+rpi1_armhf.deb) ... Selecting previously unselected package openjdk-6-jdk:armhf. Unpacking openjdk-6-jdk:armhf (from .../openjdk-6-jdk_6b24-1.11.1-6+rpi1_armhf.deb) ... Selecting previously unselected package sbuild-build-depends-libhmsbeagle-dummy. Unpacking sbuild-build-depends-libhmsbeagle-dummy (from .../sbuild-build-depends-libhmsbeagle-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libssl1.0.0:armhf (1.0.1c-1) ... Setting up libgpg-error0:armhf (1.10-3) ... Setting up libgcrypt11:armhf (1.5.0-3) ... Setting up libp11-kit0:armhf (0.12-3) ... Setting up libtasn1-3:armhf (2.12-1) ... Setting up libgnutls26:armhf (2.12.19-1) ... Setting up libkeyutils1:armhf (1.5.5-2) ... Setting up libkrb5support0:armhf (1.10.1+dfsg-1) ... Setting up libk5crypto3:armhf (1.10.1+dfsg-1) ... Setting up libkrb5-3:armhf (1.10.1+dfsg-1) ... Setting up libgssapi-krb5-2:armhf (1.10.1+dfsg-1) ... Setting up libsasl2-2:armhf (2.1.25.dfsg1-4) ... Setting up libldap-2.4-2:armhf (2.4.28-1.1+rpi1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libsqlite3-0:armhf (3.7.12.1-1) ... Setting up libwrap0:armhf (7.6.q-23) ... Setting up libxml2:armhf (2.7.8.dfsg-9.1) ... Setting up libasound2:armhf (1.0.25-3) ... Setting up libasyncns0:armhf (0.8-4) ... Setting up libdbus-1-3:armhf (1.5.12-1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libdbus-glib-1-2:armhf (0.98-1) ... Setting up gconf2-common (3.2.5-1) ... Creating config file /etc/gconf/2/path with new version Setting up libgconf-2-4:armhf (3.2.5-1) ... Setting up gconf-service (3.2.5-1) ... Setting up libatk1.0-data (2.4.0-2) ... Setting up libatk1.0-0:armhf (2.4.0-2) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.9.0-5) ... Setting up libfontconfig1:armhf (2.9.0-5) ... Setting up libpixman-1-0:armhf (0.24.4-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.99.901-2) ... Setting up libx11-6:armhf (2:1.4.99.901-2) ... Setting up libxcb-render0:armhf (1.8.1-1) ... Setting up libxcb-shm0:armhf (1.8.1-1) ... Setting up libxrender1:armhf (1:0.9.7-1) ... Setting up libcairo2:armhf (1.12.2-1) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libjasper1:armhf (1.900.1-13) ... Setting up libjbig0:armhf (2.0-2) ... Setting up libtiff4:armhf (3.9.6-5) ... Setting up libgdk-pixbuf2.0-common (2.26.1-1) ... Setting up libgdk-pixbuf2.0-0:armhf (2.26.1-1) ... Setting up libgtk2.0-common (2.24.10-1) ... Setting up libavahi-common-data:armhf (0.6.31-1) ... Setting up libavahi-common3:armhf (0.6.31-1) ... Setting up libavahi-client3:armhf (0.6.31-1) ... Setting up libcups2:armhf (1.5.3-1) ... Setting up libthai-data (0.1.17-1) ... Setting up libdatrie1:armhf (0.2.5-3) ... Setting up libthai0:armhf (0.1.17-1) ... Setting up libxft2:armhf (2.2.0-3) ... Setting up fontconfig (2.9.0-5) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libpango1.0-0:armhf (1.30.0-1) ... Setting up libxcomposite1:armhf (1:0.4.3-2) ... Setting up libxfixes3:armhf (1:5.0-4) ... Setting up libxcursor1:armhf (1:1.1.13-1) ... Setting up libxdamage1:armhf (1:1.1.3-2) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxi6:armhf (2:1.6.1-1) ... Setting up libxinerama1:armhf (2:1.1.2-1) ... Setting up libxrandr2:armhf (2:1.3.2-2) ... Setting up shared-mime-info (0.90-1.1) ... Setting up libgtk2.0-0:armhf (2.24.10-1) ... Setting up libatk-wrapper-java (0.30.4-1) ... Setting up libatk-wrapper-java-jni:armhf (0.30.4-1) ... Setting up libcroco3:armhf (0.6.5-1) ... Setting up libogg0 (1.3.0-2) ... Setting up libflac8:armhf (1.2.1-6) ... Setting up x11-common (1:7.6+13) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.8-2) ... Setting up libnspr4:armhf (2:4.9-3) ... Setting up libnss3:armhf (2:3.13.4-3) ... Setting up libpcsclite1:armhf (1.8.3-3) ... Setting up libcap2 (1:2.22-1) ... Setting up libjson0:armhf (0.9-1.1) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libvorbis0a:armhf (1.3.2-1.3) ... Setting up libvorbisenc2:armhf (1.3.2-1.3) ... Setting up libsndfile1:armhf (1.0.25-4) ... Setting up libx11-xcb1:armhf (2:1.4.99.901-2) ... Setting up libxtst6:armhf (2:1.2.1-1) ... Setting up libpulse0:armhf (2.0-3) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up openssl (1.0.1c-1) ... Setting up ca-certificates (20120212) ... Updating certificates in /etc/ssl/certs... 151 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d....done. Setting up libnss3-1d:armhf (2:3.13.4-3) ... Setting up tzdata-java (2012c-1) ... Setting up java-common (0.47) ... Setting up bsdmainutils (9.0.2) ... 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 (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up m4 (1.4.16-3) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.3~rc2-2.1) ... Setting up python2.7 (2.7.3~rc2-2.1) ... Setting up python-minimal (2.7.2-10) ... Setting up python (2.7.2-10) ... Setting up libxml-commons-resolver1.1-java (1.2-7) ... Setting up libxml-commons-external-java (1.4.01-2) ... Setting up libxerces2-java (2.11.0-5) ... Setting up autoconf (2.69-1) ... Setting up autotools-dev (20120210.1) ... Setting up automake (1:1.11.5-1) ... update-alternatives: using /usr/bin/automake-1.11 to provide /usr/bin/automake (automake) in auto mode. Setting up dctrl-tools (2.22) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up devscripts (2.11.7) ... Setting up libtool (2.4.2-1+b2) ... Setting up dh-autoreconf (6) ... Setting up doxygen (1.8.1-1) ... Setting up libarchive-zip-perl (1.30-6) ... Setting up javahelper (0.41) ... Setting up libgif4 (4.1.6-9.1) ... Setting up openjdk-6-jre-lib (6b24-1.11.1-6+rpi1) ... Setting up ca-certificates-java (20120225) ... Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/EBG_Elektronik_Sertifika_Hizmet_Sa??lay??c??s??.pem. Message: /etc/ssl/certs/EBG_Elektronik_Sertifika_Hizmet_Sa??lay??c??s??.pem (No such file or directory) Adding debian:QuoVadis_Root_CA.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:Certum_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:RSA_Root_Certificate_1.pem Adding debian:Thawte_Premium_Server_CA.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/NetLock_Arany_=Class_Gold=_F??tan??s??tv??ny.pem. Message: /etc/ssl/certs/NetLock_Arany_=Class_Gold=_F??tan??s??tv??ny.pem (No such file or directory) Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:CNNIC_ROOT.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DST_Root_CA_X3.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Wells_Fargo_Root_CA.pem Adding debian:Entrust.net_Secure_Server_CA.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:ComSign_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:spi-ca-2003.pem Adding debian:Juur-SK.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:Thawte_Server_CA.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:TDC_OCES_Root_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:America_Online_Root_Certification_Authority_2.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/T??B??TAK_UEKAE_K??k_Sertifika_Hizmet_Sa??lay??c??s??_-_S??r??m_3.pem. Message: /etc/ssl/certs/T??B??TAK_UEKAE_K??k_Sertifika_Hizmet_Sa??lay??c??s??_-_S??r??m_3.pem (No such file or directory) Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Secure_Global_CA.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:Certigna.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:ValiCert_Class_1_VA.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:ValiCert_Class_2_VA.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Izenpe.com.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Taiwan_GRCA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:CA_Disig.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/AC_Ra??z_Certic??mara_S.A..pem. Message: /etc/ssl/certs/AC_Ra??z_Certic??mara_S.A..pem (No such file or directory) Adding debian:QuoVadis_Root_CA_3.pem Adding debian:ca.pem Adding debian:ComSign_Secured_CA.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:A-Trust-nQual-03.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:TDC_Internet_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:America_Online_Root_Certification_Authority_1.pem Adding debian:Firmaprofesional_Root_CA.pem Adding debian:IGC_A.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:SecureTrust_CA.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Equifax_Secure_eBusiness_CA_2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:TC_TrustCenter_Universal_CA_III.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:spi-cacert-2008.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Equifax_Secure_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Warning: there was a problem reading the certificate file /etc/ssl/certs/Certinomis_-_Autorit??_Racine.pem. Message: /etc/ssl/certs/Certinomis_-_Autorit??_Racine.pem (No such file or directory) Adding debian:XRamp_Global_CA_Root.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:GeoTrust_Global_CA_2.pem Adding debian:EC-ACC.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:cacert.org.pem Adding debian:ACEDICOM_Root.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem done. Setting up openjdk-6-jre-headless:armhf (6b24-1.11.1-6+rpi1) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/java to provide /usr/bin/java (java) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode. Setting up ant (1.8.2-4) ... Setting up openjdk-6-jre:armhf (6b24-1.11.1-6+rpi1) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode. Setting up openjdk-6-jdk:armhf (6b24-1.11.1-6+rpi1) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/javah to provide /usr/bin/javah (javah) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode. update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode. Setting up sbuild-build-depends-libhmsbeagle-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.3 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.17-1 Package versions: ant_1.8.2-4 apt_0.9.3+rpi1 autoconf_2.69-1 automake_1:1.11.5-1 autotools-dev_20120210.1 base-files_6.9 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.2 bsdutils_1:2.20.1-5 build-essential_11.5+b1 bzip2_1.0.6-1 ca-certificates_20120212 ca-certificates-java_20120225 coreutils_8.13-3.2 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 dctrl-tools_2.22 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2012.3 debianutils_4.3 devscripts_2.11.7 dh-autoreconf_6 diffutils_1:3.2-6 doxygen_1.8.1-1 dpkg_1.16.3 dpkg-dev_1.16.3 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig_2.9.0-5 fontconfig-config_2.9.0-5 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gconf-service_3.2.5-1 gconf2-common_3.2.5-1 gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 java-common_0.47 javahelper_0.41 libacl1_2.2.51-7 libapt-pkg4.12_0.9.3+rpi1 libarchive-zip-perl_1.30-6 libasound2_1.0.25-3 libasyncns0_0.8-4 libatk-wrapper-java_0.30.4-1 libatk-wrapper-java-jni_0.30.4-1 libatk1.0-0_2.4.0-2 libatk1.0-data_2.4.0-2 libattr1_1:2.4.46-7 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libblkid1_2.20.1-5 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libcairo2_1.12.2-1 libcap2_1:2.22-1 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libcups2_1.5.3-1 libdatrie1_0.2.5-3 libdb5.1_5.1.29-1 libdbus-1-3_1.5.12-1 libdbus-glib-1-2_0.98-1 libdpkg-perl_1.16.3 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libflac8_1.2.1-6 libfontconfig1_2.9.0-5 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgconf-2-4_3.2.5-1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libgdk-pixbuf2.0-0_2.26.1-1 libgdk-pixbuf2.0-common_2.26.1-1 libgif4_4.1.6-9.1 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-1.1 libgnutls26_2.12.19-1 libgomp1_4.7.0-1.1+rpi libgpg-error0_1.10-3 libgssapi-krb5-2_1.10.1+dfsg-1 libgtk2.0-0_2.24.10-1 libgtk2.0-common_2.24.10-1 libice6_2:1.0.8-2 libjasper1_1.900.1-13 libjbig0_2.0-2 libjpeg8_8d-1 libjson0_0.9-1.1 libk5crypto3_1.10.1+dfsg-1 libkeyutils1_1.5.5-2 libkrb5-3_1.10.1+dfsg-1 libkrb5support0_1.10.1+dfsg-1 libldap-2.4-2_2.4.28-1.1+rpi1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-7 libncursesw5_5.9-7 libnspr4_2:4.9-3 libnss3_2:3.13.4-3 libnss3-1d_2:3.13.4-3 libogg0_1.3.0-2 libp11-kit0_0.12-3 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpango1.0-0_1.30.0-1 libpcre3_1:8.30-5 libpcsclite1_1.8.3-3 libpipeline1_1.2.1-1 libpixman-1-0_0.24.4-1 libpng12-0_1.2.49-1 libpulse0_2.0-3 libreadline6_6.2-8 libsasl2-2_2.1.25.dfsg1-4 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-10 libsm6_2:1.2.1-2 libsndfile1_1.0.25-4 libsqlite3-0_3.7.12.1-1 libss2_1.42.2-2 libssl1.0.0_1.0.1c-1 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtasn1-3_2.12-1 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.17-1 libthai0_0.1.17-1 libtiff4_3.9.6-5 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libtool_2.4.2-1+b2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-5 libvorbis0a_1.3.2-1.3 libvorbisenc2_1.3.2-1.3 libwrap0_7.6.q-23 libx11-6_2:1.4.99.901-2 libx11-data_2:1.4.99.901-2 libx11-xcb1_2:1.4.99.901-2 libxau6_1:1.0.7-1 libxcb-render0_1.8.1-1 libxcb-shm0_1.8.1-1 libxcb1_1.8.1-1 libxcomposite1_1:0.4.3-2 libxcursor1_1:1.1.13-1 libxdamage1_1:1.1.3-2 libxdmcp6_1:1.1.1-1 libxerces2-java_2.11.0-5 libxext6_2:1.3.1-2 libxfixes3_1:5.0-4 libxft2_2.2.0-3 libxi6_2:1.6.1-1 libxinerama1_2:1.1.2-1 libxml-commons-external-java_1.4.01-2 libxml-commons-resolver1.1-java_1.2-7 libxml2_2.7.8.dfsg-9.1 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.7-1 libxtst6_2:1.2.1-1 linux-libc-dev_3.2.17-1 login_1:4.1.5-1 lsb-base_4.1+Debian4 m4_1.4.16-3 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-5 multiarch-support_2.13-32 ncurses-base_5.9-7 ncurses-bin_5.9-7 openjdk-6-jdk_6b24-1.11.1-6+rpi1 openjdk-6-jre_6b24-1.11.1-6+rpi1 openjdk-6-jre-headless_6b24-1.11.1-6+rpi1 openjdk-6-jre-lib_6b24-1.11.1-6+rpi1 openssl_1.0.1c-1 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.3~rc2-2.1 python2.7-minimal_2.7.3~rc2-2.1 raspbian-archive-keyring_20120528.2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libhmsbeagle-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.7 shared-mime-info_0.90-1.1 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 ttf-dejavu-core_2.33-2 tzdata_2012c-1 tzdata-java_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5 x11-common_1:7.6+13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-11 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri May 25 12:43:42 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./libhmsbeagle_1.0-6.dsc dpkg-source: info: extracting libhmsbeagle in libhmsbeagle-1.0 dpkg-source: info: unpacking libhmsbeagle_1.0.orig.tar.gz dpkg-source: info: unpacking libhmsbeagle_1.0-6.debian.tar.gz dpkg-source: info: applying enable_static.patch dpkg-source: info: applying disable_cpu_sse_plugin.patch dpkg-source: info: applying gcc-4.7.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-1bc90566-2fb5-47cb-bd14-7d708bcffab1 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package libhmsbeagle dpkg-buildpackage: source version 1.0-6 dpkg-source --before-build libhmsbeagle-1.0 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with autoreconf --with javahelper dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -f Makefile distclean || true make[2]: Entering directory `/«PKGBUILDDIR»' make[2]: Makefile: No such file or directory make[2]: *** No rule to make target `Makefile'. Stop. make[2]: Leaving directory `/«PKGBUILDDIR»' rm -rf doc .config configure rm -rf lib build make[1]: Leaving directory `/«PKGBUILDDIR»' dh_autoreconf_clean jh_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf --with javahelper dh_testdir -a dh_autoreconf -a libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.config'. libtoolize: copying file `.config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' configure.ac:64: installing `.config/config.guess' configure.ac:64: installing `.config/config.sub' configure.ac:56: installing `.config/install-sh' configure.ac:56: installing `.config/missing' examples/complextest/Makefile.am: installing `.config/depcomp' Makefile.am: installing `./INSTALL' debian/rules override_dh_auto_configure make[1]: Entering directory `/«PKGBUILDDIR»' ./autogen.sh libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.config'. libtoolize: copying file `.config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'. libtoolize: copying file `m4/libtool.m4' libtoolize: copying file `m4/ltoptions.m4' libtoolize: copying file `m4/ltsugar.m4' libtoolize: copying file `m4/ltversion.m4' libtoolize: copying file `m4/lt~obsolete.m4' dh_auto_configure -- --enable-doxygen-man --enable-march-native=no --enable-sse=no configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking whether ln -s works... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 805306365 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for library containing lt_dlinit... no checking for library containing dlopen... -ldl checking if gcc accepts -dumpversion option... yes checking gcc version... 4.6 checking for /usr/local/cuda/... no checking for /usr/local/cuda/include... no checking for /usr/local/cuda/lib... no checking for javac... javac checking for javac... /usr/bin/javac checking symlink for /usr/bin/javac... /etc/alternatives/javac checking symlink for /etc/alternatives/javac... /usr/lib/jvm/java-6-openjdk-armhf/bin/javac checking for doxygen... /usr/bin/doxygen checking for perl... /usr/bin/perl checking for dot... no configure: WARNING: dot not found - will not generate graphics for doxygen documentation configure: creating ./config.status config.status: creating Makefile config.status: creating hmsbeagle-1.pc config.status: creating libhmsbeagle/Makefile config.status: creating libhmsbeagle/GPU/Makefile config.status: creating libhmsbeagle/GPU/kernels/Makefile config.status: creating libhmsbeagle/CPU/Makefile config.status: creating libhmsbeagle/plugin/Makefile config.status: creating examples/Makefile config.status: creating examples/tinytest/Makefile config.status: creating examples/complextest/Makefile config.status: creating examples/oddstatetest/Makefile config.status: creating examples/fourtaxon/Makefile config.status: creating examples/genomictest/Makefile config.status: creating examples/matrixtest/Makefile config.status: creating libhmsbeagle/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode configure: WARNING: NVIDIA CUDA nvcc compiler not found. CUDA support will not be built. Check the path to CUDA and specify --with-cuda=/path/to/cuda make[1]: Leaving directory `/«PKGBUILDDIR»' jh_linkjars -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make make[2]: Entering directory `/«PKGBUILDDIR»' Making all in libhmsbeagle make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' /usr/bin/make all-recursive make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' Making all in GPU make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' /usr/bin/make all-recursive make[6]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making all in kernels make[7]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' /usr/bin/make all-am make[8]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[8]: Nothing to be done for `all-am'. make[8]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[7]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[7]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[7]: Nothing to be done for `all-am'. make[7]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[6]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making all in CPU make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/«PKGBUILDDIR» -I/«PKGBUILDDIR» -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o libhmsbeagle_cpu_la-BeagleCPUPlugin.lo `test -f 'BeagleCPUPlugin.cpp' || echo './'`BeagleCPUPlugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/«PKGBUILDDIR» -I/«PKGBUILDDIR» -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c BeagleCPUPlugin.cpp -fPIC -DPIC -o .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/«PKGBUILDDIR» -I/«PKGBUILDDIR» -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c BeagleCPUPlugin.cpp -o libhmsbeagle_cpu_la-BeagleCPUPlugin.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -version-info 1:0:0 -o libhmsbeagle-cpu.la -rpath /usr/lib libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtbeginS.o .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o -ldl -L/usr/lib/gcc/arm-linux-gnueabihf/4.6 -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crtn.o -O3 -Wl,-soname -Wl,libhmsbeagle-cpu.so.1 -o .libs/libhmsbeagle-cpu.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu.so.1" && ln -s "libhmsbeagle-cpu.so.1.0.0" "libhmsbeagle-cpu.so.1") libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu.so" && ln -s "libhmsbeagle-cpu.so.1.0.0" "libhmsbeagle-cpu.so") libtool: link: ar cru .libs/libhmsbeagle-cpu.a libhmsbeagle_cpu_la-BeagleCPUPlugin.o libtool: link: ranlib .libs/libhmsbeagle-cpu.a libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu.la" && ln -s "../libhmsbeagle-cpu.la" "libhmsbeagle-cpu.la" ) make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' Making all in plugin make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o libplugin_la-Plugin.lo `test -f 'Plugin.cpp' || echo './'`Plugin.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c Plugin.cpp -fPIC -DPIC -o .libs/libplugin_la-Plugin.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c Plugin.cpp -o libplugin_la-Plugin.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o libplugin_la-UnixSharedLibrary.lo `test -f 'UnixSharedLibrary.cpp' || echo './'`UnixSharedLibrary.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c UnixSharedLibrary.cpp -fPIC -DPIC -o .libs/libplugin_la-UnixSharedLibrary.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c UnixSharedLibrary.cpp -o libplugin_la-UnixSharedLibrary.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o libplugin.la libplugin_la-Plugin.lo libplugin_la-UnixSharedLibrary.lo -ldl libtool: link: ar cru .libs/libplugin.a .libs/libplugin_la-Plugin.o .libs/libplugin_la-UnixSharedLibrary.o libtool: link: ranlib .libs/libplugin.a libtool: link: ( cd ".libs" && rm -f "libplugin.la" && ln -s "../libplugin.la" "libplugin.la" ) make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o libhmsbeagle_la-beagle.lo `test -f 'beagle.cpp' || echo './'`beagle.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c beagle.cpp -fPIC -DPIC -o .libs/libhmsbeagle_la-beagle.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c beagle.cpp -o libhmsbeagle_la-beagle.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -version-info 1:0:0 -o libhmsbeagle.la -rpath /usr/lib libhmsbeagle_la-beagle.lo plugin/libplugin.la -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtbeginS.o .libs/libhmsbeagle_la-beagle.o -Wl,--whole-archive plugin/.libs/libplugin.a -Wl,--no-whole-archive -ldl -L/usr/lib/gcc/arm-linux-gnueabihf/4.6 -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crtn.o -O3 -Wl,-soname -Wl,libhmsbeagle.so.1 -o .libs/libhmsbeagle.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libhmsbeagle.so.1" && ln -s "libhmsbeagle.so.1.0.0" "libhmsbeagle.so.1") libtool: link: (cd ".libs" && rm -f "libhmsbeagle.so" && ln -s "libhmsbeagle.so.1.0.0" "libhmsbeagle.so") libtool: link: (cd .libs/libhmsbeagle.lax/libplugin.a && ar x "/«PKGBUILDDIR»/libhmsbeagle/plugin/.libs/libplugin.a") libtool: link: ar cru .libs/libhmsbeagle.a libhmsbeagle_la-beagle.o .libs/libhmsbeagle.lax/libplugin.a/libplugin_la-Plugin.o .libs/libhmsbeagle.lax/libplugin.a/libplugin_la-UnixSharedLibrary.o libtool: link: ranlib .libs/libhmsbeagle.a libtool: link: rm -fr .libs/libhmsbeagle.lax libtool: link: ( cd ".libs" && rm -f "libhmsbeagle.la" && ln -s "../libhmsbeagle.la" "libhmsbeagle.la" ) /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo `test -f 'JNI/beagle_BeagleJNIWrapper.cpp' || echo './'`JNI/beagle_BeagleJNIWrapper.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c JNI/beagle_BeagleJNIWrapper.cpp -fPIC -DPIC -o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o In file included from JNI/beagle_BeagleJNIWrapper.cpp:9:0: /usr/lib/jvm/java-6-openjdk-armhf/include/jni.h:876:13: note: the mangling of 'va_list' has changed in GCC 4.4 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c JNI/beagle_BeagleJNIWrapper.cpp -o libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -module -avoid-version -o libhmsbeagle-jni.la -rpath /usr/lib libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -lhmsbeagle -ldl libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtbeginS.o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o -Wl,-rpath -Wl,/«PKGBUILDDIR»/libhmsbeagle/.libs /«PKGBUILDDIR»/libhmsbeagle/.libs/libhmsbeagle.so -ldl -L/usr/lib/gcc/arm-linux-gnueabihf/4.6 -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crtn.o -O3 -Wl,-soname -Wl,libhmsbeagle-jni.so -o .libs/libhmsbeagle-jni.so libtool: link: ar cru .libs/libhmsbeagle-jni.a libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o libtool: link: ranlib .libs/libhmsbeagle-jni.a libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-jni.la" && ln -s "../libhmsbeagle-jni.la" "libhmsbeagle-jni.la" ) make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' Making all in examples make[3]: Entering directory `/«PKGBUILDDIR»/examples' Making all in genomictest make[4]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' Making all in tinytest make[4]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' Making all in oddstatetest make[4]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' Making all in complextest make[4]: Entering directory `/«PKGBUILDDIR»/examples/complextest' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' Making all in fourtaxon make[4]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' Making all in matrixtest make[4]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make[4]: Entering directory `/«PKGBUILDDIR»/examples' make[4]: Nothing to be done for `all-am'. make[4]: Leaving directory `/«PKGBUILDDIR»/examples' make[3]: Leaving directory `/«PKGBUILDDIR»/examples' make[3]: Entering directory `/«PKGBUILDDIR»' make[3]: Nothing to be done for `all-am'. make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' /usr/bin/make doxygen-doc make[2]: Entering directory `/«PKGBUILDDIR»' rm -rf doc SRCDIR='.' PROJECT='libhmsbeagle' DOCDIR='doc' VERSION='1.0.0' PERL_PATH='/usr/bin/perl' HAVE_DOT='NO' GENERATE_MAN='YES' GENERATE_RTF='NO' GENERATE_XML='NO' GENERATE_HTMLHELP='NO' GENERATE_CHI='NO' GENERATE_HTML='YES' GENERATE_LATEX='NO' /usr/bin/doxygen ./beagle.dox warning: Tag `DETAILS_AT_TOP' at line 163 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `SHOW_DIRECTORIES' at line 453 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `HTML_ALIGN_MEMBERS' at line 765 of file ./beagle.dox has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Notice: Output directory `doc' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for files to exclude Searching for files to process... Searching for files in directory /«PKGBUILDDIR» Searching for files in directory /«PKGBUILDDIR»/autom4te.cache Searching for files in directory /«PKGBUILDDIR»/config Searching for files in directory /«PKGBUILDDIR»/debian Searching for files in directory /«PKGBUILDDIR»/debian/patches Searching for files in directory /«PKGBUILDDIR»/debian/source Searching for files in directory /«PKGBUILDDIR»/dist Searching for files in directory /«PKGBUILDDIR»/doc Searching for files in directory /«PKGBUILDDIR»/examples Searching for files in directory /«PKGBUILDDIR»/examples/complextest Searching for files in directory /«PKGBUILDDIR»/examples/fourtaxon Searching for files in directory /«PKGBUILDDIR»/examples/genomictest Searching for files in directory /«PKGBUILDDIR»/examples/matrixtest Searching for files in directory /«PKGBUILDDIR»/examples/oddstatetest Searching for files in directory /«PKGBUILDDIR»/examples/standalone Searching for files in directory /«PKGBUILDDIR»/examples/standalone/hellobeagle Searching for files in directory /«PKGBUILDDIR»/examples/standalone/hellobeagle/src Searching for files in directory /«PKGBUILDDIR»/examples/tinytest Searching for files in directory /«PKGBUILDDIR»/java Searching for files in directory /«PKGBUILDDIR»/java/beagle Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle/CPU Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle/GPU Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle/GPU/kernels Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle/JNI Searching for files in directory /«PKGBUILDDIR»/libhmsbeagle/plugin Searching for files in directory /«PKGBUILDDIR»/m4 Searching for files in directory /«PKGBUILDDIR»/tests Reading and parsing tag files Preprocessing /«PKGBUILDDIR»/beagle.dox... Parsing file /«PKGBUILDDIR»/beagle.dox... Preprocessing /«PKGBUILDDIR»/examples/complextest/complextest.cpp... Parsing file /«PKGBUILDDIR»/examples/complextest/complextest.cpp... Preprocessing /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.cpp... Parsing file /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.cpp... Preprocessing /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.h... Parsing file /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.h... Preprocessing /«PKGBUILDDIR»/examples/genomictest/genomictest.cpp... Parsing file /«PKGBUILDDIR»/examples/genomictest/genomictest.cpp... Preprocessing /«PKGBUILDDIR»/examples/genomictest/linalg.cpp... Parsing file /«PKGBUILDDIR»/examples/genomictest/linalg.cpp... Preprocessing /«PKGBUILDDIR»/examples/genomictest/linalg.h... Parsing file /«PKGBUILDDIR»/examples/genomictest/linalg.h... Preprocessing /«PKGBUILDDIR»/examples/matrixtest/matrixtest.cpp... Parsing file /«PKGBUILDDIR»/examples/matrixtest/matrixtest.cpp... Preprocessing /«PKGBUILDDIR»/examples/oddstatetest/oddstatetest.cpp... Parsing file /«PKGBUILDDIR»/examples/oddstatetest/oddstatetest.cpp... Preprocessing /«PKGBUILDDIR»/examples/standalone/hellobeagle/src/hello.cpp... Parsing file /«PKGBUILDDIR»/examples/standalone/hellobeagle/src/hello.cpp... Preprocessing /«PKGBUILDDIR»/examples/tinytest/tinytest.cpp... Parsing file /«PKGBUILDDIR»/examples/tinytest/tinytest.cpp... Reading /«PKGBUILDDIR»/java/beagle/Beagle.java... Parsing file /«PKGBUILDDIR»/java/beagle/Beagle.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleException.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleException.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleFactory.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleFactory.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleFlag.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleFlag.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleInfo.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleInfo.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java... Reading /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java... Parsing file /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java... Reading /«PKGBUILDDIR»/java/beagle/DependencyAwareBeagleImpl.java... Parsing file /«PKGBUILDDIR»/java/beagle/DependencyAwareBeagleImpl.java... Reading /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java... Parsing file /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java... Reading /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java... Parsing file /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java... Reading /«PKGBUILDDIR»/java/beagle/InstanceDetails.java... Parsing file /«PKGBUILDDIR»/java/beagle/InstanceDetails.java... Reading /«PKGBUILDDIR»/java/beagle/ResourceDetails.java... Parsing file /«PKGBUILDDIR»/java/beagle/ResourceDetails.java... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/beagle.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/beagle.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/beagle.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/beagle.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/config.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/config.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUPlugin.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUPlugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUPlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUPlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEPlugin.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEPlugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEPlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEPlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/Precision.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/Precision.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/CPU/SSEDefinitions.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/CPU/SSEDefinitions.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/CUDAPlugin.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/CUDAPlugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/CUDAPlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/CUDAPlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplHelper.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplHelper.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplHelper.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplHelper.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceCUDA.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceCUDA.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/OpenCLPlugin.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/OpenCLPlugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/OpenCLPlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/OpenCLPlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/GPU/Precision.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/GPU/Precision.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/JNI/beagle_BeagleJNIWrapper.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/JNI/beagle_BeagleJNIWrapper.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/JNI/beagle_BeagleJNIWrapper.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/JNI/beagle_BeagleJNIWrapper.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/platform.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/platform.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/BeaglePlugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/BeaglePlugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/LibtoolSharedLibrary.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/LibtoolSharedLibrary.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.cpp... QGDict::hashAsciiKey: Invalid null key QGDict::hashAsciiKey: Invalid null key /«PKGBUILDDIR»/java/beagle/DependencyAwareBeagleImpl.java:3: warning: Compound beagle::DependencyAwareBeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:57: warning: Compound beagle::cpu::BeagleCPUSSEImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:3: warning: Compound beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java:5: warning: Compound beagle::FourStateBeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:29: warning: Compound KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.h:27: warning: Compound beagle::cpu::BeagleCPUOpenMPPlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:135: warning: Compound beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:56: warning: Compound beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:72: warning: Compound beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:17: warning: Compound beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:146: warning: Compound beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:37: warning: Compound KernelLauncher is not documented. /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.h:18: warning: Compound FourTaxonExample is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:218: warning: Compound beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/OpenCLPlugin.h:22: warning: Compound beagle::gpu::OpenCLPlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:216: warning: Compound beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:54: warning: Compound beagle::plugin::PluginManager is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:17: warning: Compound beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:26: warning: Compound beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:156: warning: Compound beagle::BeagleImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:49: warning: Compound beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:42: warning: Compound beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/CUDAPlugin.h:22: warning: Compound beagle::gpu::CUDAPlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/SSEDefinitions.h:78: warning: Compound VecUnion is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:58: warning: Compound GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:54: warning: Compound beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.h:27: warning: Compound beagle::plugin::UnixSharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:21: warning: Compound beagle::plugin::SharedLibraryException is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/BeaglePlugin.h:13: warning: Compound beagle::BeaglePlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEPlugin.h:22: warning: Compound beagle::cpu::BeagleCPUSSEPlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h:287: warning: Compound Dim3Int is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:265: warning: Compound beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:30: warning: Compound beagle::plugin::SharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h:17: warning: Compound beagle::cpu::EigenDecompositionCube is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUPlugin.h:22: warning: Compound beagle::cpu::BeagleCPUPlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:46: warning: Compound beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:50: warning: Compound beagle::cpu::BeagleCPU4StateSSEImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:154: warning: Compound beagle::cpu::BeagleCPU4StateImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.h:26: warning: Compound beagle::plugin::WinSharedLibrary is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:16: warning: Compound beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:402: warning: Compound beagle::cpu::BeagleCPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:472: warning: Compound BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceCUDA.cpp:667: warning: documented function `const char * GPUInterface::GetCUDAErrorDescription' was not declared or defined. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp:278: warning: no matching class member found for void GPUInterface::PrintfDeviceVector(GPUPtr dPtr, int length) Possible candidates: template < Real > void GPUInterface::PrintfDeviceVector(GPUPtr dPtr, int length, Real r) template < Real > void GPUInterface::PrintfDeviceVector(GPUPtr dPtr, int length, double checkValue, Real r) template < Real > void GPUInterface::PrintfDeviceVector(GPUPtr dPtr, int length, double checkValue, int *signal, Real r) /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp:303: warning: documented function `const char * GPUInterface::GetCLErrorDescription' was not declared or defined. Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.h... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.cpp... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.cpp... Preprocessing /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.h... Parsing file /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Creating members for template instances... Computing class relations... Add enum values to enums... Searching for member function documentation... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Combining using relations... Adding members to index pages... Generating style sheet... Generating example documentation... Generating file sources... Generating code for file examples/fourtaxon/fourtaxon.h... Generating code for file examples/genomictest/linalg.h... Generating code for file libhmsbeagle/beagle.h... Generating code for file libhmsbeagle/BeagleImpl.h... Generating code for file libhmsbeagle/config.h... Generating code for file libhmsbeagle/CPU/BeagleCPU4StateImpl.h... Generating code for file libhmsbeagle/CPU/BeagleCPU4StateImpl.hpp... Generating code for file libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h... Generating code for file libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp... Generating code for file libhmsbeagle/CPU/BeagleCPUImpl.h... Generating code for file libhmsbeagle/CPU/BeagleCPUImpl.hpp... Generating code for file libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.h... Generating code for file libhmsbeagle/CPU/BeagleCPUPlugin.h... Generating code for file libhmsbeagle/CPU/BeagleCPUSSEImpl.h... Generating code for file libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp... Generating code for file libhmsbeagle/CPU/BeagleCPUSSEPlugin.h... Generating code for file libhmsbeagle/CPU/EigenDecomposition.h... Generating code for file libhmsbeagle/CPU/EigenDecompositionCube.h... Generating code for file libhmsbeagle/CPU/EigenDecompositionCube.hpp... /«PKGBUILDDIR»/libhmsbeagle/beagle.h:473: warning: Member destinationPartials (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:474: warning: Member destinationScaleWrite (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:475: warning: Member destinationScaleRead (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:476: warning: Member child1Partials (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:477: warning: Member child1TransitionMatrix (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:478: warning: Member child2Partials (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.h:479: warning: Member child2TransitionMatrix (variable) of class BeagleOperation is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h:288: warning: Member x (variable) of class Dim3Int is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h:288: warning: Member y (variable) of class Dim3Int is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUImplDefs.h:288: warning: Member z (variable) of class Dim3Int is not documented. /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.h:21: warning: Member interpretCommandLineParameters(int argc, char *argv[]) (function) of class FourTaxonExample is not documented. /«PKGBUILDDIR»/examples/fourtaxon/fourtaxon.h:22: warning: Member run() (function) of class FourTaxonExample is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:80: warning: Member Initialize() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:82: warning: Member GetDeviceCount() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:88: warning: Member SetDevice(int deviceNumber, int paddedStateCount, int categoryCount, int patternCount, long flags) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:90: warning: Member Synchronize() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:92: warning: Member GetFunction(const char *functionName) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:99: warning: Member LaunchKernel(GPUFunction deviceFunction, Dim3Int block, Dim3Int grid, int parameterCountV, int totalParameterCount,...) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:101: warning: Member MallocHost(size_t memSize) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:103: warning: Member CallocHost(size_t size, size_t length) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:107: warning: Member AllocatePinnedHostMemory(size_t memSize, bool writeCombined, bool mapped) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:109: warning: Member AllocateMemory(size_t memSize) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:111: warning: Member AllocateRealMemory(size_t length) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:113: warning: Member AllocateIntMemory(size_t length) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:117: warning: Member MemsetShort(GPUPtr dest, unsigned short val, size_t count) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:121: warning: Member MemcpyHostToDevice(GPUPtr dest, const void *src, size_t memSize) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:125: warning: Member MemcpyDeviceToHost(void *dest, const GPUPtr src, size_t memSize) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:129: warning: Member MemcpyDeviceToDevice(GPUPtr dest, GPUPtr src, size_t memSize) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:131: warning: Member FreeHostMemory(void *hPtr) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:133: warning: Member FreePinnedHostMemory(void *hPtr) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:135: warning: Member FreeMemory(GPUPtr dPtr) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:137: warning: Member GetDevicePointer(void *hPtr) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:139: warning: Member GetAvailableMemory() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:143: warning: Member GetDeviceName(int deviceNumber, char *deviceName, int nameLength) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:146: warning: Member GetDeviceDescription(int deviceNumber, char *deviceDescription) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:148: warning: Member GetSupportsDoublePrecision(int deviceNumber) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:151: warning: Member PrintfDeviceVector(GPUPtr dPtr, int length, Real r) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:157: warning: Member PrintfDeviceVector(GPUPtr dPtr, int length, double checkValue, Real r) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:164: warning: Member PrintfDeviceVector(GPUPtr dPtr, int length, double checkValue, int *signal, Real r) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:196: warning: Member PrintfDeviceInt(GPUPtr dPtr, int length) (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:198: warning: Member DestroyKernelMap() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:200: warning: Member kernelResource (variable) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:203: warning: Member InitializeKernelMap() (function) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:205: warning: Member resourceMap (variable) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/GPUInterface.h:207: warning: Member supportDoublePrecision (variable) of class GPUInterface is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:103: warning: Member KernelLauncher(GPUInterface *inGpu) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:140: warning: Member GetTransitionProbabilitiesSquare(GPUPtr dPtr, GPUPtr dEvec, GPUPtr dIevc, GPUPtr dEigenValues, GPUPtr distanceQueue, unsigned int totalMatrix, unsigned int index) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:158: warning: Member PartialsPartialsPruningDynamicCheckScaling(GPUPtr partials1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, int writeScalingIndex, int readScalingIndex, int cumulativeScalingIndex, GPUPtr *dScalingFactors, GPUPtr *dScalingFactorsMaster, unsigned int patternCount, unsigned int categoryCount, int doRescaling, int *hRescalingTrigger, GPUPtr dRescalingTrigger, int sizeReal) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:169: warning: Member PartialsPartialsPruningDynamicScaling(GPUPtr partials1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:180: warning: Member StatesPartialsPruningDynamicScaling(GPUPtr states1, GPUPtr partials2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:191: warning: Member StatesStatesPruningDynamicScaling(GPUPtr states1, GPUPtr states2, GPUPtr partials3, GPUPtr matrices1, GPUPtr matrices2, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, int doRescaling) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:199: warning: Member IntegrateLikelihoodsDynamicScaling(GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:207: warning: Member IntegrateLikelihoodsAutoScaling(GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:219: warning: Member IntegrateLikelihoodsDynamicScalingSecondDeriv(GPUPtr dResult, GPUPtr dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials, GPUPtr dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dRootScalingFactors, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:226: warning: Member PartialsPartialsEdgeLikelihoods(GPUPtr dPartialsTmp, GPUPtr dParentPartials, GPUPtr dChildParials, GPUPtr dTransMatrix, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:237: warning: Member PartialsPartialsEdgeLikelihoodsSecondDeriv(GPUPtr dPartialsTmp, GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr dChildParials, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:245: warning: Member StatesPartialsEdgeLikelihoods(GPUPtr dPartialsTmp, GPUPtr dParentPartials, GPUPtr dChildStates, GPUPtr dTransMatrix, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:256: warning: Member StatesPartialsEdgeLikelihoodsSecondDeriv(GPUPtr dPartialsTmp, GPUPtr dFirstDerivTmp, GPUPtr dSecondDerivTmp, GPUPtr dParentPartials, GPUPtr dChildStates, GPUPtr dTransMatrix, GPUPtr dFirstDerivMatrix, GPUPtr dSecondDerivMatrix, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:262: warning: Member AccumulateFactorsDynamicScaling(GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:269: warning: Member AccumulateFactorsAutoScaling(GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount, unsigned int scaleBufferSize) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:275: warning: Member RemoveFactorsDynamicScaling(GPUPtr dScalingFactors, GPUPtr dNodePtrQueue, GPUPtr dRootScalingFactors, unsigned int nodeCount, unsigned int patternCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:282: warning: Member RescalePartials(GPUPtr partials3, GPUPtr scalingFactors, GPUPtr cumulativeScaling, unsigned int patternCount, unsigned int categoryCount, unsigned int fillWithOnes) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:289: warning: Member IntegrateLikelihoods(GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:300: warning: Member IntegrateLikelihoodsSecondDeriv(GPUPtr dResult, GPUPtr dFirstDerivResult, GPUPtr dSecondDerivResult, GPUPtr dRootPartials, GPUPtr dRootFirstDeriv, GPUPtr dRootSecondDeriv, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:308: warning: Member IntegrateLikelihoodsMulti(GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, unsigned int patternCount, unsigned int categoryCount, unsigned int takeLog) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:321: warning: Member IntegrateLikelihoodsFixedScaleMulti(GPUPtr dResult, GPUPtr dRootPartials, GPUPtr dWeights, GPUPtr dFrequencies, GPUPtr dScalingFactors, GPUPtr dPtrQueue, GPUPtr dMaxScalingFactors, GPUPtr dIndexMaxScalingFactors, unsigned int patternCount, unsigned int categoryCount, unsigned int subsetCount, unsigned int subsetIndex) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:326: warning: Member SumSites1(GPUPtr dArray1, GPUPtr dSum1, GPUPtr dPatternWeights, unsigned int patternCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:333: warning: Member SumSites2(GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr dSum2, GPUPtr dPatternWeights, unsigned int patternCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:342: warning: Member SumSites3(GPUPtr dArray1, GPUPtr dSum1, GPUPtr dArray2, GPUPtr dSum2, GPUPtr dArray3, GPUPtr dSum3, GPUPtr dPatternWeights, unsigned int patternCount) (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:344: warning: Member SetupKernelBlocksAndGrids() (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelLauncher.h:347: warning: Member LoadKernels() (function) of class KernelLauncher is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:44: warning: Member KernelResource(int inPaddedStateCount, char *inKernelString, int inPatternBlockSize, int inMatrixBlockSize, int inBlockPeelingSize, int inSlowReweighing, int inMultiplyBlockSize, int inCategoryCount, int inPatternCount, long inFlags) (function) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:47: warning: Member KernelResource(const KernelResource &krIn, char *inKernelCode) (function) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:64: warning: Member copy() (function) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:51: warning: Member paddedStateCount (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:52: warning: Member categoryCount (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:53: warning: Member patternCount (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:54: warning: Member kernelCode (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:55: warning: Member patternBlockSize (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:56: warning: Member matrixBlockSize (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:57: warning: Member blockPeelingSize (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:58: warning: Member isPowerOfTwo (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:59: warning: Member smallestPowerOfTwo (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:60: warning: Member slowReweighing (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:61: warning: Member multiplyBlockSize (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/KernelResource.h:62: warning: Member flags (variable) of class KernelResource is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/SSEDefinitions.h:79: warning: Member x[REALS_PER_VEC] (variable) of class VecUnion is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/SSEDefinitions.h:80: warning: Member vx (variable) of class VecUnion is not documented. /«PKGBUILDDIR»/libhmsbeagle/beagle.cpp:61: warning: Member getBeagleInstance(int instanceIndex) (function) of namespace beagle is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp:2: warning: Found unknown command `\TODO' /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp:4: warning: Found unknown command `\API' /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp:4: warning: Found unknown command `\API' /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUOpenMPPlugin.cpp:4: warning: Found unknown command `\API' /«PKGBUILDDIR»/java/beagle/Beagle.java:23: warning: Member OPERATION_TUPLE_SIZE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:24: warning: Member NONE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:270: warning: argument 'instance' of command @param is not found in the argument list of beagle.Beagle::copyScaleFactors(int destScalingIndex, int srcScalingIndex) /«PKGBUILDDIR»/java/beagle/Beagle.java:181: warning: The following parameters of beagle.Beagle.setTransitionMatrix(int matrixIndex, final double[] inMatrix, double paddedValue) are not documented: parameter 'paddedValue' /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:19: warning: Member BeagleErrorCode(int errCode, String meaning) (function) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:24: warning: Member getErrCode() (function) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:28: warning: Member getMeaning() (function) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:9: warning: Member NO_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:10: warning: Member GENERAL_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:11: warning: Member OUT_OF_MEMORY_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:12: warning: Member UNIDENTIFIED_EXCEPTION_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:13: warning: Member UNINITIALIZED_INSTANCE_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:14: warning: Member OUT_OF_RANGE_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:15: warning: Member NO_RESOURCE_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:16: warning: Member NO_IMPLEMENTATION_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleErrorCode.java:17: warning: Member FLOATING_POINT_ERROR (variable) of class beagle::BeagleErrorCode is not documented. /«PKGBUILDDIR»/java/beagle/BeagleException.java:8: warning: Member BeagleException(String functionName, int errCode) (function) of class beagle::BeagleException is not documented. /«PKGBUILDDIR»/java/beagle/BeagleException.java:14: warning: Member getMessage() (function) of class beagle::BeagleException is not documented. /«PKGBUILDDIR»/java/beagle/BeagleException.java:27: warning: Member getFunctionName() (function) of class beagle::BeagleException is not documented. /«PKGBUILDDIR»/java/beagle/BeagleException.java:31: warning: Member getErrCode() (function) of class beagle::BeagleException is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFactory.java:18: warning: Member getResourceDetails() (function) of class beagle::BeagleFactory is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFactory.java:24: warning: Member getResourceDetails(int resourceNumber) (function) of class beagle::BeagleFactory is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFactory.java:43: warning: Member loadBeagleInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int[] resourceList, long preferenceFlags, long requirementFlags) (function) of class beagle::BeagleFactory is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:37: warning: Member BeagleFlag(long mask, String meaning) (function) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:42: warning: Member getMask() (function) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:46: warning: Member getMeaning() (function) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:50: warning: Member isSet(long flags) (function) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:54: warning: Member toString(long flags) (function) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:9: warning: Member PRECISION_SINGLE (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:10: warning: Member PRECISION_DOUBLE (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:12: warning: Member COMPUTATION_SYNCH (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:13: warning: Member COMPUTATION_ASYNCH (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:15: warning: Member EIGEN_REAL (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:16: warning: Member EIGEN_COMPLEX (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:18: warning: Member SCALING_MANUAL (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:19: warning: Member SCALING_AUTO (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:20: warning: Member SCALING_ALWAYS (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:21: warning: Member SCALING_DYNAMIC (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:23: warning: Member SCALERS_RAW (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:24: warning: Member SCALERS_LOG (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:26: warning: Member VECTOR_SSE (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:27: warning: Member VECTOR_NONE (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:29: warning: Member THREADING_OPENMP (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:30: warning: Member THREADING_NONE (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:32: warning: Member PROCESSOR_CPU (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:33: warning: Member PROCESSOR_GPU (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:34: warning: Member PROCESSOR_FPGA (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleFlag.java:35: warning: Member PROCESSOR_CELL (variable) of class beagle::BeagleFlag is not documented. /«PKGBUILDDIR»/java/beagle/BeagleInfo.java:12: warning: Member printResourceList() (function) of class beagle::BeagleInfo is not documented. /«PKGBUILDDIR»/java/beagle/BeagleInfo.java:24: warning: Member main(String[] argv) (function) of class beagle::BeagleInfo is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:32: warning: Member BeagleJNIImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, long preferenceFlags, long requirementFlags) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:134: warning: Member setCategoryRates(double[] inCategoryRates) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:148: warning: Member getTransitionMatrix(int matrixIndex, final double[] outMatrix) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:171: warning: Member updatePartials(final int[] operations, final int operationCount, final int cumulativeScaleIndex) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:185: warning: Member removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:211: warning: Member calculateRootLogLikelihoods(int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:236: warning: Member calculateEdgeLogLikelihoods(final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:255: warning: Member getSiteLogLikelihoods(final double[] outLogLikelihoods) (function) of class beagle::BeagleJNIImpl is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:23: warning: Member OPERATION_TUPLE_SIZE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:24: warning: Member NONE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIImpl.java:192: warning: argument 'instance' of command @param is not found in the argument list of beagle.BeagleJNIImpl::copyScaleFactors(int destScalingIndex, int srcScalingIndex) inherited from member copyScaleFactors at line 270 in file /«PKGBUILDDIR»/java/beagle/Beagle.java /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:27: warning: Member getResourceList() (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:43: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, int resourceCount, long preferenceFlags, long requirementFlags, InstanceDetails returnInfo) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:45: warning: Member finalize(int instance) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:48: warning: Member setPatternWeights(int instance, final double[] patternWeights) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:50: warning: Member setTipStates(int instance, int tipIndex, final int[] inStates) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:52: warning: Member getTipStates(int instance, int tipIndex, final int[] inStates) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:54: warning: Member setTipPartials(int instance, int tipIndex, final double[] inPartials) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:56: warning: Member setPartials(int instance, int bufferIndex, final double[] inPartials) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:59: warning: Member getPartials(int instance, int bufferIndex, int scaleIndex, final double[] outPartials) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:66: warning: Member setEigenDecomposition(int instance, int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final double[] eigenValues) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:70: warning: Member setStateFrequencies(int instance, int stateFrequenciesIndex, final double[] stateFrequencies) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:74: warning: Member setCategoryWeights(int instance, int categoryWeightsIndex, final double[] categoryWeights) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:77: warning: Member setCategoryRates(int instance, final double[] inCategoryRates) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:79: warning: Member setTransitionMatrix(int instance, int matrixIndex, final double[] inMatrix, double paddedValue) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:81: warning: Member getTransitionMatrix(int instance, int matrixIndex, final double[] outMatrix) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:88: warning: Member updateTransitionMatrices(int instance, int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, int count) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:93: warning: Member updatePartials(final int instance, final int[] operations, int operationCount, int cumulativeScalingIndex) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:97: warning: Member waitForPartials(final int instance, final int[] destinationPartials, int destinationPartialsCount) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:102: warning: Member accumulateScaleFactors(final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:107: warning: Member removeScaleFactors(final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:110: warning: Member resetScaleFactors(final int instance, final int cumulativeScalingIndex) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:114: warning: Member copyScaleFactors(final int instance, final int destScalingIndex, final int srcScalingIndex) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:122: warning: Member calculateRootLogLikelihoods(int instance, final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:136: warning: Member calculateEdgeLogLikelihoods(int instance, final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] scalingFactorsIndices, int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:139: warning: Member getSiteLogLikelihoods(final int instance, final double[] outLogLikelihoods) (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:154: warning: Member loadBeagleLibrary() (function) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:19: warning: Member LIBRARY_NAME (variable) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/BeagleJNIWrapper.java:167: warning: Member INSTANCE (variable) of class beagle::BeagleJNIWrapper is not documented. /«PKGBUILDDIR»/java/beagle/DependencyAwareBeagleImpl.java:5: warning: Member DependencyAwareBeagleImpl(final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int stateCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount) (function) of class beagle::DependencyAwareBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:156: warning: Member getTipStates(int tipIndex, int[] states) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:164: warning: Member setTipPartials(int tipIndex, double[] inPartials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:176: warning: Member setPartials(final int bufferIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:181: warning: Member getPartials(final int bufferIndex, final int scaleIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:185: warning: Member setEigenDecomposition(int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:198: warning: Member setStateFrequencies(final int stateFrequenciesIndex, final double[] stateFrequencies) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:202: warning: Member setCategoryWeights(final int categoryWeightsIndex, final double[] categoryWeights) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:206: warning: Member setCategoryRates(double[] categoryRates) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:210: warning: Member setTransitionMatrix(final int matrixIndex, final double[] inMatrix, final double paddedValue) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:214: warning: Member getTransitionMatrix(final int matrixIndex, final double[] outMatrix) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:223: warning: Member updateTransitionMatrices(final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:360: warning: Member accumulateScaleFactors(int[] scaleIndices, int count, int outScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:365: warning: Member removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:613: warning: Member calculateRootLogLikelihoods(final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:671: warning: Member calculateEdgeLogLikelihoods(final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:675: warning: Member getSiteLogLikelihoods(final double[] outLogLikelihoods) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:5: warning: Member DEBUG (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:6: warning: Member SCALING (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:10: warning: Member SCALING_FACTOR_COUNT (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:11: warning: Member SCALING_FACTOR_OFFSET (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:23: warning: Member OPERATION_TUPLE_SIZE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:24: warning: Member NONE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:542: warning: Member updatePartialsPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:14: warning: Member tipCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:15: warning: Member partialsBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:16: warning: Member compactBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:17: warning: Member stateCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:18: warning: Member patternCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:19: warning: Member eigenBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:20: warning: Member matrixBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:21: warning: Member categoryCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:23: warning: Member partialsSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:24: warning: Member matrixSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:26: warning: Member cMatrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:27: warning: Member eigenValues (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:29: warning: Member stateFrequencies (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:31: warning: Member categoryRates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:32: warning: Member categoryWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:34: warning: Member patternWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:35: warning: Member partials (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:36: warning: Member scalingFactorCounts (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:38: warning: Member tipStates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:40: warning: Member matrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:45: warning: Member scalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:46: warning: Member logScalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java:9: warning: Member FourStateBeagleImpl(final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount) (function) of class beagle::FourStateBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java:325: warning: Member calculateRootLogLikelihoods(final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) (function) of class beagle::FourStateBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:156: warning: Member getTipStates(int tipIndex, int[] states) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:164: warning: Member setTipPartials(int tipIndex, double[] inPartials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:176: warning: Member setPartials(final int bufferIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:181: warning: Member getPartials(final int bufferIndex, final int scaleIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:185: warning: Member setEigenDecomposition(int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:198: warning: Member setStateFrequencies(final int stateFrequenciesIndex, final double[] stateFrequencies) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:202: warning: Member setCategoryWeights(final int categoryWeightsIndex, final double[] categoryWeights) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:206: warning: Member setCategoryRates(double[] categoryRates) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:210: warning: Member setTransitionMatrix(final int matrixIndex, final double[] inMatrix, final double paddedValue) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:214: warning: Member getTransitionMatrix(final int matrixIndex, final double[] outMatrix) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:223: warning: Member updateTransitionMatrices(final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:360: warning: Member accumulateScaleFactors(int[] scaleIndices, int count, int outScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:365: warning: Member removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:671: warning: Member calculateEdgeLogLikelihoods(final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:675: warning: Member getSiteLogLikelihoods(final double[] outLogLikelihoods) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java:7: warning: Member DEBUG (variable) of class beagle::FourStateBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:6: warning: Member SCALING (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:10: warning: Member SCALING_FACTOR_COUNT (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:11: warning: Member SCALING_FACTOR_OFFSET (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:23: warning: Member OPERATION_TUPLE_SIZE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:24: warning: Member NONE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/FourStateBeagleImpl.java:229: warning: Member updatePartialsPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) (function) of class beagle::FourStateBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:14: warning: Member tipCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:15: warning: Member partialsBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:16: warning: Member compactBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:17: warning: Member stateCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:18: warning: Member patternCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:19: warning: Member eigenBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:20: warning: Member matrixBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:21: warning: Member categoryCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:23: warning: Member partialsSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:24: warning: Member matrixSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:26: warning: Member cMatrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:27: warning: Member eigenValues (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:29: warning: Member stateFrequencies (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:31: warning: Member categoryRates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:32: warning: Member categoryWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:34: warning: Member patternWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:35: warning: Member partials (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:36: warning: Member scalingFactorCounts (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:38: warning: Member tipStates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:40: warning: Member matrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:45: warning: Member scalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:46: warning: Member logScalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:156: warning: Member getTipStates(int tipIndex, int[] states) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:164: warning: Member setTipPartials(int tipIndex, double[] inPartials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:176: warning: Member setPartials(final int bufferIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:181: warning: Member getPartials(final int bufferIndex, final int scaleIndex, final double[] partials) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:185: warning: Member setEigenDecomposition(int eigenIndex, double[] eigenVectors, double[] inverseEigenValues, double[] eigenValues) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:198: warning: Member setStateFrequencies(final int stateFrequenciesIndex, final double[] stateFrequencies) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:202: warning: Member setCategoryWeights(final int categoryWeightsIndex, final double[] categoryWeights) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:206: warning: Member setCategoryRates(double[] categoryRates) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:210: warning: Member setTransitionMatrix(final int matrixIndex, final double[] inMatrix, final double paddedValue) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:214: warning: Member getTransitionMatrix(final int matrixIndex, final double[] outMatrix) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:223: warning: Member updateTransitionMatrices(final int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDervativeIndices, final double[] edgeLengths, final int count) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:360: warning: Member accumulateScaleFactors(int[] scaleIndices, int count, int outScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:365: warning: Member removeScaleFactors(int[] scaleIndices, int count, int cumulativeScaleIndex) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:613: warning: Member calculateRootLogLikelihoods(final int[] bufferIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:671: warning: Member calculateEdgeLogLikelihoods(final int[] parentBufferIndices, final int[] childBufferIndices, final int[] probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final int[] stateFrequenciesIndices, final int[] cumulativeScaleIndices, final int count, final double[] outSumLogLikelihood, final double[] outSumFirstDerivative, final double[] outSumSecondDerivative) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:675: warning: Member getSiteLogLikelihoods(final double[] outLogLikelihoods) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:5: warning: Member DEBUG (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:6: warning: Member SCALING (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:10: warning: Member SCALING_FACTOR_COUNT (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:11: warning: Member SCALING_FACTOR_OFFSET (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:23: warning: Member OPERATION_TUPLE_SIZE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/Beagle.java:24: warning: Member NONE (variable) of class beagle::Beagle is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:542: warning: Member updatePartialsPartials(int bufferIndex1, int matrixIndex1, int bufferIndex2, int matrixIndex2, int bufferIndex3) (function) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:14: warning: Member tipCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:15: warning: Member partialsBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:16: warning: Member compactBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:17: warning: Member stateCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:18: warning: Member patternCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:19: warning: Member eigenBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:20: warning: Member matrixBufferCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:21: warning: Member categoryCount (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:23: warning: Member partialsSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:24: warning: Member matrixSize (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:26: warning: Member cMatrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:27: warning: Member eigenValues (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:29: warning: Member stateFrequencies (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:31: warning: Member categoryRates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:32: warning: Member categoryWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:34: warning: Member patternWeights (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:35: warning: Member partials (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:36: warning: Member scalingFactorCounts (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:38: warning: Member tipStates (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:40: warning: Member matrices (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:45: warning: Member scalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:46: warning: Member logScalingFactors (variable) of class beagle::GeneralBeagleImpl is not documented. /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:49: warning: The following parameters of beagle.GeneralBeagleImpl.GeneralBeagleImpl(final int tipCount, final int partialsBufferCount, final int compactBufferCount, final int stateCount, final int patternCount, final int eigenBufferCount, final int matrixBufferCount, final int categoryCount, final int scaleBufferCount) are not documented: parameter 'tipCount' parameter 'partialsBufferCount' parameter 'compactBufferCount' parameter 'patternCount' parameter 'eigenBufferCount' parameter 'matrixBufferCount' parameter 'categoryCount' parameter 'scaleBufferCount' /«PKGBUILDDIR»/java/beagle/GeneralBeagleImpl.java:369: warning: argument 'instance' of command @param is not found in the argument list of beagle.GeneralBeagleImpl::copyScaleFactors(int destScalingIndex, int srcScalingIndex) inherited from member copyScaleFactors at line 270 in file /«PKGBUILDDIR»/java/beagle/Beagle.java /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:15: warning: Member getResourceNumber() (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:19: warning: Member setResourceNumber(int resourceNumber) (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:23: warning: Member getResourceName() (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:27: warning: Member setResourceName(String resourceName) (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:31: warning: Member getImplementationName() (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:35: warning: Member setImplementationName(String implementationName) (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:39: warning: Member getFlags() (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:43: warning: Member setFlags(long flags) (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/InstanceDetails.java:48: warning: Member toString() (function) of class beagle::InstanceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:11: warning: Member ResourceDetails(int number) (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:15: warning: Member getNumber() (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:19: warning: Member getName() (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:23: warning: Member setName(String name) (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:27: warning: Member getDescription() (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:31: warning: Member setDescription(String description) (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:35: warning: Member getFlags() (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:39: warning: Member setFlags(long flags) (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/java/beagle/ResourceDetails.java:44: warning: Member toString() (function) of class beagle::ResourceDetails is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:57: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:59: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:62: warning: Member setTipStates(int tipIndex, const int *inStates)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:65: warning: Member setTipPartials(int tipIndex, const double *inPartials)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:68: warning: Member setPartials(int bufferIndex, const double *inPartials)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:72: warning: Member getPartials(int bufferIndex, int scaleIndex, double *outPartials)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:77: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:80: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:83: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:85: warning: Member setPatternWeights(const double *inPatternWeights)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:87: warning: Member setCategoryRates(const double *inCategoryRates)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:91: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:96: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:99: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:106: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:110: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:113: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:117: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:121: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:123: warning: Member resetScaleFactors(int cumulativeScalingIndex)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:126: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:133: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:146: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:148: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:151: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives)=0 (function) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:153: warning: Member resourceNumber (variable) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:170: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode)=0 (function) of class beagle::BeagleImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:172: warning: Member getName()=0 (function) of class beagle::BeagleImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:174: warning: Member getFlags()=0 (function) of class beagle::BeagleImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/BeaglePlugin.h:16: warning: Member BeaglePlugin(const char *plugin_name) (function) of class beagle::BeaglePlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/BeaglePlugin.h:17: warning: Member getSayHelloString() const =0 (function) of class beagle::BeaglePlugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:70: warning: Member getName() (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:77: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:83: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:89: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:95: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:102: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:110: warning: Member calcEdgeLogLikelihoods(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:117: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:124: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:131: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:138: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:144: warning: Member integrateOutStatesAndScale(const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:149: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class beagle::cpu::BeagleCPU4StateImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:134: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:137: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:144: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:151: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:155: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:159: warning: Member getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:170: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:173: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:176: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:178: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:183: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:187: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:192: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:195: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:208: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:218: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:234: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:239: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:243: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:245: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:248: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:259: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:274: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:276: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:279: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:281: warning: Member block(void) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:285: warning: Member getFlags() (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:335: warning: Member calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:345: warning: Member calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:357: warning: Member calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:393: warning: Member autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:395: warning: Member getPaddedPatternsModulus() (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:397: warning: Member mallocAligned(size_t size) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:59: warning: Member kBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:69: warning: Member kPartialsPaddedStateCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:70: warning: Member kEigenDecompCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:72: warning: Member kScaleBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:74: warning: Member kPartialsSize (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:79: warning: Member kFlags (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:81: warning: Member realtypeMin (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:82: warning: Member scalingExponentThreshhold (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:84: warning: Member gEigenDecomposition (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:86: warning: Member gCategoryRates (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:87: warning: Member gPatternWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:89: warning: Member gCategoryWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:90: warning: Member gStateFrequencies (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:95: warning: Member gPartials (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:96: warning: Member gTipStates (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:97: warning: Member gScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:99: warning: Member gAutoScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:101: warning: Member gActiveScalingFactors (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:106: warning: Member gTransitionMatrices (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:108: warning: Member integrationTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:109: warning: Member firstDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:110: warning: Member secondDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:112: warning: Member outLogLikelihoodsTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:113: warning: Member outFirstDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:114: warning: Member outSecondDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:116: warning: Member ones (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:117: warning: Member zeros (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:168: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) (function) of class beagle::cpu::BeagleCPU4StateImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:170: warning: Member getName() (function) of class beagle::cpu::BeagleCPU4StateImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:171: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:70: warning: Member getName() (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:77: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:83: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:89: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:95: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:102: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:110: warning: Member calcEdgeLogLikelihoods(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:117: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:124: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:131: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:138: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:144: warning: Member integrateOutStatesAndScale(const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:149: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:75: warning: Member getName() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:77: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:77: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:83: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:89: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:95: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:102: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:117: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:124: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:131: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:138: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:144: warning: Member integrateOutStatesAndScale(const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:149: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:80: warning: Member getPaddedPatternsModulus() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:156: warning: Member getName() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:158: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:77: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:83: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:89: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:95: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:102: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:117: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:124: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:131: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:138: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *child0Partials, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, int *activateScaling) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:144: warning: Member integrateOutStatesAndScale(const REALTYPE *integrationTmp, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateImpl.h:149: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPU4StateImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:161: warning: Member getPaddedPatternsModulus() (function) of class beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:230: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) (function) of class beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:232: warning: Member getName() (function) of class beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.h:233: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:768: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPU4StateSSEImpl.hpp:781: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPU4StateSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:134: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:137: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:144: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:151: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:155: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:159: warning: Member getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:170: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:173: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:176: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:178: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:183: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:187: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:192: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:195: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:208: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:218: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:234: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:239: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:243: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:245: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:248: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:259: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:274: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:276: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:279: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:281: warning: Member block(void) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:283: warning: Member getName() (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:285: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:292: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:299: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:305: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:311: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:318: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:326: warning: Member calcEdgeLogLikelihoods(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:335: warning: Member calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:345: warning: Member calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:357: warning: Member calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:364: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:371: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:378: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:385: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:390: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:393: warning: Member autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:395: warning: Member getPaddedPatternsModulus() (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:397: warning: Member mallocAligned(size_t size) (function) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:59: warning: Member kBufferCount (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:69: warning: Member kPartialsPaddedStateCount (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:70: warning: Member kEigenDecompCount (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:72: warning: Member kScaleBufferCount (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:74: warning: Member kPartialsSize (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:79: warning: Member kFlags (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:81: warning: Member realtypeMin (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:82: warning: Member scalingExponentThreshhold (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:84: warning: Member gEigenDecomposition (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:86: warning: Member gCategoryRates (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:87: warning: Member gPatternWeights (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:89: warning: Member gCategoryWeights (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:90: warning: Member gStateFrequencies (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:95: warning: Member gPartials (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:96: warning: Member gTipStates (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:97: warning: Member gScaleBuffers (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:99: warning: Member gAutoScaleBuffers (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:101: warning: Member gActiveScalingFactors (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:106: warning: Member gTransitionMatrices (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:108: warning: Member integrationTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:109: warning: Member firstDerivTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:110: warning: Member secondDerivTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:112: warning: Member outLogLikelihoodsTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:113: warning: Member outFirstDerivativesTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:114: warning: Member outSecondDerivativesTmp (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:116: warning: Member ones (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:117: warning: Member zeros (variable) of class beagle::cpu::BeagleCPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:153: warning: Member resourceNumber (variable) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:416: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) (function) of class beagle::cpu::BeagleCPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:418: warning: Member getName() (function) of class beagle::cpu::BeagleCPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:419: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:134: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:137: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:144: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:151: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:155: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:159: warning: Member getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:170: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:173: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:176: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:178: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:183: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:187: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:192: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:195: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:208: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:218: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:234: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:239: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:243: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:245: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:248: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:259: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:274: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:276: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:279: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:281: warning: Member block(void) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:283: warning: Member getName() (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:285: warning: Member getFlags() (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:292: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:299: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:305: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:311: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:318: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:326: warning: Member calcEdgeLogLikelihoods(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:335: warning: Member calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:345: warning: Member calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:357: warning: Member calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:364: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:371: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:378: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:385: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:390: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:393: warning: Member autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:395: warning: Member getPaddedPatternsModulus() (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:397: warning: Member mallocAligned(size_t size) (function) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:59: warning: Member kBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:69: warning: Member kPartialsPaddedStateCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:70: warning: Member kEigenDecompCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:72: warning: Member kScaleBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:74: warning: Member kPartialsSize (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:79: warning: Member kFlags (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:81: warning: Member realtypeMin (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:82: warning: Member scalingExponentThreshhold (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:84: warning: Member gEigenDecomposition (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:86: warning: Member gCategoryRates (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:87: warning: Member gPatternWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:89: warning: Member gCategoryWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:90: warning: Member gStateFrequencies (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:95: warning: Member gPartials (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:96: warning: Member gTipStates (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:97: warning: Member gScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:99: warning: Member gAutoScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:101: warning: Member gActiveScalingFactors (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:106: warning: Member gTransitionMatrices (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:108: warning: Member integrationTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:109: warning: Member firstDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:110: warning: Member secondDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:112: warning: Member outLogLikelihoodsTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:113: warning: Member outFirstDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:114: warning: Member outSecondDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:116: warning: Member ones (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:117: warning: Member zeros (variable) of class BeagleCPUImpl< BEAGLE_CPU_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:93: warning: Member getName() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:95: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:134: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:137: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:144: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:151: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:155: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:159: warning: Member getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:170: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:173: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:176: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:178: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:183: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:187: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:192: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:195: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:208: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:218: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:234: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:239: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:243: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:245: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:248: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:259: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:274: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:276: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:279: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:281: warning: Member block(void) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:98: warning: Member getPaddedPatternsModulus() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:292: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:299: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:305: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:311: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:318: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:335: warning: Member calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:345: warning: Member calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:357: warning: Member calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:364: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:371: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:378: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:385: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:390: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:393: warning: Member autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:397: warning: Member mallocAligned(size_t size) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:59: warning: Member kBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:69: warning: Member kPartialsPaddedStateCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:70: warning: Member kEigenDecompCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:72: warning: Member kScaleBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:74: warning: Member kPartialsSize (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:79: warning: Member kFlags (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:81: warning: Member realtypeMin (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:82: warning: Member scalingExponentThreshhold (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:84: warning: Member gEigenDecomposition (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:86: warning: Member gCategoryRates (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:87: warning: Member gPatternWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:89: warning: Member gCategoryWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:90: warning: Member gStateFrequencies (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:95: warning: Member gPartials (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:96: warning: Member gTipStates (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:97: warning: Member gScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:99: warning: Member gAutoScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:101: warning: Member gActiveScalingFactors (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:106: warning: Member gTransitionMatrices (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:108: warning: Member integrationTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:109: warning: Member firstDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:110: warning: Member secondDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:112: warning: Member outLogLikelihoodsTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:113: warning: Member outFirstDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:114: warning: Member outSecondDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:116: warning: Member ones (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:117: warning: Member zeros (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_FLOAT > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:167: warning: Member getName() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:169: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:134: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:137: warning: Member getInstanceDetails(BeagleInstanceDetails *returnInfo) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:144: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:151: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:155: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:159: warning: Member getPartials(int bufferIndex, int scaleBuffer, double *outPartials) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:170: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:173: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:176: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:178: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:183: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:187: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:192: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:195: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:208: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:218: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:234: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:239: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:243: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:245: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:248: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:259: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:274: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:276: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:279: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:281: warning: Member block(void) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:172: warning: Member getPaddedPatternsModulus() (function) of class beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:292: warning: Member calcStatesStates(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const int *states2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:299: warning: Member calcStatesPartials(REALTYPE *destP, const int *states1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:305: warning: Member calcPartialsPartials(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:311: warning: Member calcRootLogLikelihoods(const int bufferIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scaleBufferIndex, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:318: warning: Member calcRootLogLikelihoodsMulti(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scaleBufferIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:335: warning: Member calcEdgeLogLikelihoodsMulti(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:345: warning: Member calcEdgeLogLikelihoodsFirstDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:357: warning: Member calcEdgeLogLikelihoodsSecondDeriv(const int parentBufferIndex, const int childBufferIndex, const int probabilityIndex, const int firstDerivativeIndex, const int secondDerivativeIndex, const int categoryWeightsIndex, const int stateFrequenciesIndex, const int scalingFactorsIndex, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:364: warning: Member calcStatesStatesFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const int *child1States, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:371: warning: Member calcStatesPartialsFixedScaling(REALTYPE *destP, const int *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:378: warning: Member calcPartialsPartialsFixedScaling(REALTYPE *destP, const REALTYPE *child0States, const REALTYPE *child0TransMat, const REALTYPE *child1Partials, const REALTYPE *child1TransMat, const REALTYPE *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:385: warning: Member calcPartialsPartialsAutoScaling(REALTYPE *destP, const REALTYPE *partials1, const REALTYPE *matrices1, const REALTYPE *partials2, const REALTYPE *matrices2, int *activateScaling) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:390: warning: Member rescalePartials(REALTYPE *destP, REALTYPE *scaleFactors, REALTYPE *cumulativeScaleFactors, const int fillWithOnes) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:393: warning: Member autoRescalePartials(REALTYPE *destP, signed short *scaleFactors) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:397: warning: Member mallocAligned(size_t size) (function) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:59: warning: Member kBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:69: warning: Member kPartialsPaddedStateCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:70: warning: Member kEigenDecompCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:72: warning: Member kScaleBufferCount (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:74: warning: Member kPartialsSize (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:79: warning: Member kFlags (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:81: warning: Member realtypeMin (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:82: warning: Member scalingExponentThreshhold (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:84: warning: Member gEigenDecomposition (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:86: warning: Member gCategoryRates (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:87: warning: Member gPatternWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:89: warning: Member gCategoryWeights (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:90: warning: Member gStateFrequencies (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:95: warning: Member gPartials (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:96: warning: Member gTipStates (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:97: warning: Member gScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:99: warning: Member gAutoScaleBuffers (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:101: warning: Member gActiveScalingFactors (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:106: warning: Member gTransitionMatrices (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:108: warning: Member integrationTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:109: warning: Member firstDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:110: warning: Member secondDerivTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:112: warning: Member outLogLikelihoodsTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:113: warning: Member outFirstDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:114: warning: Member outSecondDerivativesTmp (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:116: warning: Member ones (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUImpl.h:117: warning: Member zeros (variable) of class BeagleCPUImpl< BEAGLE_CPU_SSE_DOUBLE > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:232: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) (function) of class beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:234: warning: Member getName() (function) of class beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.h:235: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp:620: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/BeagleCPUSSEImpl.hpp:633: warning: Member getFlags() (function) of class beagle::cpu::BeagleCPUSSEImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:43: warning: Member EigenDecomposition(int decompositionCount, int stateCount, int categoryCount, long flags) (function) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:62: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)=0 (function) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:77: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, const double *categoryRates, REALTYPE **transitionMatrices, int count)=0 (function) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:29: warning: Member gEigenValues (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:30: warning: Member kStateCount (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:31: warning: Member kEigenDecompCount (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:32: warning: Member kCategoryCount (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:33: warning: Member kFlags (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:34: warning: Member matrixTmp (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:35: warning: Member firstDerivTmp (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:36: warning: Member secondDerivTmp (variable) of class beagle::cpu::EigenDecomposition is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h:35: warning: Member EigenDecompositionCube(int decompositionCount, int stateCount, int categoryCount, long flags) (function) of class beagle::cpu::EigenDecompositionCube is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h:42: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class beagle::cpu::EigenDecompositionCube is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h:51: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, const double *categoryRates, REALTYPE **transitionMatrices, int count) (function) of class beagle::cpu::EigenDecompositionCube is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:43: warning: Member EigenDecomposition(int decompositionCount, int stateCount, int categoryCount, long flags) (function) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionCube.h:29: warning: Member gCMatrices (variable) of class beagle::cpu::EigenDecompositionCube is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:29: warning: Member gEigenValues (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:30: warning: Member kStateCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:31: warning: Member kEigenDecompCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:32: warning: Member kCategoryCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:33: warning: Member kFlags (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:34: warning: Member matrixTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:35: warning: Member firstDerivTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:36: warning: Member secondDerivTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. Generating code for file libhmsbeagle/CPU/EigenDecompositionSquare.h... Generating code for file libhmsbeagle/CPU/EigenDecompositionSquare.hpp... Generating code for file libhmsbeagle/CPU/Precision.h... Generating code for file libhmsbeagle/GPU/Precision.h... Generating code for file libhmsbeagle/CPU/SSEDefinitions.h... Generating code for file libhmsbeagle/GPU/BeagleGPUImpl.h... Generating code for file libhmsbeagle/GPU/BeagleGPUImpl.hpp... Generating code for file libhmsbeagle/GPU/CUDAPlugin.h... Generating code for file libhmsbeagle/GPU/GPUImplDefs.h... Generating code for file libhmsbeagle/GPU/GPUImplHelper.h... Generating code for file libhmsbeagle/GPU/GPUInterface.h... Generating code for file libhmsbeagle/GPU/KernelLauncher.h... Generating code for file libhmsbeagle/GPU/KernelResource.h... Generating code for file libhmsbeagle/GPU/OpenCLPlugin.h... Generating code for file libhmsbeagle/JNI/beagle_BeagleJNIWrapper.h... Generating code for file libhmsbeagle/platform.h... Generating code for file libhmsbeagle/plugin/BeaglePlugin.h... Generating code for file libhmsbeagle/plugin/LibtoolSharedLibrary.h... Generating code for file libhmsbeagle/plugin/Plugin.h... Generating code for file libhmsbeagle/plugin/SharedLibrary.h... Generating code for file libhmsbeagle/plugin/UnixSharedLibrary.h... Generating code for file libhmsbeagle/plugin/WinSharedLibrary.h... Generating file documentation... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound BeagleInstanceDetails... Generating docs for compound BeagleOperation... Generating docs for compound BeagleResource... Generating docs for compound BeagleResourceList... Generating docs for compound Dim3Int... Generating docs for compound FourTaxonExample... Generating docs for compound GPUInterface... Generating docs for compound KernelLauncher... Generating docs for compound KernelResource... Generating docs for compound VecUnion... Generating namespace index... Generating docs for namespace beagle Generating docs for compound beagle::Beagle... Generating docs for compound beagle::BeagleErrorCode... Generating docs for compound beagle::BeagleException... Generating docs for compound beagle::BeagleFactory... Generating docs for compound beagle::BeagleFlag... Generating docs for compound beagle::BeagleInfo... Generating docs for compound beagle::BeagleJNIImpl... Generating docs for compound beagle::BeagleJNIWrapper... Generating docs for compound beagle::DependencyAwareBeagleImpl... Generating docs for compound beagle::FourStateBeagleImpl... Generating docs for compound beagle::GeneralBeagleImpl... Generating docs for compound beagle::InstanceDetails... Generating docs for compound beagle::ResourceDetails... Generating docs for compound beagle::BeagleImpl... Generating docs for compound beagle::BeagleImplFactory... Generating docs for compound beagle::BeaglePlugin... Generating docs for compound beagle::cpu::BeagleCPU4StateImpl... Generating docs for compound beagle::cpu::BeagleCPU4StateImplFactory... Generating docs for compound beagle::cpu::BeagleCPU4StateSSEImpl... Generating docs for compound beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_FLOAT >... Generating docs for compound beagle::cpu::BeagleCPU4StateSSEImpl< BEAGLE_CPU_4_SSE_DOUBLE >... Generating docs for compound beagle::cpu::BeagleCPU4StateSSEImplFactory... Generating docs for compound beagle::cpu::BeagleCPUImpl... Generating docs for compound beagle::cpu::BeagleCPUImplFactory... Generating docs for compound beagle::cpu::BeagleCPUOpenMPPlugin... Generating docs for compound beagle::cpu::BeagleCPUPlugin... Generating docs for compound beagle::cpu::BeagleCPUSSEImpl... Generating docs for compound beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_FLOAT >... Generating docs for compound beagle::cpu::BeagleCPUSSEImpl< BEAGLE_CPU_SSE_DOUBLE >... Generating docs for compound beagle::cpu::BeagleCPUSSEImplFactory... Generating docs for compound beagle::cpu::BeagleCPUSSEPlugin... Generating docs for compound beagle::cpu::EigenDecomposition... Generating docs for compound beagle::cpu::EigenDecompositionCube... /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:36: warning: Member EigenDecompositionSquare(int decompositionCount, int stateCount, int categoryCount, long flags) (function) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:43: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:52: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, const double *categoryRates, REALTYPE **transitionMatrices, int count) (function) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:43: warning: Member EigenDecomposition(int decompositionCount, int stateCount, int categoryCount, long flags) (function) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:27: warning: Member gEMatrices (variable) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:28: warning: Member gIMatrices (variable) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:29: warning: Member isComplex (variable) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecompositionSquare.h:30: warning: Member kEigenValuesSize (variable) of class beagle::cpu::EigenDecompositionSquare is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:29: warning: Member gEigenValues (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:30: warning: Member kStateCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:31: warning: Member kEigenDecompCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:32: warning: Member kCategoryCount (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:33: warning: Member kFlags (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:34: warning: Member matrixTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:35: warning: Member firstDerivTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/CPU/EigenDecomposition.h:36: warning: Member secondDerivTmp (variable) of class EigenDecomposition< BEAGLE_CPU_EIGEN_GENERIC > is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:162: warning: Member createInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenDecompositionCount, int matrixCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:164: warning: Member getInstanceDetails(BeagleInstanceDetails *retunInfo) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:167: warning: Member setTipStates(int tipIndex, const int *inStates) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:170: warning: Member setTipPartials(int tipIndex, const double *inPartials) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:173: warning: Member setPartials(int bufferIndex, const double *inPartials) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:177: warning: Member getPartials(int bufferIndex, int scaleIndex, double *outPartials) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:182: warning: Member setEigenDecomposition(int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:185: warning: Member setStateFrequencies(int stateFrequenciesIndex, const double *inStateFrequencies) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:188: warning: Member setCategoryWeights(int categoryWeightsIndex, const double *inCategoryWeights) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:190: warning: Member setPatternWeights(const double *inPatternWeights) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:193: warning: Member setCategoryRates(const double *inCategoryRates) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:197: warning: Member setTransitionMatrix(int matrixIndex, const double *inMatrix, double paddedValue) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:202: warning: Member setTransitionMatrices(const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:205: warning: Member getTransitionMatrix(int matrixIndex, double *outMatrix) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:212: warning: Member updateTransitionMatrices(int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:216: warning: Member updatePartials(const int *operations, int operationCount, int cumulativeScalingIndex) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:219: warning: Member waitForPartials(const int *destinationPartials, int destinationPartialsCount) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:223: warning: Member accumulateScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:227: warning: Member removeScaleFactors(const int *scalingIndices, int count, int cumulativeScalingIndex) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:229: warning: Member resetScaleFactors(int cumulativeScalingIndex) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:232: warning: Member copyScaleFactors(int destScalingIndex, int srcScalingIndex) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:239: warning: Member calculateRootLogLikelihoods(const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:252: warning: Member calculateEdgeLogLikelihoods(const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:254: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:257: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:1932: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:1954: warning: Member getSiteLogLikelihoods(double *outLogLikelihoods) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:1976: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:2008: warning: Member getSiteDerivatives(double *outFirstDerivatives, double *outSecondDerivatives) (function) of class beagle::gpu::BeagleGPUImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/BeagleImpl.h:153: warning: Member resourceNumber (variable) of class beagle::BeagleImpl is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:279: warning: Member createImpl(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long requirementFlags, int *errorCode) (function) of class beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:281: warning: Member getName() (function) of class beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.h:282: warning: Member getFlags() (function) of class beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:2081: warning: Member getName() (function) of class beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/GPU/BeagleGPUImpl.hpp:2086: warning: Member getName() (function) of class beagle::gpu::BeagleGPUImplFactory is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:36: warning: Member Plugin(const char *plugin_name, const char *plugin_type) (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:38: warning: Member pluginName() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:39: warning: Member pluginType() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:41: warning: Member getBeagleFactories() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:42: warning: Member getBeagleResources() const (function) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:45: warning: Member beagleFactories (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:46: warning: Member beagleResources (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:47: warning: Member m_plugin_name (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:48: warning: Member m_plugin_type (variable) of class beagle::plugin::Plugin is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:59: warning: Member findPlugin(const char *name) (function) of class beagle::plugin::PluginManager is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/Plugin.h:56: warning: Member instance() (function) of class beagle::plugin::PluginManager is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:23: warning: Member SharedLibraryException(const char *error) (function) of class beagle::plugin::SharedLibraryException is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:24: warning: Member getError() const (function) of class beagle::plugin::SharedLibraryException is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:34: warning: Member findSymbol(const char *name)=0 (function) of class beagle::plugin::SharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:32: warning: Member openSharedLibrary(const char *name) (function) of class beagle::plugin::SharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.h:29: warning: Member UnixSharedLibrary(const char *name) (function) of class beagle::plugin::UnixSharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/UnixSharedLibrary.h:32: warning: Member findSymbol(const char *name) (function) of class beagle::plugin::UnixSharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:32: warning: Member openSharedLibrary(const char *name) (function) of class beagle::plugin::SharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.h:29: warning: Member WinSharedLibrary(const char *name) (function) of class beagle::plugin::WinSharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/WinSharedLibrary.h:33: warning: Member findSymbol(const char *name) (function) of class beagle::plugin::WinSharedLibrary is not documented. /«PKGBUILDDIR»/libhmsbeagle/plugin/SharedLibrary.h:32: warning: Member openSharedLibrary(const char *name) (function) of class beagle::plugin::SharedLibrary is not documented. Generating docs for compound beagle::cpu::EigenDecompositionSquare... Generating docs for compound beagle::gpu::BeagleGPUImpl... Generating docs for compound beagle::gpu::BeagleGPUImplFactory... Generating docs for compound beagle::gpu::CUDAPlugin... Generating docs for compound beagle::gpu::OpenCLPlugin... Generating docs for compound beagle::plugin::Plugin... Generating docs for compound beagle::plugin::PluginManager... Generating docs for compound beagle::plugin::SharedLibraryException... Generating docs for compound beagle::plugin::SharedLibrary... Generating docs for compound beagle::plugin::UnixSharedLibrary... Generating docs for compound beagle::plugin::WinSharedLibrary... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... symbol cache used 1599/65536 hits=84557 misses=1599 lookup cache used 1561/65536 hits=12464 misses=1634 finished... make[2]: Leaving directory `/«PKGBUILDDIR»' ant Buildfile: /«PKGBUILDDIR»/build.xml init: [mkdir] Created dir: /«PKGBUILDDIR»/build [mkdir] Created dir: /«PKGBUILDDIR»/lib compile: [javac] /«PKGBUILDDIR»/build.xml:37: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 13 source files to /«PKGBUILDDIR»/build dist: [jar] Building jar: /«PKGBUILDDIR»/lib/beagle.jar BUILD SUCCESSFUL Total time: 10 seconds make[1]: Leaving directory `/«PKGBUILDDIR»' jh_build -a dh_auto_test -a make[1]: Entering directory `/«PKGBUILDDIR»' Making check in libhmsbeagle make[2]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' Making check in GPU make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make check-recursive make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making check in kernels make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make check-am make[6]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[6]: Nothing to be done for `check-am'. make[6]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[5]: Nothing to be done for `check-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making check in CPU make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' Making check in plugin make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[3]: Nothing to be done for `check'. make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' make[3]: Nothing to be done for `check-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' make[2]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' Making check in examples make[2]: Entering directory `/«PKGBUILDDIR»/examples' Making check in genomictest make[3]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' make genomictest genomictest.sh make[4]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o genomictest.o genomictest.cpp g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o linalg.o linalg.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o genomictest genomictest.o linalg.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/genomictest genomictest.o linalg.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl echo './genomictest' > genomictest.sh echo './genomictest --states 64 --sites 100 --taxa 10' >> genomictest.sh chmod +x genomictest.sh make[4]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' Simulating genomic DNA with 16 taxa and 10000 site patterns (5 reps) Unable to load CPU plugin! Please check for proper libhmsbeagle installation. Simulating genomic 64-state data with 10 taxa and 100 site patterns (5 reps) Unable to load CPU plugin! Please check for proper libhmsbeagle installation. PASS: genomictest.sh ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' Making check in tinytest make[3]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' make tinytest make[4]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o tinytest.o tinytest.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o tinytest tinytest.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/tinytest tinytest.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl make[4]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' Available resources: Resource 0: Name : CPU Desc : Flags: PROCESSOR_CPU PRECISION_DOUBLE PRECISION_SINGLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALING_DYNAMIC SCALERS_RAW SCALERS_LOG VECTOR_NONE THREADING_NONE Using resource 0: Rsrc Name : CPU Impl Name : CPU-4State-Double Impl Desc : none Flags: PROCESSOR_CPU PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE logL = -1498.89812 (PAUP logL = -1498.89812) sumLogL = -1498.89812 PASS: tinytest ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' Making check in oddstatetest make[3]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' make oddstatetest make[4]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o oddstatetest.o oddstatetest.cpp oddstatetest.cpp: In function 'int main(int, const char**)': oddstatetest.cpp:444:36: warning: passing NULL to non-pointer argument 1 of 'void runBeagle(int, int, int, int, bool, bool, int)' [-Wconversion-null] /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o oddstatetest oddstatetest.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/oddstatetest oddstatetest.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl make[4]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' Simulating genomic 5-state data with 29 taxa and 10000 site patterns Using resource 0: Rsrc Name : CPU Impl Name : CPU-Double logL = -636971.54276 Took 0.001709 and 2.14418 seconds PASS: oddstatetest ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' Making check in complextest make[3]: Entering directory `/«PKGBUILDDIR»/examples/complextest' make complextest make[4]: Entering directory `/«PKGBUILDDIR»/examples/complextest' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o complextest.o complextest.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o complextest complextest.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/complextest complextest.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl make[4]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/complextest' Using resource 0: Rsrc Name : CPU Impl Name : CPU-4State-Double Impl Desc : none logL = -1665.38544 (BEAST = -1665.38544) PASS: complextest ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' Making check in fourtaxon make[3]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' make fourtaxon fourtaxonrun.sh make[4]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o fourtaxon.o fourtaxon.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o fourtaxon fourtaxon.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/fourtaxon fourtaxon.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl echo './fourtaxon --niters 4 --filename ./fourtaxon.dat' > fourtaxonrun.sh chmod +x fourtaxonrun.sh make[4]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' niters option: 4 niters = 4 quiet = false number of iterations = 4 data file name = ./fourtaxon.dat Using resource 0: Rsrc Name : CPU Impl Name : CPU-4State-Double iter log-likelihood tree length 0 -4636.84054 0.05000 1 -4208.23102 0.25600 2 -4036.79286 0.39883 3 -3998.27704 0.47025 4 -3988.78135 0.51592 PASS: fourtaxonrun.sh ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' Making check in matrixtest make[3]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' make matrixtest make[4]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/usr/lib/jvm/java-6-openjdk-armhf/include -I/usr/lib/jvm/java-6-openjdk-armhf/include/linux -O3 -c -o matrixtest.o matrixtest.cpp /bin/bash ../../libtool --tag=CXX --mode=link g++ -O3 -o matrixtest matrixtest.o ../../libhmsbeagle/libhmsbeagle.la -ldl libtool: link: g++ -O3 -o .libs/matrixtest matrixtest.o ../../libhmsbeagle/.libs/libhmsbeagle.so -ldl make[4]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make check-TESTS make[4]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' Using resource 0: Rsrc Name : CPU Impl : CPU-4State-Double Impl Desc : none logL = -1574.63623 (PAUP = -1574.63623) PASS: matrixtest ============= 1 test passed ============= make[4]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make[3]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make[3]: Entering directory `/«PKGBUILDDIR»/examples' make[3]: Nothing to be done for `check-am'. make[3]: Leaving directory `/«PKGBUILDDIR»/examples' make[2]: Leaving directory `/«PKGBUILDDIR»/examples' make[2]: Entering directory `/«PKGBUILDDIR»' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/«PKGBUILDDIR»' make[1]: Leaving directory `/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch --with autoreconf --with javahelper dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory `/«PKGBUILDDIR»' dh_auto_install make[2]: Entering directory `/«PKGBUILDDIR»' Making install in libhmsbeagle make[3]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' Making install in GPU make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make install-recursive make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making install in kernels make[6]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make install-am make[7]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[8]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[8]: Nothing to be done for `install-exec-am'. make[8]: Nothing to be done for `install-data-am'. make[8]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[7]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[6]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU/kernels' make[6]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[7]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[7]: Nothing to be done for `install-data-am'. make[7]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[6]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/GPU' Making install in CPU make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libhmsbeagle-cpu.la '/«PKGBUILDDIR»/debian/tmp/usr/lib' libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu.so.1.0.0 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-cpu.so.1.0.0 libtool: install: (cd /«PKGBUILDDIR»/debian/tmp/usr/lib && { ln -s -f libhmsbeagle-cpu.so.1.0.0 libhmsbeagle-cpu.so.1 || { rm -f libhmsbeagle-cpu.so.1 && ln -s libhmsbeagle-cpu.so.1.0.0 libhmsbeagle-cpu.so.1; }; }) libtool: install: (cd /«PKGBUILDDIR»/debian/tmp/usr/lib && { ln -s -f libhmsbeagle-cpu.so.1.0.0 libhmsbeagle-cpu.so || { rm -f libhmsbeagle-cpu.so && ln -s libhmsbeagle-cpu.so.1.0.0 libhmsbeagle-cpu.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-cpu.la libtool: install: /usr/bin/install -c .libs/libhmsbeagle-cpu.a /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-cpu.a libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-cpu.a libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-cpu.a libtool: install: warning: remember to run `libtool --finish /usr/lib' make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/CPU' Making install in plugin make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle/plugin' make[4]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' make[5]: Entering directory `/«PKGBUILDDIR»/libhmsbeagle' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c libhmsbeagle.la libhmsbeagle-jni.la '/«PKGBUILDDIR»/debian/tmp/usr/lib' libtool: install: /usr/bin/install -c .libs/libhmsbeagle.so.1.0.0 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle.so.1.0.0 libtool: install: (cd /«PKGBUILDDIR»/debian/tmp/usr/lib && { ln -s -f libhmsbeagle.so.1.0.0 libhmsbeagle.so.1 || { rm -f libhmsbeagle.so.1 && ln -s libhmsbeagle.so.1.0.0 libhmsbeagle.so.1; }; }) libtool: install: (cd /«PKGBUILDDIR»/debian/tmp/usr/lib && { ln -s -f libhmsbeagle.so.1.0.0 libhmsbeagle.so || { rm -f libhmsbeagle.so && ln -s libhmsbeagle.so.1.0.0 libhmsbeagle.so; }; }) libtool: install: /usr/bin/install -c .libs/libhmsbeagle.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle.la libtool: install: warning: relinking `libhmsbeagle-jni.la' libtool: install: (cd /«PKGBUILDDIR»/libhmsbeagle; /bin/bash /«PKGBUILDDIR»/libtool --tag CXX --mode=relink g++ -O3 -module -avoid-version -o libhmsbeagle-jni.la -rpath /usr/lib libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -lhmsbeagle -ldl -inst-prefix-dir /«PKGBUILDDIR»/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtbeginS.o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o -L/«PKGBUILDDIR»/debian/tmp/usr/lib -L/usr/lib -lhmsbeagle -ldl -L/usr/lib/gcc/arm-linux-gnueabihf/4.6 -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/4.6/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crtn.o -O3 -Wl,-soname -Wl,libhmsbeagle-jni.so -o .libs/libhmsbeagle-jni.so libtool: install: /usr/bin/install -c .libs/libhmsbeagle-jni.soT /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-jni.so libtool: install: /usr/bin/install -c .libs/libhmsbeagle-jni.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-jni.la libtool: install: /usr/bin/install -c .libs/libhmsbeagle.a /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle.a libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle.a libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle.a libtool: install: /usr/bin/install -c .libs/libhmsbeagle-jni.a /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-jni.a libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-jni.a libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/libhmsbeagle-jni.a libtool: install: warning: remember to run `libtool --finish /usr/lib' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/libhmsbeagle-1/libhmsbeagle' /usr/bin/install -c -m 644 beagle.h platform.h '/«PKGBUILDDIR»/debian/tmp/usr/include/libhmsbeagle-1/libhmsbeagle' make[5]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' make[4]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' make[3]: Leaving directory `/«PKGBUILDDIR»/libhmsbeagle' Making install in examples make[3]: Entering directory `/«PKGBUILDDIR»/examples' Making install in genomictest make[4]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' make[5]: Entering directory `/«PKGBUILDDIR»/examples/genomictest' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/genomictest' Making install in tinytest make[4]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' make[5]: Entering directory `/«PKGBUILDDIR»/examples/tinytest' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/tinytest' Making install in oddstatetest make[4]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' make[5]: Entering directory `/«PKGBUILDDIR»/examples/oddstatetest' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/oddstatetest' Making install in complextest make[4]: Entering directory `/«PKGBUILDDIR»/examples/complextest' make[5]: Entering directory `/«PKGBUILDDIR»/examples/complextest' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/complextest' Making install in fourtaxon make[4]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' make[5]: Entering directory `/«PKGBUILDDIR»/examples/fourtaxon' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/fourtaxon' Making install in matrixtest make[4]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' make[5]: Entering directory `/«PKGBUILDDIR»/examples/matrixtest' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make[4]: Leaving directory `/«PKGBUILDDIR»/examples/matrixtest' make[4]: Entering directory `/«PKGBUILDDIR»/examples' make[5]: Entering directory `/«PKGBUILDDIR»/examples' make[5]: Nothing to be done for `install-exec-am'. make[5]: Nothing to be done for `install-data-am'. make[5]: Leaving directory `/«PKGBUILDDIR»/examples' make[4]: Leaving directory `/«PKGBUILDDIR»/examples' make[3]: Leaving directory `/«PKGBUILDDIR»/examples' make[3]: Entering directory `/«PKGBUILDDIR»' make[4]: Entering directory `/«PKGBUILDDIR»' make[4]: Nothing to be done for `install-exec-am'. /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib/pkgconfig' /usr/bin/install -c -m 644 hmsbeagle-1.pc '/«PKGBUILDDIR»/debian/tmp/usr/lib/pkgconfig' make[4]: Leaving directory `/«PKGBUILDDIR»' make[3]: Leaving directory `/«PKGBUILDDIR»' make[2]: Leaving directory `/«PKGBUILDDIR»' #Shunt jni .so to jni directory. mkdir -p -m755 debian/tmp/usr/lib/jni mv debian/tmp/usr/lib/*jni.* debian/tmp/usr/lib/jni # will be removed later anyway (see below) # sed -i "s/libdir='\/usr\/lib'/libdir='\/usr\/lib\/jni'/" debian/tmp/usr/lib/jni/libhmsbeagle-jni.la # Remove unneeded *.la files according to # http://lists.debian.org/debian-devel/2009/08/msg00783.html # Release goal: Getting rid of unneeded *.la / emptying dependency_libs find debian -name "*.la" -delete make[1]: Leaving directory `/«PKGBUILDDIR»' dh_install -a jh_installjavadoc -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a debian/rules override_dh_installman make[1]: Entering directory `/«PKGBUILDDIR»' # Fix whatis entry of doxygen generated man pages if possible find doc/man/man3 -name "*.3" -exec sed -i "/^.SH NAME/{;N;N;N;s/\(.SH NAME\)[[:space:]]*\([A-Za-z].*-\).*.PP[[:space:]]*\([A-Za-z].*\)/\1\n\2 \3/g;}" \{\} \; dh_installman make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a jh_installlibs -a jh_classpath -a jh_manifest -a jh_exec -a jh_depends -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/libhmsbeagle1/usr/lib/jni/libhmsbeagle-jni.so contains an unresolvable reference to symbol __aeabi_unwind_cpp_pr1@GCC_3.5: it's probably a plugin. dpkg-shlibdeps: warning: symbol __aeabi_unwind_cpp_pr1@GCC_3.5 used by debian/libhmsbeagle1/usr/lib/libhmsbeagle.so.1.0.0 found in none of the libraries. dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libhmsbeagle-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: Depends field of package libhmsbeagle-java: unknown substitution variable ${shlibs:Depends} dh_md5sums -a dh_builddeb -a dpkg-deb: building package `libhmsbeagle-dev' in `../libhmsbeagle-dev_1.0-6_armhf.deb'. dpkg-deb: building package `libhmsbeagle1' in `../libhmsbeagle1_1.0-6_armhf.deb'. dpkg-deb: building package `libhmsbeagle-java' in `../libhmsbeagle-java_1.0-6_armhf.deb'. dpkg-genchanges -B -mbuildd >../libhmsbeagle_1.0-6_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build libhmsbeagle-1.0 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120605-1109 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ libhmsbeagle_1.0-6_armhf.changes: ───────────────────────────────── Format: 1.8 Date: Wed, 09 May 2012 15:08:00 +0200 Source: libhmsbeagle Binary: libhmsbeagle-dev libhmsbeagle1 libhmsbeagle-java Architecture: armhf Version: 1.0-6 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Andreas Tille Description: libhmsbeagle-dev - High-performance lib for Bayesian and Maximum Likelihood phylogen libhmsbeagle-java - High-performance lib for Bayesian and Maximum Likelihood phylogen libhmsbeagle1 - High-performance lib for Bayesian and Maximum Likelihood phylogen Closes: 672015 Changes: libhmsbeagle (1.0-6) unstable; urgency=low . * debian/upstream: - Make authors BibTeX compliant - Add some publication info (volume, number, pages) * debian/get-orig-source: Try harder to get reproducible tarballs * debian/patches/gcc-4.7.patch: Fix gcc 4.7 build issue Closes: #672015 Checksums-Sha1: 68601e4e442fe3c430ed7ecb34a3a9665e6985ec 534778 libhmsbeagle-dev_1.0-6_armhf.deb ac64da72b20bd9c91ec9c9ab86d5656768cf42d4 64020 libhmsbeagle1_1.0-6_armhf.deb fc75dd86b9fcc9810ec239af530dc29efc6fd8c3 20902 libhmsbeagle-java_1.0-6_armhf.deb Checksums-Sha256: a194841bbe8f8fce53a54ba8776e9a2bcfa661235dd3fa43de5a2887b75def42 534778 libhmsbeagle-dev_1.0-6_armhf.deb f5946f68e3e673cf8679ab66f125c7047f5558288213512fb2787b37e0dbaf3b 64020 libhmsbeagle1_1.0-6_armhf.deb b5fd3e21772c177745055c645ffccef36e91795ac645028e64454af0607b8dfd 20902 libhmsbeagle-java_1.0-6_armhf.deb Files: a9f629d86a8691929eba95f0fdec98ac 534778 libdevel extra libhmsbeagle-dev_1.0-6_armhf.deb 4aaf55932bf4b1b81097bed530ebbf15 64020 libs extra libhmsbeagle1_1.0-6_armhf.deb 922449658ab60693dc7f4a8a91ab735f 20902 java extra libhmsbeagle-java_1.0-6_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ libhmsbeagle-dev_1.0-6_armhf.deb ──────────────────────────────── new debian package, version 2.0. size 534778 bytes: control archive= 10001 bytes. 1216 bytes, 26 lines control 34169 bytes, 320 lines md5sums Package: libhmsbeagle-dev Source: libhmsbeagle Version: 1.0-6 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 3752 Depends: libhmsbeagle1 (= 1.0-6) Section: libdevel Priority: extra Homepage: http://code.google.com/p/beagle-lib Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs. . The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. . The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units. . This package contains development files needed to build against Beagle library. drwxr-xr-x root/root 0 2012-06-05 11:08 ./ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/include/ drwxr-xr-x root/root 0 2012-06-05 11:07 ./usr/include/libhmsbeagle-1/ drwxr-xr-x root/root 0 2012-06-05 11:07 ./usr/include/libhmsbeagle-1/libhmsbeagle/ -rw-r--r-- root/root 30386 2012-06-05 11:07 ./usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h -rw-r--r-- root/root 1629 2012-06-05 11:07 ./usr/include/libhmsbeagle-1/libhmsbeagle/platform.h drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/lintian/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 5030 2012-01-19 13:29 ./usr/share/lintian/overrides/libhmsbeagle-dev drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/man/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/man/man3/ -rw-r--r-- root/root 209 2012-06-05 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51111 2012-06-05 11:06 ./usr/share/doc/libhmsbeagle-dev/html/interfacebeagle_1_1_beagle.html -rw-r--r-- root/root 3983 2012-06-05 11:06 ./usr/share/doc/libhmsbeagle-dev/html/classbeagle_1_1_beagle_exception-members.html drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/lib/ -rw-r--r-- root/root 232364 2012-06-05 11:08 ./usr/lib/libhmsbeagle-cpu.a -rw-r--r-- root/root 44208 2012-06-05 11:08 ./usr/lib/libhmsbeagle.a drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/lib/pkgconfig/ -rw-r--r-- root/root 268 2012-06-05 11:08 ./usr/lib/pkgconfig/hmsbeagle-1.pc lrwxrwxrwx root/root 0 2012-06-05 11:08 ./usr/lib/libhmsbeagle-cpu.so -> libhmsbeagle-cpu.so.1.0.0 lrwxrwxrwx root/root 0 2012-06-05 11:08 ./usr/lib/libhmsbeagle.so -> libhmsbeagle.so.1.0.0 libhmsbeagle1_1.0-6_armhf.deb ───────────────────────────── new debian package, version 2.0. size 64020 bytes: control archive= 1177 bytes. 1162 bytes, 24 lines control 352 bytes, 5 lines md5sums 135 bytes, 7 lines * postinst #!/bin/sh 132 bytes, 7 lines * postrm #!/bin/sh 93 bytes, 3 lines shlibs Package: libhmsbeagle1 Source: libhmsbeagle Version: 1.0-6 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 185 Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.6) Section: libs Priority: extra Homepage: http://code.google.com/p/beagle-lib Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs. . The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. . The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units. drwxr-xr-x root/root 0 2012-06-05 11:08 ./ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/doc/libhmsbeagle1/ -rw-r--r-- root/root 1250 2012-05-25 05:38 ./usr/share/doc/libhmsbeagle1/changelog.Debian.gz -rw-r--r-- root/root 1262 2012-03-05 01:09 ./usr/share/doc/libhmsbeagle1/copyright drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/lib/ -rw-r--r-- root/root 29384 2012-06-05 11:08 ./usr/lib/libhmsbeagle.so.1.0.0 drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/lib/jni/ -rw-r--r-- root/root 12976 2012-06-05 11:08 ./usr/lib/jni/libhmsbeagle-jni.so -rw-r--r-- root/root 110736 2012-06-05 11:08 ./usr/lib/libhmsbeagle-cpu.so.1.0.0 lrwxrwxrwx root/root 0 2012-06-05 11:08 ./usr/lib/libhmsbeagle-cpu.so.1 -> libhmsbeagle-cpu.so.1.0.0 lrwxrwxrwx root/root 0 2012-06-05 11:08 ./usr/lib/libhmsbeagle.so.1 -> libhmsbeagle.so.1.0.0 libhmsbeagle-java_1.0-6_armhf.deb ───────────────────────────────── new debian package, version 2.0. size 20902 bytes: control archive= 903 bytes. 1140 bytes, 25 lines control 226 bytes, 3 lines md5sums Package: libhmsbeagle-java Source: libhmsbeagle Version: 1.0-6 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 49 Section: java Priority: extra Homepage: http://code.google.com/p/beagle-lib Description: High-performance lib for Bayesian and Maximum Likelihood phylogenetics BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs. . The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. . The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units. . This package contains the Java interface. drwxr-xr-x root/root 0 2012-06-05 11:08 ./ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/java/ -rw-r--r-- root/root 18581 2012-06-05 11:08 ./usr/share/java/beagle-1.0.jar drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-06-05 11:08 ./usr/share/doc/libhmsbeagle-java/ -rw-r--r-- root/root 1250 2012-05-25 05:38 ./usr/share/doc/libhmsbeagle-java/changelog.Debian.gz -rw-r--r-- root/root 1262 2012-03-05 01:09 ./usr/share/doc/libhmsbeagle-java/copyright lrwxrwxrwx root/root 0 2012-06-05 11:08 ./usr/share/java/beagle.jar -> beagle-1.0.jar ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ant* autoconf* automake* autotools-dev* bsdmainutils* ca-certificates* ca-certificates-java* dctrl-tools* debhelper* devscripts* dh-autoreconf* doxygen* file* fontconfig* fontconfig-config* gconf-service* gconf2-common* gettext* gettext-base* groff-base* html2text* intltool-debian* java-common* javahelper* libarchive-zip-perl* libasound2* libasyncns0* libatk-wrapper-java* libatk-wrapper-java-jni* libatk1.0-0* libatk1.0-data* libavahi-client3* libavahi-common-data* libavahi-common3* libcairo2* libcap2* libcroco3* libcups2* libdatrie1* libdbus-1-3* libdbus-glib-1-2* libexpat1* libffi5* libflac8* libfontconfig1* libfreetype6* libgconf-2-4* libgcrypt11* libgdk-pixbuf2.0-0* libgdk-pixbuf2.0-common* libgif4* libglib2.0-0* libgnutls26* libgpg-error0* libgssapi-krb5-2* libgtk2.0-0* libgtk2.0-common* libice6* libjasper1* libjbig0* libjpeg8* libjson0* libk5crypto3* libkeyutils1* libkrb5-3* libkrb5support0* libldap-2.4-2* libmagic1* libnspr4* libnss3* libnss3-1d* libogg0* libp11-kit0* libpango1.0-0* libpcre3* libpcsclite1* libpipeline1* libpixman-1-0* libpng12-0* libpulse0* libsasl2-2* libsm6* libsndfile1* libsqlite3-0* libssl1.0.0* libtasn1-3* libthai-data* libthai0* libtiff4* libtool* libunistring0* libvorbis0a* libvorbisenc2* libwrap0* libx11-6* libx11-data* libx11-xcb1* libxau6* libxcb-render0* libxcb-shm0* libxcb1* libxcomposite1* libxcursor1* libxdamage1* libxdmcp6* libxerces2-java* libxext6* libxfixes3* libxft2* libxi6* libxinerama1* libxml-commons-external-java* libxml-commons-resolver1.1-java* libxml2* libxrandr2* libxrender1* libxtst6* m4* man-db* mime-support* openjdk-6-jdk* openjdk-6-jre* openjdk-6-jre-headless* openjdk-6-jre-lib* openssl* po-debconf* python* python-minimal* python2.7* python2.7-minimal* sbuild-build-depends-core-dummy* sbuild-build-depends-libhmsbeagle-dummy* shared-mime-info* ttf-dejavu-core* tzdata-java* x11-common* 0 upgraded, 0 newly installed, 136 to remove and 2 not upgraded. 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Removing tzdata-java ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 20068 Build-Time: 504 Distribution: testing Install-Time: 263 Job: libhmsbeagle_1.0-6 Package: libhmsbeagle Package-Time: 785 Source-Version: 1.0-6 Space: 20068 Status: successful Version: 1.0-6 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120605-1109 Build needed 00:13:05, 20068k disc space