RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 3.2.0-1415-omap4 #20-Ubuntu SMP PREEMPT Mon Jun 18 19:03:59 UTC 2012 armv7l Buildd toolchain package versions: launchpad-buildd_114-0~53~0.IS.08.04 python-lpbuildd_114-0~53~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 1 Aug 12:21:22 ntpdate[24758]: adjust time server 10.211.37.1 offset 0.002320 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2', '/home/buildd/filecache-default/bd8d7f780b59f98d54682530582a91ef731bc9b2'] Unpacking chroot for build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2'] Mounting chroot for build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2', 'deb http://ftpmaster.internal/ubuntu quantal main restricted universe multiverse'] Overriding sources.list in build-38f5e3dc2ee43462f26db802c1d4ecab2752b5e2 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2', 'armhf'] Updating debian chroot for build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2 Ign http://ftpmaster.internal quantal InRelease Get:1 http://ftpmaster.internal quantal Release.gpg [198 B] Get:2 http://ftpmaster.internal quantal Release [49.6 kB] Get:3 http://ftpmaster.internal quantal/main armhf Packages [1136 kB] Get:4 http://ftpmaster.internal quantal/restricted armhf Packages [1103 B] Get:5 http://ftpmaster.internal quantal/universe armhf Packages [5179 kB] Get:6 http://ftpmaster.internal quantal/multiverse armhf Packages [110 kB] Get:7 http://ftpmaster.internal quantal/main Translation-en [659 kB] Get:8 http://ftpmaster.internal quantal/multiverse Translation-en [97.2 kB] Get:9 http://ftpmaster.internal quantal/restricted Translation-en [2401 B] Get:10 http://ftpmaster.internal quantal/universe Translation-en [3671 kB] Fetched 10.9 MB in 25s (421 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: gnupg gpgv initscripts libglib2.0-0 libldap-2.4-2 libp11-kit0 libprocps0 linux-libc-dev procps python2.7-minimal sysv-rc sysvinit-utils tzdata 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5348 kB of archives. After this operation, 2048 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! libglib2.0-0 libprocps0 libldap-2.4-2 libp11-kit0 gpgv gnupg tzdata sysvinit-utils sysv-rc initscripts procps python2.7-minimal linux-libc-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ quantal/main libglib2.0-0 armhf 2.33.6-1 [1048 kB] Get:2 http://ftpmaster.internal/ubuntu/ quantal/main libprocps0 armhf 1:3.3.3-2ubuntu3 [32.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ quantal/main libldap-2.4-2 armhf 2.4.31-1ubuntu1 [153 kB] Get:4 http://ftpmaster.internal/ubuntu/ quantal/main libp11-kit0 armhf 0.13-1 [30.3 kB] Get:5 http://ftpmaster.internal/ubuntu/ quantal/main gpgv armhf 1.4.11-3ubuntu3 [152 kB] Get:6 http://ftpmaster.internal/ubuntu/ quantal/main gnupg armhf 1.4.11-3ubuntu3 [714 kB] Get:7 http://ftpmaster.internal/ubuntu/ quantal/main tzdata all 2012d-1 [459 kB] Get:8 http://ftpmaster.internal/ubuntu/ quantal/main sysvinit-utils armhf 2.88dsf-13.10ubuntu13 [53.5 kB] Get:9 http://ftpmaster.internal/ubuntu/ quantal/main sysv-rc all 2.88dsf-13.10ubuntu13 [44.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ quantal/main initscripts armhf 2.88dsf-13.10ubuntu13 [27.9 kB] Get:11 http://ftpmaster.internal/ubuntu/ quantal/main procps armhf 1:3.3.3-2ubuntu3 [218 kB] Get:12 http://ftpmaster.internal/ubuntu/ quantal/main python2.7-minimal armhf 2.7.3-0ubuntu4 [1561 kB] Get:13 http://ftpmaster.internal/ubuntu/ quantal/main linux-libc-dev armhf 3.5.0-7.7 [854 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5348 kB in 1s (3882 kB/s) (Reading database ... 12182 files and directories currently installed.) Preparing to replace libglib2.0-0:armhf 2.33.3-2 (using .../libglib2.0-0_2.33.6-1_armhf.deb) ... Unpacking replacement libglib2.0-0:armhf ... Preparing to replace libprocps0:armhf 1:3.3.3-2ubuntu2 (using .../libprocps0_1%3a3.3.3-2ubuntu3_armhf.deb) ... Unpacking replacement libprocps0:armhf ... Preparing to replace libldap-2.4-2:armhf 2.4.28-1.1ubuntu4 (using .../libldap-2.4-2_2.4.31-1ubuntu1_armhf.deb) ... Unpacking replacement libldap-2.4-2:armhf ... Preparing to replace libp11-kit0:armhf 0.12-3ubuntu1 (using .../libp11-kit0_0.13-1_armhf.deb) ... Unpacking replacement libp11-kit0:armhf ... Preparing to replace gpgv 1.4.11-3ubuntu2 (using .../gpgv_1.4.11-3ubuntu3_armhf.deb) ... Unpacking replacement gpgv ... Setting up gpgv (1.4.11-3ubuntu3) ... (Reading database ... 12181 files and directories currently installed.) Preparing to replace gnupg 1.4.11-3ubuntu2 (using .../gnupg_1.4.11-3ubuntu3_armhf.deb) ... Unpacking replacement gnupg ... Setting up gnupg (1.4.11-3ubuntu3) ... (Reading database ... 12181 files and directories currently installed.) Preparing to replace tzdata 2012c-1 (using .../tzdata_2012d-1_all.deb) ... Unpacking replacement tzdata ... Setting up tzdata (2012d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Aug 1 12:23:16 UTC 2012. Universal Time is now: Wed Aug 1 12:23:16 UTC 2012. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 12181 files and directories currently installed.) Preparing to replace sysvinit-utils 2.88dsf-13.10ubuntu11 (using .../sysvinit-utils_2.88dsf-13.10ubuntu13_armhf.deb) ... Unpacking replacement sysvinit-utils ... Preparing to replace sysv-rc 2.88dsf-13.10ubuntu11 (using .../sysv-rc_2.88dsf-13.10ubuntu13_all.deb) ... Unpacking replacement sysv-rc ... Preparing to replace initscripts 2.88dsf-13.10ubuntu11 (using .../initscripts_2.88dsf-13.10ubuntu13_armhf.deb) ... Unpacking replacement initscripts ... Preparing to replace procps 1:3.3.3-2ubuntu2 (using .../procps_1%3a3.3.3-2ubuntu3_armhf.deb) ... invoke-rc.d: policy-rc.d denied execution of stop. Unpacking replacement procps ... Preparing to replace python2.7-minimal 2.7.3-0ubuntu3 (using .../python2.7-minimal_2.7.3-0ubuntu4_armhf.deb) ... Unpacking replacement python2.7-minimal ... Preparing to replace linux-libc-dev:armhf 3.5.0-4.4 (using .../linux-libc-dev_3.5.0-7.7_armhf.deb) ... Unpacking replacement linux-libc-dev:armhf ... Setting up libglib2.0-0:armhf (2.33.6-1) ... No schema files found: doing nothing. Setting up libprocps0:armhf (1:3.3.3-2ubuntu3) ... Setting up libldap-2.4-2:armhf (2.4.31-1ubuntu1) ... Setting up libp11-kit0:armhf (0.13-1) ... Setting up sysvinit-utils (2.88dsf-13.10ubuntu13) ... Setting up sysv-rc (2.88dsf-13.10ubuntu13) ... Setting up initscripts (2.88dsf-13.10ubuntu13) ... Setting up procps (1:3.3.3-2ubuntu3) ... Installing new version of config file /etc/sysctl.d/10-magic-sysrq.conf ... invoke-rc.d: policy-rc.d denied execution of start. Setting up python2.7-minimal (2.7.3-0ubuntu4) ... Setting up linux-libc-dev:armhf (3.5.0-7.7) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2', 'armhf', 'quantal', '--nolog', '--batch', '--archive=ubuntu', '--dist=quantal', '--purpose=PRIMARY', '--architecture=armhf', '--comp=multiverse', 'beast-mcmc_1.6.2-2ubuntu1.dsc'] Initiating build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2 with 2 jobs across 2 processor cores. Kernel reported to sbuild: 3.2.0-1415-omap4 #20-Ubuntu SMP PREEMPT Mon Jun 18 19:03:59 UTC 2012 armv7l Automatic build of beast-mcmc_1.6.2-2ubuntu1 on iara by sbuild/armhf 1.170.5 Build started at 20120801-1223 ****************************************************************************** beast-mcmc_1.6.2-2ubuntu1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), javahelper (>= 0.25), ant, ant-optional, default-jdk, libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java, libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2), libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base, texlive-latex-extra Checking for already installed source dependencies... debhelper: missing javahelper: missing ant: missing ant-optional: missing default-jdk: missing libjebl2-java: missing libjam-java: missing figtree: missing liboptions-java: missing libhmsbeagle-java: missing libcolt-java: missing libmpj-java: missing r-cran-rjava: missing libcommons-math-java: missing libjdom1-java: missing junit4: missing libmtj-java: missing libitext1-java: missing texlive-latex-base: missing texlive-latex-extra: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper javahelper ant ant-optional default-jdk libjebl2-java libjam-java figtree liboptions-java libhmsbeagle-java libcolt-java libmpj-java r-cran-rjava libcommons-math-java libjdom1-java junit4 libmtj-java libitext1-java texlive-latex-base texlive-latex-extra Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: binfmt-support bsdmainutils ca-certificates-java dbus dbus-x11 dctrl-tools default-jre default-jre-headless devscripts dh-apparmor ed fastjar file fontconfig fontconfig-config gconf-service gconf-service-backend gconf2 gconf2-common gettext gettext-base groff-base html2text intltool-debian jarwrapper java-common javahelp2 junit libarchive-zip-perl libasound2 libasprintf0c2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libavahi-glib1 libbcmail-java libbcprov-java libbctsp-java libblas3 libbonobo2-0 libbonobo2-common libcairo2 libcanberra0 libconcurrent-java libcroco3 libcups2 libdatrie1 libdbus-glib-1-2 libexpat1 libflac8 libfontconfig1 libfreehep-export-java libfreehep-graphics2d-java libfreehep-graphicsio-emf-java libfreehep-graphicsio-java libfreehep-graphicsio-pdf-java libfreehep-graphicsio-ps-java libfreehep-graphicsio-svg-java libfreehep-graphicsio-swf-java libfreehep-graphicsio-tests-java libfreehep-io-java libfreehep-swing-java libfreehep-util-java libfreehep-xml-java libfreetype6 libgcj-common libgconf-2-4 libgconf2-4 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgettextpo0 libgfortran3 libgif4 libgl1-mesa-glx libglapi-mesa libgnome2-0 libgnome2-common libgnomevfs2-0 libgnomevfs2-common libgnuinet-java libgnujaf-java libgnumail-java libgraphite3 libgtk2.0-0 libgtk2.0-common libhamcrest-java libice6 libidl-common libidl0 libitext5-java libjas-plotter-java libjasper1 libjaxen-java libjbig0 libjpeg-turbo8 libjpeg8 libjson0 libkpathsea6 liblapack3 liblcms2-2 libltdl7 libmagic1 libnb-org-openide-util-java libnb-org-openide-util-lookup-java libnspr4 libnss3 libnss3-1d libogg0 liborbit2 libpango1.0-0 libpaper-utils libpaper1 libpcsclite1 libpipeline1 libpixman-1-0 libpoppler26 libpopt0 libptexenc1 libpulse0 libsm6 libsndfile1 libtablelayout-java libtdb1 libthai-data libthai0 libtiff4 libtiff5 libunistring0 libvorbis0a libvorbisenc2 libvorbisfile3 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-glx0 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 libxmu6 libxpm4 libxrandr2 libxrender1 libxss1 libxt6 libxtst6 libxxf86vm1 luatex man-db mime-support netbase openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless openjdk-7-jre-lib po-debconf preview-latex-style psmisc python python2.7 r-base-core shared-mime-info sound-theme-freedesktop tcl8.5 tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-recommended texlive-pictures tk8.5 ttf-dejavu-core tzdata-java ucf unzip x11-common xdg-utils zip Suggested packages: ant-gcj ant-doc libbsf-java liboro-java libxalan2-java libjaxp1.3-java liblog4j1.2-java libregexp-java jython antlr libbcel-java libcommons-logging-java libjdepend-java libcommons-net-java libjsch-java javacc ant-optional-gcj 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 debian-keyring equivs libcrypt-ssleay-perl libsoap-lite-perl gconf-defaults-service gettext-doc groff javahelp2-doc cvs gawk tofrodos junit-doc libasound2-plugins libasound2-python java-virtual-machine libbcmail-java-doc libbcmail-java-gcj libbcprov-java-doc libbcprov-java-gcj libbctsp-java-doc libbctsp-java-gcj libbonobo2-bin libcanberra-gtk0 libcanberra-pulse cups-common desktop-base libgnomevfs2-bin libgnomevfs2-extra gamin fam gnome-mime-data libgnumail-java-doc librsvg2-common libjasper-runtime libjdom1-java-doc liblcms2-utils ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp pcscd poppler-data pulseaudio libxerces2-java-doc libxerces2-java-gcj libxml-commons-resolver1.1-java-doc less www-browser icedtea-plugin libnss-mdns sun-java6-fonts fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts-core ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts openjdk-7-demo openjdk-7-source visualvm icedtea6-plugin libmail-box-perl python-doc python-tk python2.7-doc r-doc-info r-doc-pdf r-mathlib r-base-html tcl-tclreadline perl-tk xpdf-reader pdf-viewer ghostscript gv postscript-viewer libfile-which-perl dot2tex gvfs-bin Recommended packages: at curl wget dput dupload libdistro-info-perl libjson-perl libparse-debcontrol-perl liburi-perl libwww-perl lintian patchutils python-debian python-magic strace wdiff libgl1-mesa-dri gvfs hicolor-icon-theme libgtk2.0-bin libdom4j-java libxom-java tcpd xml-core texlive-luatex ttf-dejavu-extra icedtea-netx icedtea-6-jre-cacao icedtea-6-jre-jamvm libxt-dev icedtea-7-jre-cacao icedtea-7-jre-jamvm libmail-sendmail-perl doc-base r-recommended r-base-dev r-doc-html lmodern ruby wish texlive-latex-base-doc texlive-latex-extra-doc latex-xcolor texlive-latex-recommended-doc latex-beamer prosper texlive-pictures-doc pgf xterm x-terminal-emulator libfile-mimeinfo-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ant ant-optional binfmt-support bsdmainutils ca-certificates-java dbus dbus-x11 dctrl-tools debhelper default-jdk default-jre default-jre-headless devscripts dh-apparmor ed fastjar figtree file fontconfig fontconfig-config gconf-service gconf-service-backend gconf2 gconf2-common gettext gettext-base groff-base html2text intltool-debian jarwrapper java-common javahelp2 javahelper junit junit4 libarchive-zip-perl libasound2 libasprintf0c2 libasyncns0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libavahi-glib1 libbcmail-java libbcprov-java libbctsp-java libblas3 libbonobo2-0 libbonobo2-common libcairo2 libcanberra0 libcolt-java libcommons-math-java libconcurrent-java libcroco3 libcups2 libdatrie1 libdbus-glib-1-2 libexpat1 libflac8 libfontconfig1 libfreehep-export-java libfreehep-graphics2d-java libfreehep-graphicsio-emf-java libfreehep-graphicsio-java libfreehep-graphicsio-pdf-java libfreehep-graphicsio-ps-java libfreehep-graphicsio-svg-java libfreehep-graphicsio-swf-java libfreehep-graphicsio-tests-java libfreehep-io-java libfreehep-swing-java libfreehep-util-java libfreehep-xml-java libfreetype6 libgcj-common libgconf-2-4 libgconf2-4 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgettextpo0 libgfortran3 libgif4 libgl1-mesa-glx libglapi-mesa libgnome2-0 libgnome2-common libgnomevfs2-0 libgnomevfs2-common libgnuinet-java libgnujaf-java libgnumail-java libgraphite3 libgtk2.0-0 libgtk2.0-common libhamcrest-java libhmsbeagle-java libice6 libidl-common libidl0 libitext1-java libitext5-java libjam-java libjas-plotter-java libjasper1 libjaxen-java libjbig0 libjdom1-java libjebl2-java libjpeg-turbo8 libjpeg8 libjson0 libkpathsea6 liblapack3 liblcms2-2 libltdl7 libmagic1 libmpj-java libmtj-java libnb-org-openide-util-java libnb-org-openide-util-lookup-java libnspr4 libnss3 libnss3-1d libogg0 liboptions-java liborbit2 libpango1.0-0 libpaper-utils libpaper1 libpcsclite1 libpipeline1 libpixman-1-0 libpoppler26 libpopt0 libptexenc1 libpulse0 libsm6 libsndfile1 libtablelayout-java libtdb1 libthai-data libthai0 libtiff4 libtiff5 libunistring0 libvorbis0a libvorbisenc2 libvorbisfile3 libwrap0 libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-glx0 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 libxmu6 libxpm4 libxrandr2 libxrender1 libxss1 libxt6 libxtst6 libxxf86vm1 luatex man-db mime-support netbase openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless openjdk-7-jre-lib po-debconf preview-latex-style psmisc python python2.7 r-base-core r-cran-rjava shared-mime-info sound-theme-freedesktop tcl8.5 tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures tk8.5 ttf-dejavu-core tzdata-java ucf unzip x11-common xdg-utils zip 0 upgraded, 222 newly installed, 0 to remove and 0 not upgraded. Need to get 192 MB of archives. After this operation, 503 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libmagic1 libpopt0 libasprintf0c2 libdbus-glib-1-2 libpipeline1 libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxext6 libxml2 libasound2 libasyncns0 libatk1.0-data libatk1.0-0 libgtk2.0-common libfreetype6 ucf ttf-dejavu-core fontconfig-config libfontconfig1 libpixman-1-0 libxcb-render0 libxcb-shm0 libxrender1 libcairo2 libavahi-common-data libavahi-common3 libavahi-client3 libcups2 libjpeg-turbo8 libjpeg8 libjasper1 libjbig0 libtiff5 libgdk-pixbuf2.0-common libgdk-pixbuf2.0-0 libthai-data libdatrie1 libthai0 libxft2 fontconfig libpango1.0-0 libxcomposite1 libxfixes3 libxcursor1 libxdamage1 libxi6 libxinerama1 libxrandr2 shared-mime-info libgtk2.0-0 openjdk-7-jre-lib openjdk-6-jre-lib tzdata-java java-common libnspr4 libnss3 libnss3-1d libpcsclite1 openjdk-6-jre-headless ca-certificates-java liblcms2-2 openjdk-7-jre-headless default-jre-headless libgif4 libjson0 libogg0 libflac8 libvorbis0a libvorbisenc2 libsndfile1 libwrap0 libpulse0 x11-common libxtst6 libbonobo2-common libidl-common libidl0 liborbit2 libbonobo2-0 libltdl7 libtdb1 libvorbisfile3 sound-theme-freedesktop libcanberra0 gconf2-common libgconf-2-4 gconf-service-backend gconf-service libgconf2-4 libavahi-glib1 netbase dbus psmisc dbus-x11 mime-support python2.7 python gconf2 libgnomevfs2-common libgnomevfs2-0 libgnome2-common libgnome2-0 libglapi-mesa libx11-xcb1 libxcb-glx0 libxxf86vm1 libgl1-mesa-glx openjdk-7-jre default-jre openjdk-6-jre libatk-wrapper-java libatk-wrapper-java-jni libcroco3 libunistring0 libgettextpo0 libgfortran3 libice6 libpaper1 libpoppler26 libsm6 libtiff4 libxt6 libxmu6 libxpm4 libxaw7 libxss1 tex-common libkpathsea6 luatex file bsdmainutils ed gettext-base groff-base man-db libxml-commons-resolver1.1-java libxml-commons-external-java libxerces2-java ant ant-optional binfmt-support dctrl-tools html2text gettext intltool-debian po-debconf dh-apparmor debhelper openjdk-7-jdk default-jdk devscripts fastjar jarwrapper junit libnb-org-openide-util-lookup-java libnb-org-openide-util-java libfreehep-util-java libfreehep-swing-java libfreehep-export-java libfreehep-graphics2d-java libfreehep-io-java libfreehep-graphicsio-java javahelp2 libtablelayout-java libjas-plotter-java libfreehep-graphicsio-tests-java libjaxen-java libjdom1-java libfreehep-graphicsio-emf-java libfreehep-graphicsio-pdf-java libfreehep-graphicsio-ps-java libfreehep-xml-java libfreehep-graphicsio-svg-java libfreehep-graphicsio-swf-java libgnujaf-java libgnuinet-java libgnumail-java libbcmail-java libgcj-common libbcprov-java libbctsp-java libitext5-java libjam-java libjebl2-java figtree libarchive-zip-perl javahelper libhamcrest-java junit4 libblas3 libconcurrent-java libcolt-java libcommons-math-java libgraphite3 libitext1-java liblapack3 libmpj-java libmtj-java liboptions-java libpaper-utils libptexenc1 preview-latex-style zip unzip xdg-utils tcl8.5 tk8.5 r-base-core r-cran-rjava texlive-common texlive-doc-base texlive-binaries texlive-base texlive-latex-base texlive-latex-recommended texlive-pictures texlive-latex-extra libhmsbeagle-java Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ quantal/main libexpat1 armhf 2.1.0-1 [99.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ quantal/main libmagic1 armhf 5.11-2 [168 kB] Get:3 http://ftpmaster.internal/ubuntu/ quantal/main libpopt0 armhf 1.16-3ubuntu1 [26.1 kB] Get:4 http://ftpmaster.internal/ubuntu/ quantal/main libasprintf0c2 armhf 0.18.1.1-9ubuntu1 [6460 B] Get:5 http://ftpmaster.internal/ubuntu/ quantal/main libdbus-glib-1-2 armhf 0.98-1ubuntu1 [59.1 kB] Get:6 http://ftpmaster.internal/ubuntu/ quantal/main libpipeline1 armhf 1.2.1-1 [20.8 kB] Get:7 http://ftpmaster.internal/ubuntu/ quantal/main libxau6 armhf 1:1.0.7-1 [7394 B] Get:8 http://ftpmaster.internal/ubuntu/ quantal/main libxdmcp6 armhf 1:1.1.1-1 [11.2 kB] Get:9 http://ftpmaster.internal/ubuntu/ quantal/main libxcb1 armhf 1.8.1-1 [35.4 kB] Get:10 http://ftpmaster.internal/ubuntu/ quantal/main libx11-data all 2:1.5.0-1 [181 kB] Get:11 http://ftpmaster.internal/ubuntu/ quantal/main libx11-6 armhf 2:1.5.0-1 [686 kB] Get:12 http://ftpmaster.internal/ubuntu/ quantal/main libxext6 armhf 2:1.3.1-2 [26.8 kB] Get:13 http://ftpmaster.internal/ubuntu/ quantal/main libxml2 armhf 2.8.0+dfsg1-4ubuntu1 [554 kB] Get:14 http://ftpmaster.internal/ubuntu/ quantal/main libasound2 armhf 1.0.25-3ubuntu1 [355 kB] Get:15 http://ftpmaster.internal/ubuntu/ quantal/main libasyncns0 armhf 0.8-4 [11.3 kB] Get:16 http://ftpmaster.internal/ubuntu/ quantal/main libatk1.0-data all 2.5.4-0ubuntu1 [13.0 kB] Get:17 http://ftpmaster.internal/ubuntu/ quantal/main libatk1.0-0 armhf 2.5.4-0ubuntu1 [51.2 kB] Get:18 http://ftpmaster.internal/ubuntu/ quantal/main libgtk2.0-common all 2.24.11-0ubuntu1 [119 kB] Get:19 http://ftpmaster.internal/ubuntu/ quantal/main libfreetype6 armhf 2.4.8-1ubuntu2 [272 kB] Get:20 http://ftpmaster.internal/ubuntu/ quantal/main ucf all 3.0025+nmu3 [55.0 kB] Get:21 http://ftpmaster.internal/ubuntu/ quantal/main ttf-dejavu-core all 2.33-2ubuntu1 [1552 kB] Get:22 http://ftpmaster.internal/ubuntu/ quantal/main fontconfig-config all 2.8.0-3ubuntu9 [44.4 kB] Get:23 http://ftpmaster.internal/ubuntu/ quantal/main libfontconfig1 armhf 2.8.0-3ubuntu9 [105 kB] Get:24 http://ftpmaster.internal/ubuntu/ quantal/main libpixman-1-0 armhf 0.26.0-3 [208 kB] Get:25 http://ftpmaster.internal/ubuntu/ quantal/main libxcb-render0 armhf 1.8.1-1 [11.0 kB] Get:26 http://ftpmaster.internal/ubuntu/ quantal/main libxcb-shm0 armhf 1.8.1-1 [5170 B] Get:27 http://ftpmaster.internal/ubuntu/ quantal/main libxrender1 armhf 1:0.9.7-1 [16.7 kB] Get:28 http://ftpmaster.internal/ubuntu/ quantal/main libcairo2 armhf 1.12.2-1ubuntu1 [490 kB] Get:29 http://ftpmaster.internal/ubuntu/ quantal/main libavahi-common-data armhf 0.6.31-1ubuntu1 [21.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ quantal/main libavahi-common3 armhf 0.6.31-1ubuntu1 [22.7 kB] Get:31 http://ftpmaster.internal/ubuntu/ quantal/main libavahi-client3 armhf 0.6.31-1ubuntu1 [25.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ quantal/main libcups2 armhf 1.5.3-4build1 [146 kB] Get:33 http://ftpmaster.internal/ubuntu/ quantal/main libjpeg-turbo8 armhf 1.1.90+svn733-0ubuntu6 [82.3 kB] Get:34 http://ftpmaster.internal/ubuntu/ quantal/main libjpeg8 armhf 8c-2ubuntu7 [2118 B] Get:35 http://ftpmaster.internal/ubuntu/ quantal/main libjasper1 armhf 1.900.1-13 [129 kB] Get:36 http://ftpmaster.internal/ubuntu/ quantal/main libjbig0 armhf 2.0-2ubuntu1 [25.5 kB] Get:37 http://ftpmaster.internal/ubuntu/ quantal/main libtiff5 armhf 4.0.2-1ubuntu2 [149 kB] Get:38 http://ftpmaster.internal/ubuntu/ quantal/main libgdk-pixbuf2.0-common all 2.26.1-1ubuntu1 [7762 B] Get:39 http://ftpmaster.internal/ubuntu/ quantal/main libgdk-pixbuf2.0-0 armhf 2.26.1-1ubuntu1 [172 kB] Get:40 http://ftpmaster.internal/ubuntu/ quantal/main libthai-data all 0.1.18-1 [179 kB] Get:41 http://ftpmaster.internal/ubuntu/ quantal/main libdatrie1 armhf 0.2.5-3 [13.0 kB] Get:42 http://ftpmaster.internal/ubuntu/ quantal/main libthai0 armhf 0.1.18-1 [16.0 kB] Get:43 http://ftpmaster.internal/ubuntu/ quantal/main libxft2 armhf 2.3.1-1 [35.2 kB] Get:44 http://ftpmaster.internal/ubuntu/ quantal/main fontconfig armhf 2.8.0-3ubuntu9 [154 kB] Get:45 http://ftpmaster.internal/ubuntu/ quantal/main libpango1.0-0 armhf 1.30.1-0ubuntu3 [305 kB] Get:46 http://ftpmaster.internal/ubuntu/ quantal/main libxcomposite1 armhf 1:0.4.3-2build1 [6958 B] Get:47 http://ftpmaster.internal/ubuntu/ quantal/main libxfixes3 armhf 1:5.0-4ubuntu4 [10.4 kB] Get:48 http://ftpmaster.internal/ubuntu/ quantal/main libxcursor1 armhf 1:1.1.13-1 [19.0 kB] Get:49 http://ftpmaster.internal/ubuntu/ quantal/main libxdamage1 armhf 1:1.1.3-2build1 [6728 B] Get:50 http://ftpmaster.internal/ubuntu/ quantal/main libxi6 armhf 2:1.6.1-1 [24.8 kB] Get:51 http://ftpmaster.internal/ubuntu/ quantal/main libxinerama1 armhf 2:1.1.2-1 [7412 B] Get:52 http://ftpmaster.internal/ubuntu/ quantal/main libxrandr2 armhf 2:1.3.2-2 [14.6 kB] Get:53 http://ftpmaster.internal/ubuntu/ quantal/main shared-mime-info armhf 1.0-1ubuntu1 [450 kB] Get:54 http://ftpmaster.internal/ubuntu/ quantal/main libgtk2.0-0 armhf 2.24.11-0ubuntu1 [2293 kB] Get:55 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-7-jre-lib all 7~u3-2.1.1~pre1-1ubuntu4 [5199 kB] Get:56 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-6-jre-lib all 6b24-1.11.1-4ubuntu3 [6133 kB] Get:57 http://ftpmaster.internal/ubuntu/ quantal/main tzdata-java all 2012d-1 [139 kB] Get:58 http://ftpmaster.internal/ubuntu/ quantal/main java-common all 0.43ubuntu3 [61.7 kB] Get:59 http://ftpmaster.internal/ubuntu/ quantal/main libnspr4 armhf 4.8.9-1ubuntu2 [109 kB] Get:60 http://ftpmaster.internal/ubuntu/ quantal/main libnss3 armhf 3.13.1.with.ckbi.1.88-1ubuntu6 [934 kB] Get:61 http://ftpmaster.internal/ubuntu/ quantal/main libnss3-1d armhf 3.13.1.with.ckbi.1.88-1ubuntu6 [13.4 kB] Get:62 http://ftpmaster.internal/ubuntu/ quantal/main libpcsclite1 armhf 1.8.3-3ubuntu1 [20.5 kB] Get:63 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-6-jre-headless armhf 6b24-1.11.1-4ubuntu3 [22.9 MB] Get:64 http://ftpmaster.internal/ubuntu/ quantal/main ca-certificates-java all 20120721 [13.2 kB] Get:65 http://ftpmaster.internal/ubuntu/ quantal/main liblcms2-2 armhf 2.2+git20110628-2ubuntu4 [114 kB] Get:66 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-7-jre-headless armhf 7~u3-2.1.1~pre1-1ubuntu4 [25.5 MB] Get:67 http://ftpmaster.internal/ubuntu/ quantal/main default-jre-headless armhf 1:1.7-43ubuntu3 [3330 B] Get:68 http://ftpmaster.internal/ubuntu/ quantal/main libgif4 armhf 4.1.6-9ubuntu1 [27.6 kB] Get:69 http://ftpmaster.internal/ubuntu/ quantal/main libjson0 armhf 0.9-1.1 [13.6 kB] Get:70 http://ftpmaster.internal/ubuntu/ quantal/main libogg0 armhf 1.3.0-4 [14.5 kB] Get:71 http://ftpmaster.internal/ubuntu/ quantal/main libflac8 armhf 1.2.1-6 [129 kB] Get:72 http://ftpmaster.internal/ubuntu/ quantal/main libvorbis0a armhf 1.3.2-1.3 [93.7 kB] Get:73 http://ftpmaster.internal/ubuntu/ quantal/main libvorbisenc2 armhf 1.3.2-1.3 [114 kB] Get:74 http://ftpmaster.internal/ubuntu/ quantal/main libsndfile1 armhf 1.0.25-5 [157 kB] Get:75 http://ftpmaster.internal/ubuntu/ quantal/main libwrap0 armhf 7.6.q-23 [46.1 kB] Get:76 http://ftpmaster.internal/ubuntu/ quantal/main libpulse0 armhf 1:2.0-0ubuntu2 [243 kB] Get:77 http://ftpmaster.internal/ubuntu/ quantal/main x11-common all 1:7.7+1ubuntu1 [58.4 kB] Get:78 http://ftpmaster.internal/ubuntu/ quantal/main libxtst6 armhf 2:1.2.1-1 [11.7 kB] Get:79 http://ftpmaster.internal/ubuntu/ quantal/main libbonobo2-common all 2.32.1-0ubuntu2 [36.6 kB] Get:80 http://ftpmaster.internal/ubuntu/ quantal/main libidl-common all 0.8.14-0.2ubuntu2 [8572 B] Get:81 http://ftpmaster.internal/ubuntu/ quantal/main libidl0 armhf 0.8.14-0.2ubuntu2 [75.0 kB] Get:82 http://ftpmaster.internal/ubuntu/ quantal/main liborbit2 armhf 1:2.14.19-0.1ubuntu1 [151 kB] Get:83 http://ftpmaster.internal/ubuntu/ quantal/main libbonobo2-0 armhf 2.32.1-0ubuntu2 [232 kB] Get:84 http://ftpmaster.internal/ubuntu/ quantal/main libltdl7 armhf 2.4.2-1ubuntu1 [33.8 kB] Get:85 http://ftpmaster.internal/ubuntu/ quantal/main libtdb1 armhf 1.2.10-2 [30.0 kB] Get:86 http://ftpmaster.internal/ubuntu/ quantal/main libvorbisfile3 armhf 1.3.2-1.3 [16.4 kB] Get:87 http://ftpmaster.internal/ubuntu/ quantal/main sound-theme-freedesktop all 0.7.pristine-2 [412 kB] Get:88 http://ftpmaster.internal/ubuntu/ quantal/main libcanberra0 armhf 0.29-0ubuntu1 [42.2 kB] Get:89 http://ftpmaster.internal/ubuntu/ quantal/main gconf2-common all 3.2.5-0ubuntu2 [22.1 kB] Get:90 http://ftpmaster.internal/ubuntu/ quantal/main libgconf-2-4 armhf 3.2.5-0ubuntu2 [82.0 kB] Get:91 http://ftpmaster.internal/ubuntu/ quantal/main gconf-service-backend armhf 3.2.5-0ubuntu2 [59.5 kB] Get:92 http://ftpmaster.internal/ubuntu/ quantal/main gconf-service armhf 3.2.5-0ubuntu2 [2022 B] Get:93 http://ftpmaster.internal/ubuntu/ quantal/main libgconf2-4 armhf 3.2.5-0ubuntu2 [2026 B] Get:94 http://ftpmaster.internal/ubuntu/ quantal/main libavahi-glib1 armhf 0.6.31-1ubuntu1 [9632 B] Get:95 http://ftpmaster.internal/ubuntu/ quantal/main netbase all 5.0ubuntu1 [13.8 kB] Get:96 http://ftpmaster.internal/ubuntu/ quantal/main dbus armhf 1.4.18-1ubuntu1 [285 kB] Get:97 http://ftpmaster.internal/ubuntu/ quantal/main psmisc armhf 22.19-1ubuntu1 [49.5 kB] Get:98 http://ftpmaster.internal/ubuntu/ quantal/main dbus-x11 armhf 1.4.18-1ubuntu1 [20.0 kB] Get:99 http://ftpmaster.internal/ubuntu/ quantal/main mime-support all 3.52-1ubuntu1 [31.3 kB] Get:100 http://ftpmaster.internal/ubuntu/ quantal/main python2.7 armhf 2.7.3-0ubuntu4 [2602 kB] Get:101 http://ftpmaster.internal/ubuntu/ quantal/main python armhf 2.7.3-0ubuntu5 [163 kB] Get:102 http://ftpmaster.internal/ubuntu/ quantal/main gconf2 armhf 3.2.5-0ubuntu2 [74.9 kB] Get:103 http://ftpmaster.internal/ubuntu/ quantal/main libgnomevfs2-common all 1:2.24.4-1ubuntu2 [24.3 kB] Get:104 http://ftpmaster.internal/ubuntu/ quantal/main libgnomevfs2-0 armhf 1:2.24.4-1ubuntu2 [241 kB] Get:105 http://ftpmaster.internal/ubuntu/ quantal/main libgnome2-common all 2.32.1-2ubuntu1 [36.9 kB] Get:106 http://ftpmaster.internal/ubuntu/ quantal/main libgnome2-0 armhf 2.32.1-2ubuntu1 [57.0 kB] Get:107 http://ftpmaster.internal/ubuntu/ quantal/main libglapi-mesa armhf 8.0.3-0ubuntu1 [24.1 kB] Get:108 http://ftpmaster.internal/ubuntu/ quantal/main libx11-xcb1 armhf 2:1.5.0-1 [10.7 kB] Get:109 http://ftpmaster.internal/ubuntu/ quantal/main libxcb-glx0 armhf 1.8.1-1 [20.8 kB] Get:110 http://ftpmaster.internal/ubuntu/ quantal/main libxxf86vm1 armhf 1:1.1.2-1 [10.5 kB] Get:111 http://ftpmaster.internal/ubuntu/ quantal/main libgl1-mesa-glx armhf 8.0.3-0ubuntu1 [89.6 kB] Get:112 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-7-jre armhf 7~u3-2.1.1~pre1-1ubuntu4 [190 kB] Get:113 http://ftpmaster.internal/ubuntu/ quantal/main default-jre armhf 1:1.7-43ubuntu3 [882 B] Get:114 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-6-jre armhf 6b24-1.11.1-4ubuntu3 [195 kB] Get:115 http://ftpmaster.internal/ubuntu/ quantal/main libatk-wrapper-java all 0.30.4-0ubuntu3 [30.9 kB] Get:116 http://ftpmaster.internal/ubuntu/ quantal/main libatk-wrapper-java-jni armhf 0.30.4-0ubuntu3 [24.8 kB] Get:117 http://ftpmaster.internal/ubuntu/ quantal/main libcroco3 armhf 0.6.5-1 [82.1 kB] Get:118 http://ftpmaster.internal/ubuntu/ quantal/main libunistring0 armhf 0.9.3-5 [393 kB] Get:119 http://ftpmaster.internal/ubuntu/ quantal/main libgettextpo0 armhf 0.18.1.1-9ubuntu1 [100 kB] Get:120 http://ftpmaster.internal/ubuntu/ quantal/main libgfortran3 armhf 4.7.1-5ubuntu1 [216 kB] Get:121 http://ftpmaster.internal/ubuntu/ quantal/main libice6 armhf 2:1.0.8-2 [38.2 kB] Get:122 http://ftpmaster.internal/ubuntu/ quantal/main libpaper1 armhf 1.1.24+nmu2 [13.4 kB] Get:123 http://ftpmaster.internal/ubuntu/ quantal/main libpoppler26 armhf 0.20.2-2ubuntu2 [731 kB] Get:124 http://ftpmaster.internal/ubuntu/ quantal/main libsm6 armhf 2:1.2.1-2 [15.4 kB] Get:125 http://ftpmaster.internal/ubuntu/ quantal/universe libtiff4 armhf 3.9.6-6ubuntu1 [123 kB] Get:126 http://ftpmaster.internal/ubuntu/ quantal/main libxt6 armhf 1:1.1.3-1 [145 kB] Get:127 http://ftpmaster.internal/ubuntu/ quantal/main libxmu6 armhf 2:1.1.1-1 [43.7 kB] Get:128 http://ftpmaster.internal/ubuntu/ quantal/main libxpm4 armhf 1:3.5.10-1 [32.1 kB] Get:129 http://ftpmaster.internal/ubuntu/ quantal/main libxaw7 armhf 2:1.0.10-2 [157 kB] Get:130 http://ftpmaster.internal/ubuntu/ quantal/main libxss1 armhf 1:1.2.2-1 [7652 B] Get:131 http://ftpmaster.internal/ubuntu/ quantal/main tex-common all 3.13 [626 kB] Get:132 http://ftpmaster.internal/ubuntu/ quantal/main libkpathsea6 armhf 2012.20120628-1 [67.6 kB] Get:133 http://ftpmaster.internal/ubuntu/ quantal/main luatex armhf 0.70.1.20120524-3 [2157 kB] Get:134 http://ftpmaster.internal/ubuntu/ quantal/main file armhf 5.11-2 [17.9 kB] Get:135 http://ftpmaster.internal/ubuntu/ quantal/main bsdmainutils armhf 9.0.3ubuntu1 [194 kB] Get:136 http://ftpmaster.internal/ubuntu/ quantal/main ed armhf 1.6-2 [45.6 kB] Get:137 http://ftpmaster.internal/ubuntu/ quantal/main gettext-base armhf 0.18.1.1-9ubuntu1 [54.0 kB] Get:138 http://ftpmaster.internal/ubuntu/ quantal/main groff-base armhf 1.21-9 [927 kB] Get:139 http://ftpmaster.internal/ubuntu/ quantal/main man-db armhf 2.6.2-1 [700 kB] Get:140 http://ftpmaster.internal/ubuntu/ quantal/main libxml-commons-resolver1.1-java all 1.2-7build1 [91.6 kB] Get:141 http://ftpmaster.internal/ubuntu/ quantal/main libxml-commons-external-java all 1.4.01-2build1 [245 kB] Get:142 http://ftpmaster.internal/ubuntu/ quantal/main libxerces2-java all 2.11.0-6 [1363 kB] Get:143 http://ftpmaster.internal/ubuntu/ quantal/main ant all 1.8.2-4build2 [1836 kB] Get:144 http://ftpmaster.internal/ubuntu/ quantal/main ant-optional all 1.8.2-4build2 [326 kB] Get:145 http://ftpmaster.internal/ubuntu/ quantal/main binfmt-support armhf 2.0.10 [64.0 kB] Get:146 http://ftpmaster.internal/ubuntu/ quantal/main dctrl-tools armhf 2.22.2 [99.9 kB] Get:147 http://ftpmaster.internal/ubuntu/ quantal/main html2text armhf 1.3.2a-15 [85.8 kB] Get:148 http://ftpmaster.internal/ubuntu/ quantal/main gettext armhf 0.18.1.1-9ubuntu1 [1042 kB] Get:149 http://ftpmaster.internal/ubuntu/ quantal/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:150 http://ftpmaster.internal/ubuntu/ quantal/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:151 http://ftpmaster.internal/ubuntu/ quantal/main dh-apparmor all 2.8.0-0ubuntu1 [9578 B] Get:152 http://ftpmaster.internal/ubuntu/ quantal/main debhelper all 9.20120608ubuntu1 [623 kB] Get:153 http://ftpmaster.internal/ubuntu/ quantal/main openjdk-7-jdk armhf 7~u3-2.1.1~pre1-1ubuntu4 [9343 kB] Get:154 http://ftpmaster.internal/ubuntu/ quantal/main default-jdk armhf 1:1.7-43ubuntu3 [880 B] Get:155 http://ftpmaster.internal/ubuntu/ quantal/main devscripts armhf 2.12.1 [637 kB] Get:156 http://ftpmaster.internal/ubuntu/ quantal/main fastjar armhf 2:0.98-3 [33.7 kB] Get:157 http://ftpmaster.internal/ubuntu/ quantal/universe jarwrapper all 0.43ubuntu1 [10.6 kB] Get:158 http://ftpmaster.internal/ubuntu/ quantal/main junit all 3.8.2-8build1 [106 kB] Get:159 http://ftpmaster.internal/ubuntu/ quantal/universe libnb-org-openide-util-lookup-java all 7.0.1+dfsg1-4 [94.6 kB] Get:160 http://ftpmaster.internal/ubuntu/ quantal/universe libnb-org-openide-util-java all 7.0.1+dfsg1-4 [208 kB] Get:161 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-util-java all 2.0.2-5 [48.3 kB] Get:162 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-swing-java all 2.0.3-3 [190 kB] Get:163 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-export-java all 2.1.1-2 [21.1 kB] Get:164 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-graphics2d-java all 2.1.1-3 [122 kB] Get:165 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-io-java all 2.0.2-4 [60.6 kB] Get:166 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-graphicsio-java all 2.1.1-3 [174 kB] Get:167 http://ftpmaster.internal/ubuntu/ quantal/universe javahelp2 all 2.0.05.ds1-6 [2113 kB] Get:168 http://ftpmaster.internal/ubuntu/ quantal/universe libtablelayout-java all 20090826-2 [50.3 kB] Get:169 http://ftpmaster.internal/ubuntu/ quantal/universe libjas-plotter-java all 2.2.6+dfsg1-2 [601 kB] Get:170 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-graphicsio-tests-java all 2.1.1+dfsg1-3 [104 kB] Get:171 http://ftpmaster.internal/ubuntu/ quantal/main libjaxen-java all 1.1.3-1build1 [203 kB] Get:172 http://ftpmaster.internal/ubuntu/ quantal/main libjdom1-java all 1.1.2+dfsg-2build1 [150 kB] Get:173 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-graphicsio-emf-java all 2.1.1-emfplus+dfsg1-2 [370 kB] Get:174 http://ftpmaster.internal/ubuntu/ quantal/universe libfreehep-graphicsio-pdf-java all 2.1.1+dfsg-1 [72.0 kB] Get:175 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http://ftpmaster.internal/ubuntu/ quantal/main libptexenc1 armhf 2012.20120628-1 [36.9 kB] Get:206 http://ftpmaster.internal/ubuntu/ quantal/main preview-latex-style all 11.86-2ubuntu1 [108 kB] Get:207 http://ftpmaster.internal/ubuntu/ quantal/main zip armhf 3.0-6 [244 kB] Get:208 http://ftpmaster.internal/ubuntu/ quantal/main unzip armhf 6.0-4ubuntu1 [182 kB] Get:209 http://ftpmaster.internal/ubuntu/ quantal/main xdg-utils all 1.1.0~rc1-2ubuntu6 [66.6 kB] Get:210 http://ftpmaster.internal/ubuntu/ quantal/main tcl8.5 armhf 8.5.11-2ubuntu1 [1000 kB] Get:211 http://ftpmaster.internal/ubuntu/ quantal/main tk8.5 armhf 8.5.11-2 [896 kB] Get:212 http://ftpmaster.internal/ubuntu/ quantal/universe r-base-core armhf 2.15.1-3ubuntu1 [20.1 MB] Get:213 http://ftpmaster.internal/ubuntu/ quantal/universe r-cran-rjava armhf 0.9-3-1 [558 kB] Get:214 http://ftpmaster.internal/ubuntu/ quantal/main texlive-common all 2012.20120611-3 [191 kB] Get:215 http://ftpmaster.internal/ubuntu/ quantal/main texlive-doc-base all 2012.20120611-1 [1650 kB] Get:216 http://ftpmaster.internal/ubuntu/ quantal/main texlive-binaries armhf 2012.20120628-1 [15.9 MB] Get:217 http://ftpmaster.internal/ubuntu/ quantal/main texlive-base all 2012.20120611-3 [14.1 MB] Get:218 http://ftpmaster.internal/ubuntu/ quantal/main texlive-latex-base all 2012.20120611-3 [869 kB] Get:219 http://ftpmaster.internal/ubuntu/ quantal/main texlive-latex-recommended all 2012.20120611-3 [6777 kB] Get:220 http://ftpmaster.internal/ubuntu/ quantal/main texlive-pictures all 2012.20120611-3 [2253 kB] Get:221 http://ftpmaster.internal/ubuntu/ quantal/main texlive-latex-extra all 2012.20120611-1 [6374 kB] Get:222 http://ftpmaster.internal/ubuntu/ quantal/universe libhmsbeagle-java armhf 1.0-6 [21.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 192 MB in 47s (4030 kB/s) Selecting previously unselected package libexpat1:armhf. 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Setting up libfreetype6:armhf (2.4.8-1ubuntu2) ... Setting up ucf (3.0025+nmu3) ... Setting up ttf-dejavu-core (2.33-2ubuntu1) ... Setting up fontconfig-config (2.8.0-3ubuntu9) ... Setting up libfontconfig1:armhf (2.8.0-3ubuntu9) ... Setting up libpixman-1-0:armhf (0.26.0-3) ... 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 (1.12.2-1ubuntu1) ... Setting up libavahi-common-data:armhf (0.6.31-1ubuntu1) ... Setting up libavahi-common3:armhf (0.6.31-1ubuntu1) ... Setting up libavahi-client3:armhf (0.6.31-1ubuntu1) ... Setting up libcups2:armhf (1.5.3-4build1) ... Setting up libjpeg-turbo8:armhf (1.1.90+svn733-0ubuntu6) ... Setting up libjpeg8:armhf (8c-2ubuntu7) ... Setting up libjasper1:armhf (1.900.1-13) ... Setting up libjbig0:armhf (2.0-2ubuntu1) ... Setting up libtiff5:armhf (4.0.2-1ubuntu2) ... Setting up libgdk-pixbuf2.0-common (2.26.1-1ubuntu1) ... Setting up libgdk-pixbuf2.0-0:armhf (2.26.1-1ubuntu1) ... Setting up libthai-data (0.1.18-1) ... Setting up libdatrie1:armhf (0.2.5-3) ... Setting up libthai0:armhf (0.1.18-1) ... Setting up libxft2:armhf (2.3.1-1) ... Setting up fontconfig (2.8.0-3ubuntu9) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libpango1.0-0:armhf (1.30.1-0ubuntu3) ... Setting up libxcomposite1:armhf (1:0.4.3-2build1) ... Setting up libxfixes3:armhf (1:5.0-4ubuntu4) ... Setting up libxcursor1:armhf (1:1.1.13-1) ... Setting up libxdamage1:armhf (1:1.1.3-2build1) ... 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 (1.0-1ubuntu1) ... Setting up libgtk2.0-0:armhf (2.24.11-0ubuntu1) ... Setting up tzdata-java (2012d-1) ... Setting up java-common (0.43ubuntu3) ... Setting up liblcms2-2:armhf (2.2+git20110628-2ubuntu4) ... Setting up libnspr4:armhf (4.8.9-1ubuntu2) ... Setting up libnss3:armhf (3.13.1.with.ckbi.1.88-1ubuntu6) ... Setting up libnss3-1d:armhf (3.13.1.with.ckbi.1.88-1ubuntu6) ... Setting up libpcsclite1:armhf (1.8.3-3ubuntu1) ... Setting up libgif4:armhf (4.1.6-9ubuntu1) ... Setting up libjson0:armhf (0.9-1.1) ... Setting up libogg0:armhf (1.3.0-4) ... Setting up libflac8:armhf (1.2.1-6) ... Setting up libvorbis0a:armhf (1.3.2-1.3) ... Setting up libvorbisenc2:armhf (1.3.2-1.3) ... Setting up libsndfile1:armhf (1.0.25-5) ... Setting up libwrap0:armhf (7.6.q-23) ... Setting up libpulse0:armhf (1:2.0-0ubuntu2) ... Setting up x11-common (1:7.7+1ubuntu1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libxtst6:armhf (2:1.2.1-1) ... Setting up libbonobo2-common (2.32.1-0ubuntu2) ... Setting up libidl-common (0.8.14-0.2ubuntu2) ... Setting up libidl0:armhf (0.8.14-0.2ubuntu2) ... Setting up liborbit2:armhf (1:2.14.19-0.1ubuntu1) ... Setting up libbonobo2-0:armhf (2.32.1-0ubuntu2) ... Setting up libltdl7:armhf (2.4.2-1ubuntu1) ... Setting up libtdb1:armhf (1.2.10-2) ... Setting up libvorbisfile3:armhf (1.3.2-1.3) ... Setting up sound-theme-freedesktop (0.7.pristine-2) ... Setting up libcanberra0:armhf (0.29-0ubuntu1) ... Setting up gconf2-common (3.2.5-0ubuntu2) ... Creating config file /etc/gconf/2/path with new version Setting up libgconf-2-4:armhf (3.2.5-0ubuntu2) ... Setting up libavahi-glib1:armhf (0.6.31-1ubuntu1) ... Setting up netbase (5.0ubuntu1) ... Setting up dbus (1.4.18-1ubuntu1) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up psmisc (22.19-1ubuntu1) ... Setting up dbus-x11 (1.4.18-1ubuntu1) ... Setting up mime-support (3.52-1ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up python2.7 (2.7.3-0ubuntu4) ... Setting up python (2.7.3-0ubuntu5) ... Setting up libglapi-mesa:armhf (8.0.3-0ubuntu1) ... Setting up libx11-xcb1:armhf (2:1.5.0-1) ... Setting up libxcb-glx0:armhf (1.8.1-1) ... Setting up libxxf86vm1:armhf (1:1.1.2-1) ... Setting up libgl1-mesa-glx:armhf (8.0.3-0ubuntu1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/mesa/ld.so.conf to provide /etc/ld.so.conf.d/arm-linux-gnueabihf_GL.conf (arm-linux-gnueabihf_gl_conf) in auto mode Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libgettextpo0:armhf (0.18.1.1-9ubuntu1) ... Setting up libgfortran3:armhf (4.7.1-5ubuntu1) ... Setting up libice6:armhf (2:1.0.8-2) ... Setting up libpaper1:armhf (1.1.24+nmu2) ... Creating config file /etc/papersize with new version Setting up libpoppler26:armhf (0.20.2-2ubuntu2) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libtiff4:armhf (3.9.6-6ubuntu1) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up libxmu6:armhf (2:1.1.1-1) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up libxaw7:armhf (2:1.0.10-2) ... Setting up libxss1:armhf (1:1.2.2-1) ... Setting up tex-common (3.13) ... Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up libkpathsea6 (2012.20120628-1) ... Setting up luatex (0.70.1.20120524-3) ... texlive-base is not ready, cannot create formats Setting up file (5.11-2) ... Setting up bsdmainutils (9.0.3ubuntu1) ... 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 ed (1.6-2) ... Setting up gettext-base (0.18.1.1-9ubuntu1) ... Setting up groff-base (1.21-9) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up libxml-commons-resolver1.1-java (1.2-7build1) ... Setting up libxml-commons-external-java (1.4.01-2build1) ... Setting up libxerces2-java (2.11.0-6) ... Setting up binfmt-support (2.0.10) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up dctrl-tools (2.22.2) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up dh-apparmor (2.8.0-0ubuntu1) ... Setting up debhelper (9.20120608ubuntu1) ... Setting up devscripts (2.12.1) ... Setting up fastjar (2:0.98-3) ... Setting up jarwrapper (0.43ubuntu1) ... Setting up junit (3.8.2-8build1) ... Setting up libnb-org-openide-util-lookup-java (7.0.1+dfsg1-4) ... Setting up libnb-org-openide-util-java (7.0.1+dfsg1-4) ... Setting up libfreehep-util-java (2.0.2-5) ... Setting up libfreehep-io-java (2.0.2-4) ... Setting up libtablelayout-java (20090826-2) ... Setting up libjaxen-java (1.1.3-1build1) ... Setting up libjdom1-java (1.1.2+dfsg-2build1) ... Setting up libgnujaf-java (1.1.1-8build1) ... Setting up libgnuinet-java (1.1.2-2build1) ... Setting up libgnumail-java (1.1.2-7build1) ... Setting up libgcj-common (1:4.6.3-5ubuntu1) ... Setting up libjam-java (0.0.r297-1) ... Setting up libjebl2-java (0.0.r6-1) ... Setting up libarchive-zip-perl (1.30-6) ... Setting up javahelper (0.43ubuntu1) ... Setting up libhamcrest-java (1.2-2build1) ... Setting up libblas3 (1.2.20110419-5) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libcommons-math-java (2.2-2) ... Setting up libgraphite3 (1:2.3.1-0.2build1) ... Setting up libitext1-java (1.4-5) ... Setting up liblapack3 (3.4.1-4) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libmpj-java (0.38~dfsg-1) ... Setting up libmtj-java (0.9.14~dfsg-2) ... Setting up liboptions-java (0.0.20120113-1) ... Setting up libpaper-utils (1.1.24+nmu2) ... Setting up libptexenc1 (2012.20120628-1) ... Setting up preview-latex-style (11.86-2ubuntu1) ... Setting up zip (3.0-6) ... Setting up unzip (6.0-4ubuntu1) ... Setting up xdg-utils (1.1.0~rc1-2ubuntu6) ... Setting up tcl8.5 (8.5.11-2ubuntu1) ... update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode Setting up tk8.5 (8.5.11-2) ... update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode Setting up r-base-core (2.15.1-3ubuntu1) ... Setting R_PAPERSIZE_USER default to 'a4' Creating config file /etc/R/Renviron with new version Setting up texlive-common (2012.20120611-3) ... Setting up texlive-doc-base (2012.20120611-1) ... Setting up texlive-binaries (2012.20120628-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Building format(s) --refresh. This may take some time... done. Setting up libhmsbeagle-java (1.0-6) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2012.20120611-3) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Running mktexlsr. This may take some time... done. Building format(s) --all. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-pictures (2012.20120611-3) ... Setting up texlive-latex-base (2012.20120611-3) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-latex-recommended (2012.20120611-3) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-latex-extra (2012.20120611-1) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up gconf-service (3.2.5-0ubuntu2) ... Setting up libgconf2-4:armhf (3.2.5-0ubuntu2) ... Setting up openjdk-7-jre-headless:armhf (7~u3-2.1.1~pre1-1ubuntu4) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20120721) ... Adding debian:Juur-SK.pem Adding debian:UTN_USERFirst_Email_Root_CA.pem Adding debian:ComSign_CA.pem Adding debian:A-Trust-nQual-03.pem Adding debian:CNNIC_ROOT.pem Adding debian:EC-ACC.pem Adding debian:Security_Communication_EV_RootCA1.pem Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem Adding debian:UTN_USERFirst_Hardware_Root_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Platinum_CA_-_G2.pem Adding debian:Thawte_Premium_Server_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:spi-cacert-2008.pem Adding debian:Taiwan_GRCA.pem Adding debian:Entrust.net_Secure_Server_CA.pem Adding debian:Certum_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Firmaprofesional_Root_CA.pem Adding debian:spi-ca-2003.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:TC_TrustCenter_Class_3_CA_II.pem Adding debian:Equifax_Secure_CA.pem Adding debian:ca.pem Adding debian:Equifax_Secure_eBusiness_CA_2.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Certinomis_-_Autorité_Racine.pem Adding debian:IGC_A.pem Adding debian:Thawte_Server_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Swisscom_Root_CA_1.pem Adding debian:ComSign_Secured_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Comodo_Secure_Services_root.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Buypass_Class_3_CA_1.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:ValiCert_Class_2_VA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Wells_Fargo_Root_CA.pem Adding debian:Equifax_Secure_Global_eBusiness_CA.pem Adding debian:TC_TrustCenter_Universal_CA_III.pem Adding debian:StartCom_Certification_Authority.pem Adding debian:Sonera_Class_1_Root_CA.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:AC_Raíz_Certicámara_S.A..pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:DST_ACES_CA_X6.pem Adding debian:AffirmTrust_Premium.pem Adding debian:ApplicationCA_-_Japanese_Government.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:America_Online_Root_Certification_Authority_2.pem Adding debian:SecureTrust_CA.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Staat_der_Nederlanden_Root_CA.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Camerfirma_Global_Chambersign_Root.pem Adding debian:GTE_CyberTrust_Global_Root.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Certigna.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:America_Online_Root_Certification_Authority_1.pem Adding debian:TC_TrustCenter_Class_2_CA_II.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem Adding debian:Equifax_Secure_eBusiness_CA_1.pem Adding debian:Root_CA_Generalitat_Valenciana.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:RSA_Security_2048_v3.pem Adding debian:NetLock_Notary_=Class_A=_Root.pem Adding debian:AddTrust_Public_Services_Root.pem Adding debian:TDC_Internet_Root_CA.pem Adding debian:cacert.org.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:ValiCert_Class_1_VA.pem Adding debian:Buypass_Class_2_CA_1.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem Adding debian:DST_Root_CA_X3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Secure_Global_CA.pem Adding debian:NetLock_Express_=Class_C=_Root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Comodo_Trusted_Services_root.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem Adding debian:RSA_Root_Certificate_1.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:NetLock_Qualified_=Class_QA=_Root.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:AffirmTrust_Networking.pem Adding debian:UTN_DATACorp_SGC_Root_CA.pem Adding debian:Izenpe.com.pem Adding debian:AddTrust_Low-Value_Services_Root.pem Adding debian:Microsec_e-Szigno_Root_CA.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:TC_TrustCenter_Universal_CA_I.pem Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem Adding debian:ACEDICOM_Root.pem Adding debian:AddTrust_Qualified_Certificates_Root.pem Adding debian:NetLock_Business_=Class_B=_Root.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:TDC_OCES_Root_CA.pem Adding debian:CA_Disig.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:GeoTrust_Global_CA_2.pem done. Setting up openjdk-6-jre-headless:armhf (6b24-1.11.1-4ubuntu3) ... 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 update-binfmts: warning: current package is openjdk-6, but binary format already installed by openjdk-7 Setting up openjdk-6-jre-lib (6b24-1.11.1-4ubuntu3) ... Setting up default-jre-headless (1:1.7-43ubuntu3) ... Setting up gconf-service-backend (3.2.5-0ubuntu2) ... Setting up gconf2 (3.2.5-0ubuntu2) ... update-alternatives: using /usr/bin/gconftool-2 to provide /usr/bin/gconftool (gconftool) in auto mode Setting up libgnomevfs2-common (1:2.24.4-1ubuntu2) ... Setting up libgnomevfs2-0 (1:2.24.4-1ubuntu2) ... Setting up libgnome2-common (2.32.1-2ubuntu1) ... Setting up libgnome2-0 (2.32.1-2ubuntu1) ... Setting up libatk-wrapper-java (0.30.4-0ubuntu3) ... Setting up libatk-wrapper-java-jni:armhf (0.30.4-0ubuntu3) ... Setting up openjdk-7-jre:armhf (7~u3-2.1.1~pre1-1ubuntu4) ... update-alternatives: using /usr/lib/jvm/java-7-openjdk-armhf/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up default-jre (1:1.7-43ubuntu3) ... Setting up openjdk-6-jre:armhf (6b24-1.11.1-4ubuntu3) ... update-alternatives: using /usr/lib/jvm/java-6-openjdk-armhf/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up ant (1.8.2-4build2) ... Setting up ant-optional (1.8.2-4build2) ... 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Setting up libcolt-java (1.2.0~nojar-2) ... Setting up r-cran-rjava (0.9-3-1) ... Setting up openjdk-7-jre-lib (7~u3-2.1.1~pre1-1ubuntu4) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.15-0ubuntu15 make_3.81-8.1ubuntu1 dpkg-dev_1.16.7ubuntu3 gcc-4.7_4.7.1-5ubuntu1 g++-4.7_4.7.1-5ubuntu1 binutils_2.22.52.20120713-0ubuntu1 libstdc++6-4.7-dev_4.7.1-5ubuntu1 libstdc++6_4.7.1-5ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Wed Aug 1 10:50:04 2012 UTC using RSA key ID A0E7D8C3 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./beast-mcmc_1.6.2-2ubuntu1.dsc dpkg-source: info: extracting beast-mcmc in beast-mcmc-1.6.2 dpkg-source: info: unpacking beast-mcmc_1.6.2.orig.tar.xz dpkg-source: info: unpacking beast-mcmc_1.6.2-2ubuntu1.debian.tar.gz dpkg-source: info: applying fix_gcc_options.patch dpkg-source: info: applying fix_classpath_in_build_xml.patch dpkg-source: info: applying patch_tex_docs.patch dpkg-source: info: applying fix_classpath_in_build_tracer_xml.patch dpkg-buildpackage: source package beast-mcmc dpkg-buildpackage: source version 1.6.2-2ubuntu1 dpkg-source --before-build beast-mcmc-1.6.2 dpkg-buildpackage: host architecture armhf /usr/bin/fakeroot debian/rules clean dh clean --with javahelper dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory `/build/buildd/beast-mcmc-1.6.2' rm -f native/*\.o native/*\.so native/*\.so\.* for cleantex in \ Practical_BEAST \ BookSection \ Practical_BEAST \ Yule \ SerialSampleCoalescent \ BEAST14_Manual \ ; do \ find doc -not -name "*.tex" -a -not -name "*.bib" -and -name "${cleantex}.*" -exec rm -f \{\} \; ; \ done ant clean Buildfile: /build/buildd/beast-mcmc-1.6.2/build.xml clean: BUILD SUCCESSFUL Total time: 3 seconds make[1]: Leaving directory `/build/buildd/beast-mcmc-1.6.2' jh_clean dh_clean debian/rules build-arch dh build-arch --with javahelper dh_testdir -a dh_auto_configure -a jh_linkjars -a debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/beast-mcmc-1.6.2' # CLASSPATH=/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk/lib/tools.jar:/usr/share/java/beagle.jar:/usr/share/java/mpj.jar:/usr/share/java/org.boehn.kmlframework.jar:/usr/share/java/itext1-1.4.jar:/usr/share/java/junit4.jar:/usr/share/java/figtree.jar:lib/colt.jar:/usr/share/java/options.jar:/usr/share/java/mtj.jar:/usr/share/java/jam.jar:/usr/share/java/jdom1.jar:/usr/share/java/jebl.jar:/usr/share/java/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar ant build Buildfile: /build/buildd/beast-mcmc-1.6.2/build.xml clean: init: [echo] BEAST: /build/buildd/beast-mcmc-1.6.2/build.xml compile-all: [mkdir] Created dir: /build/buildd/beast-mcmc-1.6.2/build [javac] /build/buildd/beast-mcmc-1.6.2/build.xml:66: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 1666 source files to /build/buildd/beast-mcmc-1.6.2/build [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] /build/buildd/beast-mcmc-1.6.2/src/dr/app/beast/BeastMC3.java:367: warning: unmappable character for encoding ASCII [javac] version.getVersionString() + " ???2002-2004 Alexei Drummond & Andrew Rambaut\n" + [javac] ^ [javac] /build/buildd/beast-mcmc-1.6.2/src/dr/app/beast/BeastMC3.java:367: warning: unmappable character for encoding ASCII [javac] version.getVersionString() + " ???2002-2004 Alexei Drummond & Andrew Rambaut\n" + [javac] ^ [javac] /build/buildd/beast-mcmc-1.6.2/src/dr/app/beast/BeastMC3.java:367: warning: unmappable character for encoding ASCII [javac] version.getVersionString() + " ???2002-2004 Alexei Drummond & Andrew Rambaut\n" + [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 4 warnings [echo] Successfully complied. dist-all: [mkdir] Created dir: /build/buildd/beast-mcmc-1.6.2/build/dist [jar] Building jar: /build/buildd/beast-mcmc-1.6.2/build/dist/beast.jar [jar] Building jar: /build/buildd/beast-mcmc-1.6.2/build/dist/beauti.jar build: BUILD SUCCESSFUL Total time: 4 minutes 31 seconds ant -buildfile build_tracer.xml all Buildfile: /build/buildd/beast-mcmc-1.6.2/build_tracer.xml init: [mkdir] Created dir: /build/buildd/beast-mcmc-1.6.2/dist compile-basic: [javac] /build/buildd/beast-mcmc-1.6.2/build_tracer.xml:60: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 2 source files to /build/buildd/beast-mcmc-1.6.2/build [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] 1 warning compile-all: all: BUILD SUCCESSFUL Total time: 6 seconds # native/compileNativeLinux.sh does not create dynamic libraries cd native ; \ gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \ gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \ gcc -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \ gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so.0 libAminoAcidLikelihoodCore.o -lc AminoAcidLikelihoodCore.c: In function 'Java_dr_evomodel_treelikelihood_NativeAminoAcidLikelihoodCore_nativeStatesPartialsPruning': AminoAcidLikelihoodCore.c:281:6: warning: unused variable 'i' [-Wunused-variable] AminoAcidLikelihoodCore.c: In function 'Java_dr_evomodel_treelikelihood_NativeAminoAcidLikelihoodCore_nativePartialsPartialsPruning': AminoAcidLikelihoodCore.c:1251:6: warning: unused variable 'i' [-Wunused-variable] # # Build extra LaTeX documentation # cd doc/BookSection; pdflatex BookSection.tex; pdflatex BookSection.tex This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./BookSection.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/boxedminipage/boxedminipage.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) LaTeX Warning: Unused global option(s): [english]. No file BookSection.aux. (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) LaTeX Warning: No \author given. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file BookSection.toc. [1] [1] Chapter 18. Underfull \hbox (badness 10000) in paragraph at lines 55--66 Underfull \hbox (badness 10000) in paragraph at lines 55--66 Underfull \hbox (badness 10000) in paragraph at lines 55--66 LaTeX Warning: Citation `HR2001' on page 2 undefined on input line 78. LaTeX Warning: Citation `HR2001' on page 2 undefined on input line 85. LaTeX Warning: Citation `Kuhner2006' on page 2 undefined on input line 86. LaTeX Warning: Citation `WWB2003' on page 2 undefined on input line 87. LaTeX Warning: Citation `MRRTT1953' on page 2 undefined on input line 89. 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[3] LaTeX Warning: Reference `posterior-phi' on page 4 undefined on input line 153. Overfull \hbox (32.0387pt too wide) in paragraph at lines 166--172 []\OT1/cmr/m/n/10 To con-struct the \OT1/cmr/bx/it/10 Markov chain \OT1/cmr/m/n /10 we be-gin with an ini-tial state $\OML/cmm/m/it/10 x[] \OT1/cmr/m/n/10 = (\ OML/cmm/m/it/10 g[]; ![]; ^^^[]\OT1/cmr/m/n/10 )$. [4] LaTeX Warning: Citation `Hastings1970' on page 5 undefined on input line 191. (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Citation `HR2001' on page 5 undefined on input line 214. LaTeX Warning: Citation `SR2006' on page 5 undefined on input line 214. [5] LaTeX Warning: Citation `RD2003' on page 6 undefined on input line 252. LaTeX Warning: Citation `Shapiroetal2004' on page 6 undefined on input line 267 . [6] LaTeX Warning: Citation `ROMM1990' on page 7 undefined on input line 328. LaTeX Warning: Citation `HKY1985' on page 7 undefined on input line 329. 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[9] (/usr/share/texmf/tex/latex/R/tex/latex/omscmtt.fd) LaTeX Warning: Citation `ROMM1990' on page 10 undefined on input line 498. LaTeX Warning: Citation `HKY1985' on page 10 undefined on input line 503. LaTeX Warning: Citation `Y1994' on page 10 undefined on input line 507. Overfull \hbox (15.0pt too wide) in paragraph at lines 460--541 []$[]$ [10] Overfull \vbox (116.66109pt too high) has occurred while \output is active [11] LaTeX Warning: Citation `PDNRR2003' on page 12 undefined on input line 571. LaTeX Warning: Citation `Lemeyetal2004' on page 12 undefined on input line 571. LaTeX Warning: Citation `Shapiroetal2004' on page 12 undefined on input line 57 1. LaTeX Warning: Citation `DRSP2005' on page 12 undefined on input line 571. LaTeX Warning: Citation `LMDJH2005' on page 12 undefined on input line 571. LaTeX Warning: Citation `Zlateva2004' on page 12 undefined on input line 586. Overfull \hbox (13.58408pt too wide) in paragraph at lines 583--588 \OT1/cmr/m/n/10 this ex-er-cise is avail-able for down-load at http://www.theph ylogenetichandbook.org. [12] LaTeX Warning: Reference `fig:figure1' on page 13 undefined on input line 622. [13] LaTeX Warning: Reference `fig:figure2' on page 14 undefined on input line 641. [14 <./Fi gure18_1.png>] LaTeX Warning: Reference `fig:figure3' on page 15 undefined on input line 680. [15 <./Figure18_2.png>] [16 <./Figure18_3.png>] LaTeX Warning: Reference `fig:figure4' on page 17 undefined on input line 747. [17] [18] LaTeX Warning: Reference `fig:figure5' on page 19 undefined on input line 808. LaTeX Warning: Reference `fig:figure5' on page 19 undefined on input line 824. [19 <./Figure18_4.png>] LaTeX Warning: Reference `fig:figure5' on page 20 undefined on input line 856. [20 <./Figure18_5.png>] LaTeX Warning: Reference `fig:figure6' on page 21 undefined on input line 859. LaTeX Warning: Reference `MCMC_options' on page 21 undefined on input line 882. LaTeX Warning: Reference `fig:figure7' on page 21 undefined on input line 885. [21 <./Fig ure18_6.png>] LaTeX Warning: Reference `fig:figure8' on page 22 undefined on input line 905. LaTeX Warning: Reference `fig:figure9' on page 22 undefined on input line 923. [22 <./Fig ure18_7.png>] [23 <./Figure18_8.png> <./Figure18_9.png>] LaTeX Warning: Reference `fig:figure10' on page 24 undefined on input line 951. [24 <./Figure18_10.png>] LaTeX Warning: Reference `fig:figure11' on page 25 undefined on input line 1011 . [25] [26 <./Figure18_11.png>] [27] LaTeX Font Warning: Font shape `OT1/cmr/bx/sc' undefined (Font) using `OT1/cmr/bx/n' instead on input line 1066. [28] [29] [30] (./BookSection.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on BookSection.pdf (32 pages, 1291109 bytes). Transcript written on BookSection.log. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./BookSection.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. 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(./BookSection.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) LaTeX Warning: No \author given. [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./BookSection.toc) [1] [1] Chapter 18. Underfull \hbox (badness 10000) in paragraph at lines 55--66 Underfull \hbox (badness 10000) in paragraph at lines 55--66 Underfull \hbox (badness 10000) in paragraph at lines 55--66 [2] [3] Overfull \hbox (32.0387pt too wide) in paragraph at lines 166--172 []\OT1/cmr/m/n/10 To con-struct the \OT1/cmr/bx/it/10 Markov chain \OT1/cmr/m/n /10 we be-gin with an ini-tial state $\OML/cmm/m/it/10 x[] \OT1/cmr/m/n/10 = (\ OML/cmm/m/it/10 g[]; ![]; ^^^[]\OT1/cmr/m/n/10 )$. [4] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [5] [6] [7] [8] [9] (/usr/share/texmf/tex/latex/R/tex/latex/omscmtt.fd) Overfull \hbox (15.0pt too wide) in paragraph at lines 460--541 []$[]$ [10] Overfull \vbox (116.66109pt too high) has occurred while \output is active [11] Overfull \hbox (27.77855pt too wide) in paragraph at lines 583--588 \OT1/cmr/m/n/10 for this ex-er-cise is avail-able for down-load at http://www.t hephylogenetichandbook.org. [12] [13] [14 <./Fi gure18_1.png>] [15 <./Figure18_2.png>] [16 <./Figure1 8_3.png>] [17] [18] [19 <./Figure18_4.png>] [20 <./Figure18_5.png>] [21 <./Fig ure18_6.png>] [22 <./Figure18_7.png>] [23 <./Figure18_8.png> <./Figure18 _9.png>] [24 <./Figure18_10.png>] [25] [26 <./Figure18_11.png>] [27] LaTeX Font Warning: Font shape `OT1/cmr/bx/sc' undefined (Font) using `OT1/cmr/bx/n' instead on input line 1066. [28] [29] [30] (./BookSection.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information) Output written on BookSection.pdf (32 pages, 1284590 bytes). Transcript written on BookSection.log. cd doc/Virus\ Practical\ Tex; pdflatex Practical_BEAST.tex; pdflatex Practical_BEAST.tex This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./Practical_BEAST.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) No file Practical_BEAST.aux. (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [1{/var/lib/texmf/font s/map/pdftex/updmap/pdftex.map}] [2 <./figures1/ImportNexus.png>] [3 <./figures1/BEAUti_Data.png>] [4 <./figures1/BEAUti_Taxa.png>] [5 <./figures1/BEAUti_Subst_Model.png>] [6 <./figures1/BEAUti_Clock_Model.png>] [7 <./figures1/BEAUti_Tree.png>] [8 <./figures1/BEAUti_Prior1.png>] [9 <./figur es1/BEAUti_Prior2.png>] [10 <./figures1/BEAUti_MCMC.png>] [11] [12] [13 <./figures1/Tracer1.png>] [14] [15 <./figures1/Tracer_divergences.pn g> <./figures1/Tracer_marginalDensity.png>] [16 <./figures1/TreeAnnotator1.png>] [17 <./figures1/FigTree.png>] [18 <./figures1/SamplePriorOnly.png>] [19 <./figures2/GuessDates.png>] [20 <./figures2/BEAUTi_Subst_Model.png>] [21 <./figures2/Tracer1.png>] [22 <./figures2/Tracer2.png>] [23 <./figures2/Tracer_density.png>] [24 <./figures2/Tracer_relativeRates.png>] [25 <./figures2/TreeAnnotator.png> <./figures2/Figtr ee.png>] [26] [27 <./figures3/BEAUTi_Tree.png>] [28 <./figures3/Tracer_relativeRates.png>] [29 <./figures3/Tracer_BSP.png>] [30 <./figures3/TreeAnnotator.png> <./figures3/Figtr ee.png>] Overfull \hbox (7.4864pt too wide) in paragraph at lines 843--851 \OT1/cmr/m/n/12 moves and pro-pos-als by other MCMC soft-ware pack-ages such as Mr-Bayes and LAMARC). [31] [32] [33] [34] (./Practical_BEAST.aux) ) (see the transcript file for additional information) Output written on Practical_BEAST.pdf (34 pages, 2089936 bytes). Transcript written on Practical_BEAST.log. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./Practical_BEAST.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (./Practical_BEAST.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [1{/var/lib/texmf/font s/map/pdftex/updmap/pdftex.map}] [2 <./figures1/ImportNexus.png>] [3 <./figures1/BEAUti_Data.png>] [4 <./figures1/BEAUti_Taxa.png>] [5 <./figures1/BEAUti_Subst_Model.png>] [6 <./figures1/BEAUti_Clock_Model.png>] [7 <./figures1/BEAUti_Tree.png>] [8 <./figures1/BEAUti_Prior1.png>] [9 <./figur es1/BEAUti_Prior2.png>] [10 <./figures1/BEAUti_MCMC.png>] [11] [12] [13 <./figures1/Tracer1.png>] [14] [15 <./figures1/Tracer_divergences.pn g> <./figures1/Tracer_marginalDensity.png>] [16 <./figures1/TreeAnnotator1.png>] [17 <./figures1/FigTree.png>] [18 <./figures1/SamplePriorOnly.png>] [19 <./figures2/GuessDates.png>] [20 <./figures2/BEAUTi_Subst_Model.png>] [21 <./figures2/Tracer1.png>] [22 <./figures2/Tracer2.png>] [23 <./figures2/Tracer_density.png>] [24 <./figures2/Tracer_relativeRates.png>] [25 <./figures2/TreeAnnotator.png> <./figures2/Figtr ee.png>] [26] [27 <./figures3/BEAUTi_Tree.png>] [28 <./figures3/Tracer_relativeRates.png>] [29 <./figures3/Tracer_BSP.png>] [30 <./figures3/TreeAnnotator.png> <./figures3/Figtr ee.png>] Overfull \hbox (7.4864pt too wide) in paragraph at lines 843--851 \OT1/cmr/m/n/12 moves and pro-pos-als by other MCMC soft-ware pack-ages such as Mr-Bayes and LAMARC). [31] [32] [33] [34] (./Practical_BEAST.aux) ) (see the transcript file for additional information) Output written on Practical_BEAST.pdf (34 pages, 2089936 bytes). Transcript written on Practical_BEAST.log. cd doc; pdflatex Yule.tex; pdflatex Yule.tex This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./Yule.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. 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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (./Yule.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./Yule.aux) ) Output written on Yule.pdf (2 pages, 135156 bytes). Transcript written on Yule.log. cd doc; pdflatex SerialSampleCoalescent.tex; pdflatex SerialSampleCoalescent.tex This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./SerialSampleCoalescent.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. 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(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./SerialSampleCoalescent.aux) ) Output written on SerialSampleCoalescent.pdf (2 pages, 91738 bytes). Transcript written on SerialSampleCoalescent.log. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./SerialSampleCoalescent.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (./SerialSampleCoalescent.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./SerialSampleCoalescent.aux) ) Output written on SerialSampleCoalescent.pdf (2 pages, 91738 bytes). Transcript written on SerialSampleCoalescent.log. cd doc; pdflatex BEAST14_Manual.tex; pdflatex BEAST14_Manual.tex This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./BEAST14_Manual.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) No file BEAST14_Manual.aux. (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] No file BEAST14_Manual.toc. [2] [3] [4] [5] LaTeX Warning: Citation `GY1994' on page 6 undefined on input line 203. Overfull \hbox (2.04234pt too wide) in paragraph at lines 215--224 []\OT1/cmr/m/n/10 Selecting ``Gamma'' will per-mit sub-sti-tu-tion rate vari-a- tion among sites within [6] LaTeX Warning: Citation `Y1994' on page 7 undefined on input line 235. LaTeX Warning: Citation `SRD2006' on page 7 undefined on input line 260. [7] LaTeX Warning: Reference `priorspanel' on page 8 undefined on input line 270. LaTeX Warning: Citation `DHPR2006' on page 8 undefined on input line 287. Overfull \hbox (1.7784pt too wide) in paragraph at lines 277--288 \OT1/cmr/m/n/10 This al-lows you to se-lect the ap-pro-pri-ate model for rate v ari-a-tion among branches Overfull \hbox (21.92587pt too wide) in paragraph at lines 277--288 \OT1/cmr/m/n/10 for each node of the tree, the $\OML/cmm/m/it/10 t[]$ \OT1/cmr/ m/n/10 of taxon groups, and the []\OT1/cmtt/m/n/10 treeModel.rootHeight[] Overfull \hbox (6.4445pt too wide) in paragraph at lines 293--295 \OT1/cmr/m/n/10 sub-sti-tu-tion rate to a des-ig-nated value or by us-ing a pri or on the []\OT1/cmtt/m/n/10 clock.rate[] [8] LaTeX Warning: Citation `DRSP2005' on page 9 undefined on input line 329. LaTeX Warning: Citation `DRSP2005' on page 9 undefined on input line 336. [9] [10] Overfull \hbox (11.8342pt too wide) in paragraph at lines 391--395 \OT1/cmr/m/n/10 of growth of the pop-u-la-tion as-sum-ing ex-po-nen-tial growth . (/usr/share/texmf/tex/latex/R/tex/latex/omscmtt.fd) LaTeX Warning: Citation `ROMM1990' on page 11 undefined on input line 403. LaTeX Warning: Citation `HKY1985' on page 11 undefined on input line 408. [11] LaTeX Warning: Citation `Y1994' on page 12 undefined on input line 418. 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[18] LaTeX Warning: Reference `commandline' on page 19 undefined on input line 714. [19] [20] [21] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] [22] [23] [24] [25] Overfull \hbox (54.50574pt too wide) in paragraph at lines 1031--1031 [] \OT1/cmtt/m/n/8 [] [26] [27] Overfull \hbox (9.37088pt too wide) in paragraph at lines 1133--1133 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (14.09583pt too wide) in paragraph at lines 1133--1133 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (4.64594pt too wide) in paragraph at lines 1153--1153 [] \OT1/cmtt/m/n/9 [] [28] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1194--1194 [] \OT1/cmtt/m/n/10 [] [29] Overfull \hbox (28.27066pt too wide) in paragraph at lines 1246--1246 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (18.82077pt too wide) in paragraph at lines 1246--1246 [] \OT1/cmtt/m/n/9 [] [30] [31] [32] Overfull \hbox (18.82077pt too wide) in paragraph at lines 1419--1419 []\OT1/cmtt/m/n/9 [] [33] Overfull \hbox (37.5055pt too wide) in paragraph at lines 1472--1472 [] \OT1/cmtt/m/n/8 [] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (30.49702pt too wide) in paragraph at lines 1486--1487 []\OT1/cmr/m/n/10 see the BEAST home-page or $\OT1/cmtt/m/n/10 http : / / beast . bio . ed . ac . uk / BEAST _ XML _ Reference$ [34] [35] [36] [37] [38] LaTeX Font Warning: Font shape `OT1/cmr/bx/sc' undefined (Font) using `OT1/cmr/bx/n' instead on input line 1662. [39] [40] [41] (./BEAST14_Manual.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on BEAST14_Manual.pdf (41 pages, 331360 bytes). Transcript written on BEAST14_Manual.log. This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian) restricted \write18 enabled. entering extended mode (./BEAST14_Manual.tex LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.sty (/usr/share/texlive/texmf-dist/tex/generic/babel/english.ldf (/usr/share/texlive/texmf-dist/tex/generic/babel/babel.def))) (./BEAST14_Manual.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] (./BEAST14_Manual.toc [2]) [3] [4] [5] [6] Overfull \hbox (2.04234pt too wide) in paragraph at lines 215--224 []\OT1/cmr/m/n/10 Selecting ``Gamma'' will per-mit sub-sti-tu-tion rate vari-a- tion among sites within [7] LaTeX Warning: Citation `SRD2006' on page 8 undefined on input line 260. [8] Overfull \hbox (1.7784pt too wide) in paragraph at lines 277--288 \OT1/cmr/m/n/10 This al-lows you to se-lect the ap-pro-pri-ate model for rate v ari-a-tion among branches Overfull \hbox (21.92587pt too wide) in paragraph at lines 277--288 \OT1/cmr/m/n/10 for each node of the tree, the $\OML/cmm/m/it/10 t[]$ \OT1/cmr/ m/n/10 of taxon groups, and the []\OT1/cmtt/m/n/10 treeModel.rootHeight[] Overfull \hbox (6.4445pt too wide) in paragraph at lines 293--295 \OT1/cmr/m/n/10 sub-sti-tu-tion rate to a des-ig-nated value or by us-ing a pri or on the []\OT1/cmtt/m/n/10 clock.rate[] [9] [10] [11] Overfull \hbox (11.8342pt too wide) in paragraph at lines 391--395 \OT1/cmr/m/n/10 of growth of the pop-u-la-tion as-sum-ing ex-po-nen-tial growth . (/usr/share/texmf/tex/latex/R/tex/latex/omscmtt.fd) [12] Overfull \hbox (4.43129pt too wide) in paragraph at lines 417--420 \OT1/cmr/m/n/10 pa-ram-e-ter only ap-pears when you have se-lected Gamma [13] [14] Overfull \hbox (2.47649pt too wide) in paragraph at lines 485--488 \OT1/cmr/m/n/10 a pa-ram-e-ter such as []\OT1/cmtt/m/n/10 treeModel.rootHeight[ ] \OT1/cmr/m/n/10 or []\OT1/cmtt/m/n/10 tmrca(\OT1/cmr/m/it/10 taxon group\OT1/ cmtt/m/n/10 )[] [15] Overfull \hbox (23.05351pt too wide) in paragraph at lines 517--525 \OT1/cmr/m/n/10 weight of the each of: []\OT1/cmtt/m/n/10 upDownOperator[]\OT1/ cmr/m/n/10 , []\OT1/cmtt/m/n/10 uniformOperator[] \OT1/cmr/m/n/10 on []\OT1/cmt t/m/n/10 internalNodeHeights[]\OT1/cmr/m/n/10 , [16] [17] [18] Overfull \hbox (54.72124pt too wide) in paragraph at lines 641--644 []\OT1/cmr/m/n/10 Spelling mis-takes in the pa-ram-e-ters names de-fined in []\ OT1/cmtt/m/n/10 [] [19] [20] [21] [22] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] Overfull \hbox (1.49698pt too wide) in paragraph at lines 836--836 [] \OT1/cmtt/m/n/10 [] [23] [24] [25] [26] Overfull \hbox (54.50574pt too wide) in paragraph at lines 1031--1031 [] \OT1/cmtt/m/n/8 [] [27] [28] Overfull \hbox (9.37088pt too wide) in paragraph at lines 1133--1133 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (14.09583pt too wide) in paragraph at lines 1133--1133 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (4.64594pt too wide) in paragraph at lines 1153--1153 [] \OT1/cmtt/m/n/9 [] [29] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1194--1194 [] \OT1/cmtt/m/n/10 [] [30] Overfull \hbox (28.27066pt too wide) in paragraph at lines 1246--1246 [] \OT1/cmtt/m/n/9 [] Overfull \hbox (18.82077pt too wide) in paragraph at lines 1246--1246 [] \OT1/cmtt/m/n/9 [] [31] [32] [33] Overfull \hbox (18.82077pt too wide) in paragraph at lines 1419--1419 []\OT1/cmtt/m/n/9 [] [34] Overfull \hbox (37.5055pt too wide) in paragraph at lines 1472--1472 [] \OT1/cmtt/m/n/8 [] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Overfull \hbox (30.49702pt too wide) in paragraph at lines 1486--1487 []\OT1/cmr/m/n/10 see the BEAST home-page or $\OT1/cmtt/m/n/10 http : / / beast . bio . ed . ac . uk / BEAST _ XML _ Reference$ [35] [36] [37] [38] [39] LaTeX Font Warning: Font shape `OT1/cmr/bx/sc' undefined (Font) using `OT1/cmr/bx/n' instead on input line 1662. [40] [41] [42] (./BEAST14_Manual.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on BEAST14_Manual.pdf (42 pages, 334013 bytes). Transcript written on BEAST14_Manual.log. # ##################################################################### ## Run test suite ## ## -------------- ## ## While this test suite runs quite a bit of time (about 30min) it ## ## is recommended to be run at least once per new version upload ## ##################################################################### # # /usr/lib/jvm/default-java/bin/java -classpath /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk/lib/tools.jar:/usr/share/java/beagle.jar:/usr/share/java/mpj.jar:/usr/share/java/org.boehn.kmlframework.jar:/usr/share/java/itext1-1.4.jar:/usr/share/java/junit4.jar:/usr/share/java/figtree.jar:lib/colt.jar:/usr/share/java/options.jar:/usr/share/java/mtj.jar:/usr/share/java/jam.jar:/usr/share/java/jdom1.jar:/usr/share/java/jebl.jar:/usr/share/java/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar -Dant.home=/usr/share/ant org.apache.tools.ant.Main -Dcompile.debug=true -Dcompile.optimize=true -buildfile build.xml junit make[1]: Leaving directory `/build/buildd/beast-mcmc-1.6.2' jh_build -a dh_auto_test -a /usr/bin/fakeroot debian/rules binary-arch dh binary-arch --with javahelper dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a dh_install -a jh_installjavadoc -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a 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 debian/rules override_dh_compress make[1]: Entering directory `/build/buildd/beast-mcmc-1.6.2' dh_compress --exclude=.pdf make[1]: Leaving directory `/build/buildd/beast-mcmc-1.6.2' dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: beast-mcmc-lib dh_strip debug symbol extraction: packages to act on: beast-mcmc-lib dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: warning: '/build/buildd/beast-mcmc-1.6.2/debian/beast-mcmc-lib-dbgsym/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `beast-mcmc-lib-dbgsym' in `../beast-mcmc-lib-dbgsym_1.6.2-2ubuntu1_armhf.ddeb'. dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 116 pkgstriptranslations: processing beast-mcmc-lib (in debian/beast-mcmc-lib); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/beast-mcmc-lib/DEBIAN/control, package beast-mcmc-lib, directory debian/beast-mcmc-lib pkgstripfiles: PNG optimization for package beast-mcmc-lib took 0 s dpkg-deb: warning: 'debian/beast-mcmc-lib/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `beast-mcmc-lib' in `../beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb'. dpkg-genchanges -B -mUbuntu/armhf Build Daemon >../beast-mcmc_1.6.2-2ubuntu1_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 beast-mcmc-1.6.2 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20120801-1238 Publishing debug debs. chroot-autobuild/build/buildd/beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb: new debian package, version 2.0. size 70972 bytes: control archive= 1236 bytes. 1157 bytes, 24 lines control 382 bytes, 5 lines md5sums 135 bytes, 7 lines * postinst #!/bin/sh 132 bytes, 7 lines * postrm #!/bin/sh 89 bytes, 2 lines shlibs Package: beast-mcmc-lib Source: beast-mcmc Version: 1.6.2-2ubuntu1 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 213 Depends: libc6 (>= 2.15-0ubuntu8) Suggests: beast-mcmc-doc Section: contrib/science Priority: optional Homepage: http://beast.bio.ed.ac.uk/ Description: Bayesian MCMC phylogenetic inference BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. . This package contains an architecture dependent library. Original-Maintainer: Debian Med Packaging Team chroot-autobuild/build/buildd/beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb: drwxr-xr-x root/root 0 2012-08-01 12:37 ./ drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/ drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/share/ drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/share/doc/beast-mcmc-lib/ -rw-r--r-- root/root 1343 2012-06-07 19:19 ./usr/share/doc/beast-mcmc-lib/copyright -rw-r--r-- root/root 429 2012-08-01 10:48 ./usr/share/doc/beast-mcmc-lib/changelog.Debian.gz drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/share/lintian/ drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 299 2011-02-05 15:24 ./usr/share/lintian/overrides/beast-mcmc-lib drwxr-xr-x root/root 0 2012-08-01 12:37 ./usr/lib/ -rw-r--r-- root/root 9508 2012-08-01 12:37 ./usr/lib/libNucleotideLikelihoodCore.so.0 -rw-r--r-- root/root 169248 2012-08-01 12:37 ./usr/lib/libAminoAcidLikelihoodCore.so.0 lrwxrwxrwx root/root 0 2012-08-01 12:37 ./usr/lib/libAminoAcidLikelihoodCore.so -> libAminoAcidLikelihoodCore.so.0 lrwxrwxrwx root/root 0 2012-08-01 12:37 ./usr/lib/libNucleotideLikelihoodCore.so -> libNucleotideLikelihoodCore.so.0 beast-mcmc_1.6.2-2ubuntu1_armhf.changes: Format: 1.8 Date: Wed, 01 Aug 2012 11:48:26 +0100 Source: beast-mcmc Binary: beast-mcmc beast-mcmc-lib beast-mcmc-examples beast-mcmc-doc Architecture: armhf Version: 1.6.2-2ubuntu1 Distribution: quantal Urgency: low Maintainer: Ubuntu/armhf Build Daemon Changed-By: James Page Description: beast-mcmc - Bayesian MCMC phylogenetic inference beast-mcmc-doc - Bayesian MCMC phylogenetic inference - documentation beast-mcmc-examples - Bayesian MCMC phylogenetic inference - example data beast-mcmc-lib - Bayesian MCMC phylogenetic inference Changes: beast-mcmc (1.6.2-2ubuntu1) quantal; urgency=low . * Transition to use default java implementation: - d/control: Switch openjdk-6-{jdk|jre} -> default-{jdk|jre}. - d/rules: Use /usr/lib/jvm/default-java, explicitly export JAVA_HOME. Checksums-Sha1: b434f5eff700bf5993336beac66f94994816b172 70972 beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb Checksums-Sha256: a65f87fa42a7b061f0fac8400e51fc19facff165504c30a56525ef297bbe9551 70972 beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb Files: 84b5cad320abf56ac1d4e130e433d916 70972 contrib/science optional beast-mcmc-lib_1.6.2-2ubuntu1_armhf.deb Original-Maintainer: Debian Med Packaging Team ****************************************************************************** Built successfully ****************************************************************************** Finished at 20120801-1238 Build needed 00:08:11, 56076k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2'] Scanning for processes to kill in build /home/buildd/build-38f5e3dc2ee43462f26db802c1d4ecab2752b5e2/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2'] Unmounting chroot for build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '38f5e3dc2ee43462f26db802c1d4ecab2752b5e2'] Removing build 38f5e3dc2ee43462f26db802c1d4ecab2752b5e2