Software log

These software packages have been installed on crunch:
 * ImageMagick
 * libpng-devel
 * libxml2-devel
 * readline-devel (needed for R to link against libopenblas)
 * firefox
 * groupinstall "X Window System"
 * Xvfb
 * firefox (with firefox -createProfile webmgr2 and subsequently added "user_pref("browser.rights.3.shown", true);" to prefs.js, so as to suppress the copyright message.
 * Xephyr
 * groupinstall "KDE Desktop"
 * rubygems ruby-devel xorg-x11-font* wget
 * xorg-x11-xkb-extras, xorg-x11-xkb-utils, xorg-x11-server-Xvfb, libxkbfile-devel
 * libXtst-devel, libxcb-devel, libXinerama-devel, libXts
 * mesa-libGLU-devel (needed for package rgl)
 * gtk2-devel (needed for package RGtk2)
 * reptyr
 * libjpeg-turbo-devel-1.2.1-3.el6_5.x86_64
 * htop
 * phython-devel

Reconfigure the ld paths for rApache to make rJava run on rApache. This resolves the problem "error: unable to load shared object '/usr/lib64/R/library/rJava/libs/rJava.so'":

/usr/lib/jvm/java-1.6.0-sun-1.6.0.37.x86_64/jre/lib/amd64/server/
 * edit new file /etc/ld.so.conf.d/rApache_rJava.conf
 * put into that file the path to the libjvm.so -- the one that is used by R CMD javareconf, in our case here:
 * correction: /etc/alternatives/jre/lib/amd64/server/ is a more stable path, as it does not have to be updated with each minor java RE update (in fact fedora' autoupdater seems to set the paths nicely to point to the current version)
 * sudo /sbin/ldconfig
 * restart httpd - e voila!


 * I'm not completely sure, but i think the path set in /usr/lib64/R/etc/ldpaths in the first line is not actually evalutaed.


 * this should now be stable and should not need to be updated with every version upgrade of java


 * every once in a while R updates to an incompatible version that requires a manual update of rstudio-server:
 * in that case quite easily the command ln can break and needs to be added: sudo ln -f -s /usr/lib/rstudio-server//bin/rstudio-server /usr/sbin/rstudio-server
 * this also involves running in R: update.packages(checkBuilt=TRUE, ask=FALSE)