[R] Some install package fixes for Ubuntu Hardy

[Dirk Eddelbuettel]

On 27 March 2009 at 08:59, John C Nash wrote:
| Thanks Dirk.
| 
| I should have noted the debian sig. My question -- as Dirk recognized -- 
| was where to let folk know. Part of the issue is that Ubuntu users who are
| new to R may not find this stuff. 

No disrespect --- but we feel that it is easier for new (and even
experienced) users to install the r-cran-* binaries, not compile from source.
That is why we have been providing binary packages for all these years.

| workaround may also be a pointer for those with other Linux distros.
| 
| There is now another issue that I don't find r-cran-java as an available 
| package when I run the apt-cache search. (I do find r-cran-rgl; rgl popped up as a 
| dependency in the install.packages, but I should have looked for the debian
| package.) 

It is called r-cran-rjava, but as it was added to Debian only this winter it
has not yet made it into Ubuntu 8.10. I expect it to be in 9.04 which will be
released next month.

Dirk

| I'll post my r-cran-java query to the r-sig-debian.
| 
| JN
| 
| Dirk Eddelbuettel wrote:
| > On 26 March 2009 at 09:45, John C Nash wrote:
| > | I encountered some failures in using install.packages() to install rgl 
| > | and rJava in some of my (multiple) Ubuntu Hardy systems. A quick search 
| > | of the 'Net did not show any debian packages for these. The 
| > | install.packages messages said header or other files were missing, 
| > | suggesting path and related woes. Email with Duncan Murdoch (thanks!) 
| > | pointed the way with rgl and led to a fix for rJava in similar fashion. 
| > | It may save others some frustration to know my resolution. See below.
| > | 
| > | However, I do have a question which a brief rummage of r-project did not 
| > | answer. Where should information like this be put? My opinion is that it 
| >
| > Maybe on the r-sig-debian list that is dedicated to Debian / Ubuntu and R?
| >
| > | should go on the wiki, but possibly there is a better solution if we can 
| > | get the right messages into the package installers, though I recognize 
| > | the load that puts on maintainers.
| > | 
| > | Cheers, JN
| > | 
| > | Ubuntu Hardy rgl install fix:
| > | 
| > | The headers gl.h and glu.h are installed with the "dev" packages 
| > | libgl1-mesa-dev and libglu1-mesa-dev. So the fix is to run (in at 
| > | terminal as root)
| > | 
| > | apt-get install libgl1-mesa-dev
| > | apt-get install libglu1-mesa-dev
| >
| > Yes, which is why the r-cran-rgl package (available in Debian for over five
| > years now, and hence in Ubuntu for probably 4 1/2) has the following
| > Build-Depends (with my manual indentation here):
| >
| >   Build-Depends: debhelper (>= 5.0.0), r-base-dev (>= 2.8.1), cdbs, \
| >   	      libgl1-mesa-dev | libgl-dev, libglu1-mesa-dev | libglu-dev, \
| > 	      libpng12-dev, libx11-dev, libxt-dev, x11proto-core-dev 
| >  
| > | then
| > | R
| > | .....
| > | install.packages("rgl")
| > | 
| > | etc.
| >
| > Let's not forget the 'sudo apt-get install r-cran-rgl' alternative.
| >  
| > | Ubuntu Hardy rJava install fix:
| > | 
| > | Needed to get Sun JDK (not JRE)
| > | 
| > | Then add new
| > | ln -s /usr/java/jdkxxxxx/bin/java java
| > | and
| > | ln -s /usr/java/jdkxxxxx/bin/javac javac
| > | 
| > | where xxxxxx is the version information on the jdk directory name -- in 
| > | my case 1.6.0_13 (see below)
| > | 
| > | Then
| > | 
| > | R CMD javareconf
| > | 
| > | still fails to find the java compiler.
| > | 
| > | Seems $JAVA_HOME may not be defined.
| > | 
| > | Try
| > | export JAVA_HOME="/usr/java/jdk1.6.0_13/"
| > | 
| > | Then (as root)
| > | 
| > | R CMD javareconf
| > | 
| > | seems to work.
| > | Then rJava installed OK. I was then able to install RWeka (my original 
| > | objective) and it seems to run OK.
| >
| > Likewise, the r-cran-rjava package has 
| >
| >    Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 2.8.1), cdbs, \
| >    		  openjdk-6-jdk, automake
| >
| > and R is now configured for this Java version at the built.
| >
| >
| > Again, questions on the r-sig-debian list may have been of help.
| >
| > Hope this helps,  Dirk
| >
| >
| 
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