[R] Some install package fixes for Ubuntu Hardy

[John C Nash]

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. My
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.)

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
>
>