[R] 3.0.1 update and compiler package

[Christoph Knapp]

Hi,
I recently updated to R 3.0.1. I'm running linux ubuntu 12.04. I 
realized that I have to update all the installed packages so I run > 
update.packages(checkBuilt=TRUE)
as described here 
http://www.r-bloggers.com/r-3-0-0-is-released-whats-new-and-how-to-upgrade/ 
. The first thing it did was telling me that it will not update several 
packages. When it was finished I used the warnings function to have a 
look at what did not work. See the list below.

 > warnings()
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘boot’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘cluster’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘foreign’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘KernSmooth’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘MASS’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘Matrix’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘nlme’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘nnet’ had non-zero exit status
9: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘rpart’ had non-zero exit status
10: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘spatial’ had non-zero exit status
11: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘survival’ had non-zero exit status
12: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘class’ had non-zero exit status
13: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘epiR’ had non-zero exit status
14: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gmodels’ had non-zero exit status
15: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gplots’ had non-zero exit status
16: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘mgcv’ had non-zero exit status
17: In install.packages(update[instlib == l, "Package"], l, ... :
installation of package ‘gregmisc’ had non-zero exit status

I tried to reinstall them manually but this always failed because of a 
package dependency to the "compiler" package. Now, if I try to install 
the compiler package it tells me.

 > install.packages("compiler")
Installing package into ‘/home/christoph/R/x86_64-pc-linux-gnu-library/3.0’
(as ‘lib’ is unspecified)
Warning message:
package ‘compiler’ is not available (for R version 3.0.1)

The last line also came up all the time when the packages were updated

Doing a bit of research does not deliver much only that the compiler 
package was included into R at version 2.13.0 
(http://dirk.eddelbuettel.com/blog/2011/04/12/).

Most of those packages which do not work any more are pretty important 
for some of my scripts and I would not even know what packages replace 
the packages above.

Would anyone know how to fix this?

Regards