3.0.1 update and compiler package

On 03.06.2013 07:19, Pascal Oettli wrote:

Hi,

How did you upgraded your version of R? From source or from a Linux
package?

Actually the new R installation is just broken. It simply has to be
reinstalled carefully (watch for errors).

Best,
Uwe Ligges

Regards,
Pascal


On 05/31/2013 11:33 AM, Christoph Knapp wrote:

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