[R] 3.0.1 update and compiler package

[Pascal Oettli]

Hi,

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

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
>
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