Hi Christoph,

so what you could try to make sure it can run easily on your system is to install it from sources:

First check if you have at least gcc version 4.7.2:
gcc --version

Open a terminal and type 
wget ftp://ftp.stat.math.ethz.ch/Software/R/R-patched.tar.gz
tar -zxvf R-patched.tar.gz 
mkdir build && cd build
../R-patched/configure --prefix=/usr/opt/R --with-blas='-framework libVec' --with-lapack

Check the output at the end of the configuration process. If everything looks fine start the build:
make -j4

This should run without errors. Then check if all works fine:
make check 

If this is the case you can install it (up to here no installation have been done: so the folder /usr/opt/R does not exist  yet):
sudo make install

Start R via the shell:
/usr/opt/R/bin/R 

Install your packages and see what happens. If all is fine, add /usr/opt/R to your PATH variable, if not just delete the folder /usr/opt/R. It all worked perfectly on my scientific Linux system. 


Best

Simon


On Jun 4, 2013, at 11:50 AM, Christoph Knapp <christoph.knapp01@gmail.com> wrote:

> Usually sudo apt-get install ... Sometimes synaptic package manager. I'm using the 
> 
> http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/precise/
> http://cran.stat.ucla.edu/bin/linux/ubuntu/precise
> 
> repositories. Not sure what the differences are. I had some problems before when I installed packages from within Rstudio. It would install them in a different directory than apt-get would and it would tell me that those packages were not installed when I used the terminal to start R. Drove me crazy for a while because I could use them in Rstudio so I was sure they were installed. Do you think this could also cause this? 
> 
> Christoph
> 
> 
> On 04/06/13 21:13, Simon Zehnder wrote:
>> Hi Christoph,
>> 
>> do you install from sources? 
>> 
>> Best 
>> 
>> Simon
>> 
>> On Jun 4, 2013, at 10:41 AM, Christoph Knapp <christoph.knapp01@gmail.com> wrote:
>> 
>>> Hi,
>>> reinstalling R did not help. It still will not update the same packages. I attached the terminal output. There were no errors while I was installing R again. I might have to remove all libraries and reinstall them all. Would you agree or do you think I should try something else first which is not as extreme.
>>> 
>>> Thanks for your help
>>> 
>>> Christoph
>>> 
>>> On 03/06/13 20:32, Pascal Oettli wrote:
>>>> My mistake,
>>>> 
>>>> Regards,
>>>> Pascal
>>>> 
>>>> On 06/03/2013 04:37 PM, Uwe Ligges wrote:
>>>>> 
>>>>> 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
>>>>>>> 
>>>>>>> ______________________________________________
>>>>>>> R-help@r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>> PLEASE do read the posting guide
>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>> 
>>>>>> ______________________________________________
>>>>>> R-help@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>> <email.txt>______________________________________________
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
> 


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