[R] 3.0.1 update and compiler package

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Jun 4 12:40:05 CEST 2013 

On 04/06/2013 10:50, Christoph Knapp wrote:
> Usually sudo apt-get install ... Sometimes synaptic package manager. I'm
> using the

So you really do need to discuss this on R-sig-debian, as those OSes 
have their own non-R package layout.

Do not expect the R manuals to cover the changes made by third-party 
re-distributors, nor advice by general R users nor R bloggers.

> /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 at 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 at 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 at 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 at 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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> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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