[R] 3.0.1 update and compiler package

[Simon Zehnder]

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.