[R] 3.0.1 update and compiler package

[Pascal Oettli]

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.
>