[R] 3.0.1 update and compiler package

[Uwe Ligges]

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
>>
>> ______________________________________________
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>> 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
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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.