[R] 3.0.1 update and compiler package

[Ranjan Maitra]

Hi,

Did you try:

update.packages(installed.packages()[,1])

or 

install.packages(installed.packages()[,1])

This will reinstall the packages you have on your system and for which
updates for 3.0.1 exist.

In my experience, as recounted here earlier, update.packages()
does not always work: it breaks because it fails to also recognize the
need to update some dependencies.

If reducing bandwidth is your concern, you can update the ones that
did not update manually, but note that this is a long drawn process
with one dependency leading to another in many cases.

All this is from my experience of updating R 2.15.2 to R 3.0.0 and
later R 3.0.1: of course YMMV.

HTH,
Ranjan


On Tue, 4 Jun 2013 20:41:21 +1200 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.
> >>
> 


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