Hi Christoph, do you install from sources?
Best Simon On Jun 4, 2013, at 10:41 AM, Christoph Knapp <christoph.knap...@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@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@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@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@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.
