Usually sudo apt-get install ... Sometimes synaptic package manager. I'm using the
/http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/precise/ http://cran.stat.ucla.edu/bin/linux/ubuntu/precise repositories. Not sure what the differences are. I had some problems before when I installed packages from within Rstudio. It would install them in a different directory than apt-get would and it would tell me that those packages were not installed when I used the terminal to start R. Drove me crazy for a while because I could use them in Rstudio so I was sure they were installed. Do you think this could also cause this? Christoph / On 04/06/13 21:13, Simon Zehnder wrote: > 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. 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