Hi Christoph, so what you could try to make sure it can run easily on your system is to install it from sources:
First check if you have at least gcc version 4.7.2: gcc --version Open a terminal and type wget ftp://ftp.stat.math.ethz.ch/Software/R/R-patched.tar.gz tar -zxvf R-patched.tar.gz mkdir build && cd build ../R-patched/configure --prefix=/usr/opt/R --with-blas='-framework libVec' --with-lapack Check the output at the end of the configuration process. If everything looks fine start the build: make -j4 This should run without errors. Then check if all works fine: make check If this is the case you can install it (up to here no installation have been done: so the folder /usr/opt/R does not exist yet): sudo make install Start R via the shell: /usr/opt/R/bin/R Install your packages and see what happens. If all is fine, add /usr/opt/R to your PATH variable, if not just delete the folder /usr/opt/R. It all worked perfectly on my scientific Linux system. Best Simon On Jun 4, 2013, at 11:50 AM, Christoph Knapp <christoph.knap...@gmail.com> wrote: > 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. > [[alternative HTML version deleted]]
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