[R] Upgrading

[DEEPANKAR BASU]

Thanks for the suggestions; they resolved the problems. First I installed r-base-dev and then started R via sudo R. Now, when I used update.packages(), the process completed without any warning messages.

Deepankar

----- Original Message -----
From: Ivailo Stoyanov <istoyanov at ecolab.bas.bg>
Date: Thursday, December 21, 2006 2:53 am
Subject: Re: [R] Upgrading

> On Wed, 2006-12-20 at 11:37 -0500, DEEPANKAR BASU wrote:
> > Thanks for the comments. I had got Thomas' message wrong the 
> first time. Now, I have downloaded and re-installed the latest 
> version of R. After reading the "administration and maintenance" 
> manual, I added
> > 
> > deb http://cran.R-project.org/bin/linux/ubuntu dapper/
> > 
> > to my sources.list file and used apt-get to install the latest 
> version. After the installation, I used update.packages() from with 
> R to update all the packages. Let me know if this was what was 
> required or I made some mistake. 
> > 
> > I have two questions:
> > 1. When a new version of R is released (every 6 months or so I 
> believe) will I have to uninstall the version of R in my machine 
> and then download and install the latest version?
> > 2. When I used update.packages() from within R (after installing 
> the latest version), I still got the following warning messages:
> > 
> > Warning messages:
> > 1: installation of package 'cluster' had non-zero exit status in: 
> install.packages(update[, "Package"], instlib, contriburl = 
> contriburl,> 2: installation of package 'mgcv' had non-zero exit 
> status in: install.packages(update[, "Package"], instlib, 
> contriburl = contriburl,
> > 3: cannot create HTML package index in: 
> tools:::unix.packages.html(.Library)
> The "cannot create HTML package index" message hints toward 
> insufficientprivileges -- during "update.packages()" R should run 
> with administrator
> privileges, so you have to start it via "sudo R". The reason for the
> other error messages could be also unavailable source packages due to
> interrupted network connectivity, but generally the best approach 
> is to
> set up a larger number of scrollback lines in the terminal (the 
> defaultcould be insufficient) and to inspect the output for the 
> specific reason
> for the "non-zero exit status". Please note, that you may also need
> r-base-dev (along with some other) installed in order to successfully
> compile any of the packages available at CRAN.
> 
> HTH,
> Ivailo
> 
>