From tbooth at ceh.ac.uk  Tue Apr  1 13:15:13 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 1 Apr 2014 18:15:13 +0100
Subject: [Bio-Linux] Important for R users: [Fwd: [R-sig-Debian] Head's up:
 Renviron change in R_LIBS_USER to 3.1]
Message-ID: <1396372513.4388.360.camel@balisaur>

Hi All,

If you are using R on Bio-Linux and have installed extra modules in your
personal directory then this will affect you, as the R package has been
updated by CRAN and now looks for modules in a new path.

The short version is:

If you run "library(somlib)" in R and unexpectedly get the message
"there is no package called 'somelib'" (somelib being any actual package
you installed yourself which worked before), and R is reporting its
version as "3.1.0 beta" then try this:

cd ~/R/x86_64-pc-linux-gnu-library && mv 3.0 3.1

As far as I can tell, no recompilation of modules is necessary for this
update, just the change of directory name.

More details in Paul's post below.

Cheers,

TIM

-------- Forwarded Message --------
From: Paul Johnson <pauljohn32 at gmail.com>
To: R-SIG-DEBIAN <r-sig-debian at r-project.org>
Subject: [R-sig-Debian] Head's up: Renviron change in R_LIBS_USER to 3.1
Date: Tue, 1 Apr 2014 15:07:26 +0100

Hi

Here's a warning for you. If you start R today and it can't find any
packages in your home directory that it did find yesterday, don't
faint. You'll see something like this:
> library(data.table)
Error in library(data.table) : there is no package called 'data.table'

and your user home folder R packages will no longer appear in path:

> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"

Explanation/solution:

Yesterday on Ubuntu 13.10 I ran the package updates and R 3.0.3
installed and it altered the /etc/R/Renviron file to look for packages
here

R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/3.1'}

But  my packages are still installed in
~/R/x86_64-pc-linux-gnu-library/3.0. This seems unnecessary, on the
face of it, since R is still 3.0.3, not 3.1, but perhaps there's some
binary incompatibility they are worrying about.

I can't say for sure which package caused that particular change, but
I'm suspecting the first or second one here (from the history):

r-base (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-base-core (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-base-dev (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-base-html (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-cran-boot (1.3-10-1cran1saucy0) to 1.3-11-1saucy0
r-cran-class (7.3-9-1saucy0) to 7.3-10-1saucy0
r-cran-foreign (0.8.60-1saucy0) to 0.8.61-1saucy0
r-cran-kernsmooth (2.23-11-1saucy0) to 2.23-12-1saucy0
r-cran-mass (7.3-30-1saucy0) to 7.3-31-1saucy0
r-cran-nlme (3.1.115-1saucy0) to 3.1.116-1saucy0
r-cran-rpart (4.1-7-1saucy0) to 4.1-8-1saucy0
r-doc-html (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-mathlib (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0
r-recommended (3.0.3-1saucy0) to 3.0.3.20140328-1saucy0

Its pretty easy to change that back manually, but I expect a lot of
the people who use Ubuntu because it is "easier" are going to get
thrown for a loop.

-- 
Paul E. Johnson
Professor, Political Science      Assoc. Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas
http://pj.freefaculty.org               http://quant.ku.edu

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-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705