R SIG Debian - Apr 2014 - Head's up: Renviron change in R_LIBS_USER to 3.1

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

Paul,

Thanks for the heads-up. But please see below.

On 1 April 2014 at 09:07, Paul Johnson wrote:
| 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

Speaking __personally__ rather than as the maintainer supporting the package,
I have __always__ advised against R_LIBS_USER.  All I install goes into
/usr/local/lib/R/site-library.

Otherwise, and speaking as the maintainer, the change is AFAICT __entirely
upstream__ and this discussion may belong into r-help instead.

| 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

It is _obviously_ r-base-core. 

Do you understand that of this list about half share the same source package
and half share not.  The package description says so too.

Dirk

| 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
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com