[R-sig-Debian] Ubuntu Lucid, R 2.14.2, and ggplot2

[Dirk Eddelbuettel]

On 22 March 2012 at 14:53, Scott Smith wrote:
| 
| On Mar 22, 2012, at 2:15 PM, Michael Rutter wrote:
| 
| > On 03/22/2012 03:02 PM, Scott Smith wrote:
| >> I've just updated to the latest R (2.14.2) on my Ubuntu Lucid box, and now the ggplot2 installed as a .deb package fails to work.
| >> 
| >> $ R -e 'library(ggplot2)'
| >> Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
| >>   package ‘proto’ does not have a NAMESPACE and should be re-installed
| >> Calls: library ->  .getRequiredPackages2 ->  library
| >> Execution halted
| > 
| > This was an issue with a bunch of packages when R moved to the 2.14 series.  A number of packages had to be rebuilt to fix the NAMESPACE issue.
| > 
| 
| So I'm new to R packaging.  
| 
| If this works (It's still running for me, but others have done this and reported it works using the /usr/bin/R 2.14.2):
| R_LIBS=$HOME/myR R -e 'install.packages('ggplot2', dep = TRUE, lib="/gscuser/ssmith/myR", repos="http://cran.us.r-project.org")'
| 
| Why does cran2deb make a package (daily?) which is incompatible?
| 
| 
| > So this is an issue with your r-cran-ggplot2 package.  The problem is I am not sure where you are getting the package from.  ggplot2 is not on the CRAN Ubuntu pages and my cran2deb4ubutu project does not support lucid.  Where are you downloading the r-cran-ggplot2 package from?
| 
| I got it here:
| http://bioinformatics.rri.sari.ac.uk/cran2deb/rep/dists/testing/main/binary-amd64/
| 
| I also installed it from this server a few days ago, but the server went away, then came back again today with a different repo name, which did not exist.  This page is now down again.
| http://debian.cran.r-project.org
| 
| Perhaps an indication that this cran2deb stuff is very green?

It has been inoperational for years as you could have noticed by looking at
the version numbers of the packages you were getting, relative to CRAN.

Use http://debian-r.debian.net, which is a pretty new, well done "reboot" of
the same idea.

In case you use Ubuntu, stick to Michael's cran2deb4ubuntu.

Do not mix Debian and Ubuntu.

Dirk

| 
| It's a shame because we are funded to release our bioinformatics pipelines, and they are all carefully Debian packaged.  I can make a big blob of R_LIBS for each one of them instead of specifying R modules as dpkg dependencies, but it feels like a terrible hack.
| 
| 
| > 
| > Michael
| > 
| > 
| >> Here is what I did to ensure the packages were up-to-date:
| >> 
| >> $ sudo apt-get update
| >> $ sudo apt-get install r-base r-base-core r-cran-ggplot2 r-cran-proto
| >> 
| >> Here is what my sources list and dpkg list looks like:
| >> 
| >> $ cat /etc/apt/sources.list.d/r-cran.list
| >> deb http://cran.wustl.edu/bin/linux/ubuntu lucid/
| >> 
| >> $ dpkg -l r-base r-base-core r-cran-ggplot2 r-cran-proto
| >> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
| >> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
| >> ||/ Name                      Version                   Description
| >> +++-=========================-=========================-==================================================================
| >> ii  r-base                    2.14.2-3lucid0            GNU R statistical computation and graphics system
| >> ii  r-base-core               2.14.2-3lucid0            GNU R core of statistical computation and graphics system
| >> ii  r-cran-ggplot2            0.8.9-1cran1              GNU R package "An implementation of the Grammar of
| >> ii  r-cran-proto              0.3-9-1cran1              GNU R package "Prototype object-based programming"
| >> 
| >> _______________________________________________
| >> R-SIG-Debian mailing list
| >> R-SIG-Debian at r-project.org
| >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > 
| > 
| > -- 
| > Dr. Michael A. Rutter
| > School of Science
| > Penn State Erie, The Behrend College
| > Station Road
| > Erie, PA 16563
| > http://math.bd.psu.edu/faculty/rutter
| > 
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| 
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