
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'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"
>> 
>> _______________________________________________
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>> R-SIG-Debian@r-project.org
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> 
> 
> -- 
> 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
> 
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