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"
>>
>> _______________________________________________
>> R-SIG-Debian mailing list
>> [email protected]
>> 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
>
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