Am 29.07.2014 um 22:45 schrieb Evan Bollig:
Hey Bjoern,
I'm trying to use variant_recalibrator, xy_plot and other tools that
depend on package_r_2_11_0 and require ggplot2 to be installed. Since
CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a
better idea to update the packages the depend on those versions to R
3.0 or 3.1?
Yes, this would be a better idea!
The variant_recalibrator tool generates an Rscript
incompatible with modern versions of ggplot2, so this could be a quite
involved undertaking.
Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked
at older linux disributions, debian stable for example?
I found ggplot on download_store ;)
https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz
Is that old enough?
Meanwhile I'll look into the download_store option. You download all
of the tarballs and install them individually with R CMD INSTALL?
Not really, we have a nice routine in the toolshed for such tasks:
Have a look at:
https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10
Note: the order of the packages are important ...
Ciao,
Bjoern
Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
Hi Evan,
do you have somehow access to this tarball? Than we can put it on
https://github.com/bgruening/download_store
I use that to host R packages to save them for reproducibility.
Can I install another package_r and have packages that depend on
package_r_2_11_0 use the newer version?
I don't think so. But that depends very much on your package. Is it not
possible to use a newer R version? In either case you should save all
tarballs somehow to archive them!
Cheers,
Bjoern
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
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