docker run -ti bioconductor/devel_core:20150304 Rscript -e "biocLite('VariantAnnotation', suppressUpdates=TRUE)"
gives:
```
** preparing package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
Error in setMethod("rowRanges", "VCF", function(x, ..., fixed = TRUE) { :
no existing definition for function ‘rowRanges’
Error : unable to load R code in package ‘VariantAnnotation’
ERROR: lazy loading failed for package ‘VariantAnnotation’
* removing ‘/usr/local/lib/R/library/VariantAnnotation’
* restoring previous ‘/usr/local/lib/R/library/VariantAnnotation’
The downloaded source packages are in
‘/tmp/RtmplbkU0q/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘VariantAnnotation’ had non-zero exit status
```
posted twice by mistake, please delete it
This is a problem with the current 'devel' snapshot (GenomicRanges failed to propagate). You could install GenomicRanges from svn source, wait until later today (hopefully) for GenomicRanges to propagate, or use the bioconductor/devel_sequencing:XXX container from before Wednesday (I think).
Thanks. It was just to report the problem in case it could be useful.
Great that you're using the docker containers, and neat that they can be rolled back so easily!
absolutely, great initiative