Error installing VariantAnnotation with bioconductor/devel_core
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kforner • 0
@kforner-7188
Last seen 6.2 years ago
Switzerland
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

```

install variantannotation • 1.1k views
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posted twice by mistake, please delete it

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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).

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Thanks. It was just to report the problem in case it could be useful.

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Great that you're using the docker containers, and neat that they can be rolled back so easily!

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absolutely, great initiative

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