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Question: how to install Rsamtools in bioconductor/devel_base docker
1
3.5 years ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi,

I am trying to install Rsamtools in bioconductor/dev_base docker. When I try to install Rsamtools, it gives an error:

biocLite("Rsamtools")

installing to /usr/local/lib/R/site-library/Rsamtools/libs
** R
** inst
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
Error : unable to load R code in package ‘Rsamtools’
* removing ‘/usr/local/lib/R/site-library/Rsamtools’

How could I figure out this error? Thanks.

rsamtools docker • 869 views
written 3.5 years ago by Ou, Jianhong1.1k

Hi Jianhong,

Internal utility selectSome() was moved from BiocGenerics to S4Vectors last week. So please make sure you have the latest versions of these packages (BiocGenerics 0.15.6 and S4Vectors 0.7.12) before you try to install Rsamtools. Also please make sure that your biocLite("Rsamtools") call is downloading the latest version of Rsamtools (1.21.15).

Cheers,

H.

Oops, it seems I didn't bump S4Vectors version properly when I made that change, sorry. Just did it now (to 0.7.13) but this won't propagate before Wednesday now. If you're in a hurry, please get and install S4Vectors directly from svn.

Sorry again for the inconvenience.

H.

Hi. How do I install using the source from Github? Thanks.

biocLite("Bioconductor-mirror/S4Vectors")


But S4Vectors 0.7.13 should have propagated to the standard BioC devel repo by now (or it will in a few minutes) so you should be able to just do the usual biocLite("S4Vectors").

H.