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Question: how to install Rsamtools in bioconductor/devel_base docker
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gravatar for Ou, Jianhong
2.3 years ago by
Ou, Jianhong1000
United States
Ou, Jianhong1000 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
** preparing package for lazy loading
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'selectSome' not found
Error : unable to load R code in package ‘Rsamtools’
ERROR: lazy loading failed for package ‘Rsamtools’
* removing ‘/usr/local/lib/R/site-library/Rsamtools’

How could I figure out this error? Thanks.

ADD COMMENTlink written 2.3 years ago by Ou, Jianhong1000

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.

ADD REPLYlink written 2.3 years ago by Hervé Pagès ♦♦ 13k

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.

ADD REPLYlink written 2.3 years ago by Hervé Pagès ♦♦ 13k

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

ADD REPLYlink written 2.3 years ago by a.llave0
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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Hervé Pagès ♦♦ 13k
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