how to install Rsamtools in bioconductor/devel_base docker
0
1
Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 1 day ago
United States

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.

docker Rsamtools • 1.9k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
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 REPLY

Login before adding your answer.

Traffic: 604 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6