[Bioc-devel] problem installing VariantAnnotation devel version

[Martin Morgan]

On 08/05/2012 12:04 PM, Vincent Carey wrote:
> We would need a full sessionInfo() result.  FWIW this is the same
> problem I continue to have with my hand-built R-devel for MacOSX, and I
> have gone back to a scratch build to see if I can reproduce it even now.
>   I will provide more data on the outcome of this ASAP.

For what it's worth there is this in the svn log of Biostrings

r67139 | hpages at fhcrc.org | 2012-06-28 18:14:49 -0700 (Thu, 28 Jun 2012) 
| 3 lin
es

Rename xsbasetype() -> seqtype(), and get_xsbasetypes_conversion_lookup() ->
get_seqtype_conversion_lookup().

with ShortRead, Rsamtools, and rtracklayer using 
get_seqtype_conversion_lookup (and no mention of get_xbase* in the 
Bioconductor source tree).

>
> On Sun, Aug 5, 2012 at 2:51 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
>     On 08/05/2012 11:36 AM, Augusto Rendon wrote:
>
>         Hello,
>
>         I am trying to install the development version of the
>         VariantAnnotation
>         devel (1.3.18) package
>
>         and I keep getting this error:
>         Error : object ‘get_xsbasetypes_conversion___lookup’ is not
>         exported by
>         'namespace:Biostrings'
>         ERROR: lazy loading failed for package ‘VariantAnnotation’
>
>         any clues?
>
>
>     Likely it is an out-of-date package. Try
>
>        source('http://bioconductor.__org/biocLite.R
>     <http://bioconductor.org/biocLite.R>')
>        biocLite(character())
>
>     to be prompted to update old packages.
>
>     Does biocLite know that you are using the devel version of Bioconductor?
>
>     http://bioconductor.org/__developers/useDevel/
>     <http://bioconductor.org/developers/useDevel/>
>
>     Martin
>
>
>         thanks,
>
>         a
>
>                  [[alternative HTML version deleted]]
>
>
>
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PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793