[Bioc-sig-seq] Rsamtools problem

[Patrick Aboyoun]

Arnaud,
There have been some changes in how Biostrings, rtracklayer, (and maybe 
ShortRead?) are working with connections. If you grab the latest update 
for these three packages, this problem should be solved.


Patrick


On 2/17/10 7:45 AM, Droit Arnaud wrote:
> Dear all,
>
> I have read about Rsamtools being in dev repositories and I would like to try it.
> My working environment is Snow Leopard 64 bit and R version 2.11 (see the SessionInfo at the end). When I try to install it, I have the following error message :
>
> Attaching package: 'IRanges'
>   The following object(s) are masked from package:base :
>
>       Map,
>       cbind,
>       mapply,
>       order,
>       pmax,
>       pmax.int,
>       pmin,
>       pmin.int,
>       rbind,
>       rep.int,
>       table
>
> Error in importIntoEnv(impenv, impnames, ns, impvars) :
>    objects ''.__C__file', '.__C__connection'' are not exported by 'namespace:Biostrings'
> ERROR: lazy loading failed for package 'Rsamtools'
>
>   *   removing '/Library/Frameworks/R.framework/Resources/library/Rsamtools'
>
> Does anyone have some idea about this problem ?
>
> Thanks
>
> Arnaud.
>
>    
>> sessionInfo()
>>      
> R version 2.11.0 Under development (unstable) (2009-10-20 r50178) i386-apple-darwin10.0.0
>
> locale:
> [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.3.41   lattice_0.17-26    BSgenome_1.15.4    Biostrings_2.15.21
> [5] IRanges_1.5.46
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.8 grid_2.11.0   hwriter_1.1
>
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