[Bioc-sig-seq] Rsamtools problem

[Droit Arnaud]

Hi Patrick,

Thanks for your reply.
I have install the latest Biostrings (2.15.21), rtracklayer (1.7.4), ShortRead (1.5.15), IRanges (1.5.46), BSgenome (1.15.4) and Biostrings (2.15.21) packages and I sill received the same error message when I tried to install Rsamtools.
I have also tried it with the packages directly from the SVN account (rtracklayer 1.7.9,....) but there is still too many error that appeared.

If you have any other ideas (platform, version, 64 bit ...), please let me know?

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] rtracklayer_1.7.4  RCurl_1.2-1        bitops_1.0-4.1     ShortRead_1.5.15
[5] lattice_0.17-26    BSgenome_1.15.4    Biostrings_2.15.21 IRanges_1.5.46

loaded via a namespace (and not attached):
[1] Biobase_2.5.8 grid_2.11.0   hwriter_1.1   tools_2.11.0  XML_2.6-0


On 10-02-17 12:26 PM, "Patrick Aboyoun" <paboyoun at fhcrc.org> wrote:

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
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

_______________________________________________
Bioc-sig-sequencing mailing list
Bioc-sig-sequencing at r-project.org
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing