[BioC] rsamtools installation

[Martin Morgan]

On 11/11/2011 09:55 AM, kevin [guest] wrote:
>
> hi,
>
>     having difficulties installing Rsamtools, through biocLite:
>
> Warning: replacing previous import ‘.__C__file’ when loading ‘Biostrings’
> Warning: replacing previous import ‘.__C__connection’ when loading ‘Biostrings’
> Error : classes "file", "connection" are not exported by 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools’
> * restoring previous ‘/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools’
>
> The downloaded packages are in
> 	‘/tmp/Rtmp6N3TVN/downloaded_packages’
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>    installation of package 'Rsamtools' had non-zero exit status
>
>    and via R CMD INSTALL Rsamtools/
>
> Error : package 'bitops' does not have a name space
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools’
> * restoring previous ‘/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools
>
>
> any help will be appreciated,
> kevin
>
>   -- output of sessionInfo():
>
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biostrings_2.22.0 IRanges_1.12.1

Somehow you have managed to install Biostrings and IRanges for version 
2.14 into your version 2.12 library; biocLite is trying to install the 
version of Rsamtools for 2.12 (presumably; there isn't enough info at 
the top).

Your command line

 >    and via R CMD INSTALL Rsamtools/
 >
 > Error : package 'bitops' does not have a name space

implies that the R at the command line is version 2.14, i.e., you have 
multiple different versions of R installed on your system.

I'd suggest starting again (with current R 2-14) and sticking with biocLite.

Martin

>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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