[BioC] rsamtools installation

[Xavier de Pedro]

Hi

I was having a similar issue after upgrading to 2.14 and their 
corresponding biocoonductor packages.

And manually installing again bitops (and a few othes with a similar 
issue for me), e.g.:

biocLite("bitops")

did the trick. For some reason, the older version didn'thave the 
namespace that the new version of packages expects (for what I've noticed)

Cheers

Xavi

On 11/11/11 20:00, Martin Morgan wrote:
> 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.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor