[BioC] installation of Rsamtools

Conny [guest] guest at bioconductor.org
Fri Dec 30 11:39:46 CET 2011


I still have problems installing Rsamtools. The first idea was that my R version was too old - so I updated it to the latest version. still the installation does not work - any ideas?
this is just the end of the list after:

> biocLite("Rsamtools")
Warning: S3 methods ‘[<-.CURLOptions’, ‘[[<-.CURLOptions’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘RCurl.so’ not found
ERROR: lazy loading failed for package ‘Rsamtools’
* removing ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’
* restoring previous ‘/home/lab/R/x86_64-pc-linux-gnu-library/2.14/Rsamtools’

The downloaded packages are in
	‘/tmp/RtmpRyJ4Zm/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package ‘Rsamtools’ had non-zero exit status

farther above there was also the error:
Error : package ‘RCurl’ required by ‘rtracklayer’ could not be found
ERROR: lazy loading failed for package ‘rtracklayer’


 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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] BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] tcltk_2.14.1 tools_2.14.1


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