[BioC] Rsamtools installation error

tkhodges [guest] guest at bioconductor.org
Fri Feb 15 00:39:06 CET 2013


I am encountering a problem with trying to install Rsamtools from the latest release of Bioconductor. I am using R version 2.14 but the latest release of Bioconductor is for R version 2.15.  I am new to R and Bioconductor so I am wondering if these installation errors are due to the wrong version of R.   Unfortunately, I tried updating R (in Ubuntu 12.04) but my version of R still remains 2.14.  

I will continue try to update to R (ver 2.15) but can someone tell me if there is another potential problem based on the errors in my session output.  Thanks.

 -- output of sessionInfo(): 

> source("http://bioconductor.org/biocLite.R")
> biocLite("Rsamtools")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'Rsamtools'
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘RCurl’, ‘XML’, ‘rtracklayer’

trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-3.tar.gz'
Content type 'application/x-gzip' length 868491 bytes (848 Kb)
opened URL
==================================================
downloaded 848 Kb

trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.95-0.1.tar.gz'
Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/rtracklayer_1.14.4.tar.gz'
Content type 'application/x-gzip' length 1606020 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.3.tar.gz'
Content type 'application/x-gzip' length 2088820 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb

* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/local/lib/R/site-library/RCurl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
ERROR: dependencies ‘RCurl’, ‘XML’ are not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
ERROR: dependency ‘rtracklayer’ is not available for package ‘Rsamtools’
* removing ‘/usr/local/lib/R/site-library/Rsamtools’

The downloaded packages are in
	‘/tmp/RtmpGSb3No/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
> 


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