Hi there,

I have R version 3.0.2 on ubuntu 14.04, and I tried to install the cummeRbund package with the following commands:

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("cummeRbund")

Unfortunately, several dependencies were not installed successfully.  Not surprisingly, when I type library(cummeRbund), I got the error message -

> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

I have pasted part of the error message below that prompted after the biocLite("cummeRbund") command:

> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'cummeRbund'
also installing the dependencies ‘XML’, ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’

......

ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
* 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’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/usr/local/lib/R/site-library/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/usr/local/lib/R/site-library/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/local/lib/R/site-library/cummeRbund’

The downloaded source packages are in
    ‘/tmp/RtmplJinvC/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘biovizBase’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘Gviz’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status

Can anybody please kindly tell me how to get around this? Your assistance is greatly appreciated.

RCurl and XML have system dependencies that need to be satisfied. On linux try (your equivalent of)

sudo apt-get install libcurl4-openssl-dev libxml2-dev

Be sure to get the versions with '-dev' to include the header files.