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Question: errors when installing cummeRbund package
1
gravatar for dnajuice
3.2 years ago by
dnajuice20
dnajuice20 wrote:

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.

 

ADD COMMENTlink modified 3.2 years ago by Martin Morgan ♦♦ 20k • written 3.2 years ago by dnajuice20
1
gravatar for Martin Morgan
3.2 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Martin Morgan ♦♦ 20k
1

Thanks - it works now!

ADD REPLYlink written 3.2 years ago by dnajuice20
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