[Bioc-devel] [BioC] cummeRbund installation Error

[Dan Tenenbaum]

Hi,

On Sun, Aug 11, 2013 at 11:44 PM, Sridhar Srinivasan
<sridhar2bioinfo at gmail.com> wrote:
> Dear R Developers,
>
> I am trying to install cummeRbund library in my R latest version 3
>
> i tried giving
>
> source("http://bioconductor.org/biocLite.R")
>     biocLite("cummeRbund")
>


Can you send the FULL output of this biocLite() command?
My guess is that a clue is buried in there. Probably a missing system
dependency like xml2 or libcurl.
On ubuntu you can fix this with
sudo apt-get install libxml2-dev libcurl-dev

Dan


> After installing some package it returned with the Warning as
>
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘RCurl’ had non-zero exit status
> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘biomaRt’ had non-zero exit status
> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘rtracklayer’ had non-zero exit status
> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘GenomicFeatures’ had non-zero exit status
> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘biovizBase’ had non-zero exit status
> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘Gviz’ had non-zero exit status
> 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package ‘cummeRbund’ had non-zero exit status
>
> I searched in net regarding the issue.
>
> I am sending the Out of  following commands
> "
>
> sessionInfo()
> biocinstallRepos()
>
> "
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-redhat-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_1.10.3
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.1
>
>>biocinstallRepos()
>                                                BioCsoft
>            "http://bioconductor.org/packages/2.12/bioc"
>                                                 BioCann
> "http://bioconductor.org/packages/2.12/data/annotation"
>                                                 BioCexp
> "http://bioconductor.org/packages/2.12/data/experiment"
>                                               BioCextra
>           "http://bioconductor.org/packages/2.12/extra"
>                                                    CRAN
>                                 "http://cran.fhcrc.org"
>
>
> Could you please suggest on the same.
>
> Thanks and Regards
> Sridhar
>
>         [[alternative HTML version deleted]]
>
>
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