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Old 08-11-2013, 11:13 PM   #1
sridhar28
Member
 
Location: chennai

Join Date: May 2013
Posts: 15
Default Warning messages in software during installing library package

Dear users,
I am trying to install cummeRbund library in my R latest version 3

i tried giving

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

biocLite("cummeRbund")

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"


Your suggestion are most welcome

Thanks and Regards
sridhar
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Old 08-12-2013, 12:22 AM   #2
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
Default

Seems the original cause is that the installation of "RCurl" failed and that caused the installations of all subsequent packages that depend on it to fail, too.

Install RCurl directly and look closely for error messages.

Most likely, you are simply missing the curl header files. Install the appropriate RPM package (using the RedHat Package Manager); it's probably called "libcurl-devel" or similar.
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Old 08-12-2013, 12:44 AM   #3
sridhar28
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Location: chennai

Join Date: May 2013
Posts: 15
Default

Dear Simon,

I installed libcurl-devel and now it works.. cummeRbund is installed now..
thank you for the suggestion..

Thanks
Sridhar
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cummerbund, installation, library, package, rpackage

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