[BioC] problem when try to install GenomicFeatures packages

[Kasper Daniel Hansen]

You need curl. I assume you are under linux.  Ask you sysadmin to install curl and curl-devel

Kasper

On Jan 7, 2010, at 20:23 PM, Changbin Du wrote:

> HI, Dear,
> 
> I am a biginner of BIOconductor. When I try to install the GenomicFeatures package, I failed two times. Here is the code in R under Linux:
> 
> > biocLite("GenomicFeatures.Hsapiens.UCSC.hg18")
> Using R version 2.10.1, biocinstall version 2.5.10.
> Installing Bioconductor version 2.5 packages:
> [1] "GenomicFeatures.Hsapiens.UCSC.hg18"
> Please wait...
> 
> also installing the dependencies ‘RCurl’, ‘rtracklayer’, ‘GenomicFeatures’
> 
> trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.3-1.tar.gz'
> Content type 'application/x-gzip' length 800529 bytes (781 Kb)
> opened URL
> ==================================================
> downloaded 781 Kb
> 
> trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/rtracklayer_1.6.0.tar.gz'
> Content type 'application/x-gzip' length 1363174 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
> 
> trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GenomicFeatures_0.2.0.tar.gz'
> Content type 'application/x-gzip' length 70108 bytes (68 Kb)
> opened URL
> ==================================================
> downloaded 68 Kb
> 
> trying URL 'http://www.bioconductor.org/packages/2.5/data/experiment/src/contrib/GenomicFeatures.Hsapiens.UCSC.hg18_0.1.1.tar.gz'
> Content type 'application/x-gzip' length 19774391 bytes (18.9 Mb)
> opened URL
> ==================================================
> downloaded 18.9 Mb
> 
> * installing *source* package ‘RCurl’ ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’
> * removing ‘/home/cdu/library/RCurl’
> * installing *source* package ‘rtracklayer’ ...
> ** R
> ** data
> ** demo
> ** inst
> ** preparing package for lazy loading
> Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
> there is no package called 'RCurl'
> Error : package 'RCurl' could not be loaded
> ERROR: lazy loading failed for package ‘rtracklayer’
> * removing ‘/home/cdu/library/rtracklayer’
> * installing *source* package ‘GenomicFeatures’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
> there is no package called 'rtracklayer'
> Error : package 'rtracklayer' could not be loaded
> ERROR: lazy loading failed for package ‘GenomicFeatures’
> * removing ‘/home/cdu/library/GenomicFeatures’
> * installing *source* package ‘GenomicFeatures.Hsapiens.UCSC.hg18’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package 'GenomicFeatures' required by 'GenomicFeatures.Hsapiens.UCSC.hg18' could not be found
> ERROR: lazy loading failed for package ‘GenomicFeatures.Hsapiens.UCSC.hg18’
> * removing ‘/home/cdu/library/GenomicFeatures.Hsapiens.UCSC.hg18’
> 
> The downloaded packages are in
> ‘/tmp/Rtmp26fOPJ/downloaded_packages’
> Updating HTML index of packages in '.Library'
> 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 'rtracklayer' had non-zero exit status
> 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
> installation of package 'GenomicFeatures' had non-zero exit status
> 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
> installation of package 'GenomicFeatures.Hsapiens.UCSC.hg18' had non-zero exit status
> 
> Can you help me with this?
> 
> Thanks!
> 
> 
> -- 
> Sincerely,
> Changbin --
> 
> Changbin Du
> DOE Joint Genome Institute
> Bldg 400 Rm 457
> 2800 Mitchell Dr,  Walnut Creet, CA 94598
> Phone: 925-927-2856
> Fax: 925-296-5850
> 
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