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/GenomicFeat
ures_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
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/contri
b/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/contri
b/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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi, Changbin,
Are you using Linux or Mac OS? The reason that you cannot install the
rtracklayer and GenomicFeatures packages is because the configuration
for RCurl has failed. Either it couldn't find curl-config in your
path
or curl-config is not installed. On your X window, type "locate
libcurl" to see if "libcurl.so" is present. If not, you will have to
install curl-devel rpms (if you are using Linux) in order to install
RCurl package.
Chao-Jen
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/rtracklay
er_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/GenomicFe
atures_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/contri
b/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!
>
>
--
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org
