[Bioc-devel] Installing Geoquery on R version 2.13.1

Hi,

Thanks for your reply.

I'm still having the same problem. I removed the 2 installed packages
using remove.packages('GEOquery') and remove.packages('RCurl'), and
then started R again to try and install these packages again. Here's
the console output I got--

1.

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

BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().


2. Downloaded R Curl--

biocLite('RCurl')

Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "RCurl"
Please wait...

Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
trying URL 'http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.13/RCurl_1.7-0.tgz'
Content type 'application/x-gzip' length 680511 bytes (664 Kb)
opened URL
==================================================
downloaded 664 Kb


The downloaded packages are in
	/var/folders/OT/OTVTac26GnKM1y-L6UzkKE+++TI/-Tmp-//Rtmpd55RtQ/downloaded_packages

3. Downloaded and installed Geoquery--

biocLite('GEOquery')

Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "GEOquery"
Please wait...

Warning: unable to access index for repository
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
trying URL 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/contrib/2.13/GEOquery_2.19.4.tgz'
Content type 'application/x-gzip' length 13715323 bytes (13.1 Mb)
opened URL
==================================================
downloaded 13.1 Mb


The downloaded packages are in
	/var/folders/OT/OTVTac26GnKM1y-L6UzkKE+++TI/-Tmp-//Rtmpd55RtQ/downloaded_packages


Still experienceing the same problem--

library('GEOquery')

Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'browseVignettes()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation("pkgname")'.

Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object
'/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so':
   dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so,
6): Library not loaded:
@rpath/R.framework/Versions/2.13/Resources/lib/libR.dylib
   Referenced from:
/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so
   Reason: image not found
Error: package/namespace load failed for 'GEOquery'


Is there some problem with some path I need to set?

Thanks,
Radhika



On Mon, Nov 28, 2011 at 11:46 PM, Sean Davis<sdavis2 at mail.nih.gov>  wrote:

Hi, Radhika.
The safest way to install R/bioconductor packages is using biocLite.
  biocLite will install the appropriate dependencies.  Now that you have a
broken RCurl package, you will probably need to reinstall it.  I suggest
using biocLite('RCurl') to do so.  Let us know if you have further problems.
Sean

On Mon, Nov 28, 2011 at 11:42 PM, Radhika Malik<radhika1990 at gmail.com>
wrote:

Hi Steve,

Thanks for your reply. I'm trying to follow your instructions. First I
was getting the error that it cannot find RCurl. I downloaded the
binary for Rcurl and installed using--


I installed RCurl using R CMD INSTALL
/Users/Radhika/Desktop/RCurl_1.7-0.tgz

but now am getting this error--

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object

'/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so':

  dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so,
6): Library not loaded:
/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib
  Referenced from:

/Library/Frameworks/R.framework/Versions/2.13/Resources/library/RCurl/libs/x86_64/RCurl.so
  Reason: image not found
Error: package/namespace load failed for 'GEOquery'

What am I missing?

Thanks,
Radhika


On Mon, Nov 28, 2011 at 11:17 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com>  wrote:

Hi,

As shown here:
http://www.bioconductor.org/install/

The easiest way to install bioconductor packages is via `biocLite`.
Just:

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

This will install the appropriate version of the bioconductor packages
for your version of R.

Also, if you're not "stuck" on R-2.13.x for any particular reason, you
might as well update to the latest/greatest, which is R-2.14.0, then
do the biocLite dance.

-steve


On Mon, Nov 28, 2011 at 11:05 PM, Radhika Malik<radhika1990 at gmail.com>
wrote:

Hi,

I'm a new developer and am trying to install geoquery on R version
2.13.1 on Mac OS X 10.6.8. I got the binary GEOquery_1.7.2.tgz but am
unable to install it

1. I have tried R CMD INSTALL /Users/RM/Desktop/GEOquery_1.7.2.tgz
When I do library('GEOquery'), this gives me the error Error: package
'GEOquery' was built before R 2.10.0: please re-install it

2. I tried re-installing by running remove.packages('GEOquery')
followed by install.packages('GEOquery') but this gives me the warning
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ?GEOquery? is not available (for R version 2.13.1)

and then when I try to do library('GEOquery') it again says Error:
package 'GEOquery' was built before R 2.10.0: please re-install it

How can I load the library? Any help would be greatly appreciated;
I've been trying to just install this for several hours now..

Thanks,
Radhika

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  | Memorial Sloan-Kettering Cancer Center
  | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact