[Bioc-devel] Installing Geoquery on R version 2.13.1

[Radhika Malik]

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
>> >>
>> >> _______________________________________________
>> >> Bioc-devel at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>
>> >
>> >
>> >
>> > --
>> > 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
>> >
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>