[Bioc-devel] Installing Geoquery on R version 2.13.1

Tue Nov 29 07:44:29 CET 2011

Hi,

Your `@rpath` problem looks like you are running into the problem
spoken about in this R-sig-mac thread, here:

https://stat.ethz.ch/pipermail/r-sig-mac/2011-November/008757.html

I guess you are using R through its GUI (R.app)?
Are you somehow using R.app version from R-2.14?

Can you just install the latest version of R, and redo?
http://r.research.att.com/R-2.14-branch-leopard.pkg

Unless you have some special use case where you are trying to
reproduce some result you had previously that has changed with the
latest version of R, you really want to be following the latest R
releases anyway.

HTH,
-steve

On Tue, Nov 29, 2011 at 1:33 AM, Radhika Malik <radhika1990 at gmail.com> wrote:
> 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
>>
>>
>

-- 
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