[Bioc-devel] Installing Geoquery on R version 2.13.1

[Martin Morgan]

On 11/28/2011 10:33 PM, Radhika Malik 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

This is not the complete output. What happens next?

Martin

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


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