[Bioc-devel] Installing Geoquery on R version 2.13.1

Radhika Malik radhika1990 at gmail.com
Tue Nov 29 07:53:26 CET 2011 

Hi Steve, Sean,

I think updating it did the trick. It finally lets me load the Geoquery library.

Thanks a lot!
Radhika

On Tue, Nov 29, 2011 at 1:44 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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
>

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