[BioC] problem with using GSVA package

[Robert Castelo]

hi David,

you're right, i'm able to reproduce this error in my linux box, in the
transition to the latest released something that escaped to my eye
changed that created this problem. i'll try to find out and write back
to you with the solution. in the meantime, please let me know whether
you're on linux, windows or mac and whether you're on the latest R
version 2.14.

sorry for the inconvinience,
robert.

On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote:
> This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with
> "Cannot find the GNU Scientific Library  >= 1.6" 
> 
> I have gsl-1.14 installed and the bioc web pages states gsl>=1.12
> 
> David
> 
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Robert Castelo
> Sent: Monday, November 07, 2011 9:03 AM
> To: Wendy Qiao
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] problem with using GSVA package
> 
> hi, i think i forgot again something. those steps try to make a
> "system-wide" installation by default trying to write to parts of the
> filesystem where one need's extra privileges to do it.
> 
> please try, instead of 
> 
> make install
> 
> write
> 
> sudo make install
> 
> then the system will ask for your password, enter your password and
> hopefully everything should go fine. let me know.
> 
> cheers,
> robert.
> 
> On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote:
> > Hi Robert,
> > 
> > 
> > Thank you very much for your reply. I tried your comments. Everything
> > worked fine until "make install". This comment gives the following
> > errors. Any suggestion is appreciated. Thank you very much.
> > 
> > 
> > Making install in gsl
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > Making install in utils
> > make[2]: Nothing to be done for `install-exec-am'.
> > make[2]: Nothing to be done for `install-data-am'.
> > Making install in sys
> > make[2]: Nothing to be done for `install-exec-am'.
> > test -z "/usr/local/include/gsl" || .././install-sh -c -d
> > "/usr/local/include/gsl"
> > mkdir: /usr/local/include: Permission denied
> > mkdir: /usr/local/include: No such file or directory
> > make[2]: *** [install-pkgincludeHEADERS] Error 1
> > make[1]: *** [install-am] Error 2
> > make: *** [install-recursive] Error 1
> > 
> > 
> > Wendy
> > 
> > 
> > 
> > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA
> > <robert.castelo at upf.edu> wrote:
> >         hi Wendy,
> >         
> >         sorry about that, i forgot to say that you need to install in
> >         your computer the so-called GNU Scientific Library from:
> >         
> >         http://www.gnu.org/s/gsl
> >         
> >         this is not part of R and should be installed separately.
> >         seeing your output, i guess that you're working on an apple
> >         computer. in such a case you can just try the following:
> >         
> >         1. download the tarball in your Desktop
> >         
> >         http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz 
> >         
> >         
> >         2. open the terminal window from Applications -> Utilities ->
> >         Terminal
> >         
> >         3. write in the terminal window the following commands
> >         
> >         cd Desktop
> >         cd gsl*
> >         ./configure
> >         make
> >         make install
> >         
> >         if these commands are executed without errors, then you can go
> >         back to R and should be able to install GSVA without problems.
> >         let me know if you encounter any difficulty with this.
> >         
> >         cheers,
> >         robert.
> >         
> >         
> >         ______________________________________________________________
> >         From Wendy Qiao <wendy2.qiao at gmail.com>
> >         Sent Mon 11/7/2011 12:51 PM
> >         To bioconductor at r-project.org
> >         Subject [BioC] problem with using GSVA package
> >         
> >         
> >         Hi all, I am trying to use the GSVA package, but I encounter
> >         the following problems. library(GSVA) Error in dyn.load(file,
> >         DLLpath = DLLpath, ...) : unable to load shared object
> >         '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/libs/
> >         x86_64/GSVA.so
> >           Expected in: dynamic lookup
> >         
> >         Error: package/namespace load failed for ‘GSVA’
> >         
> >         I tried to re-install the package and recompile all the packages, but it
> >         still gave the same error. Could anybody please help? Thank you so much!
> >         
> >         Wendy
> >         
> >         	[[alternative HTML version deleted]]
> >         
> >         
> >         
> >         ______________________________________________________________
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> >
> 
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