[BioC] problem with using GSVA package
Robert Castelo
robert.castelo at upf.edu
Mon Nov 7 18:49:31 CET 2011
hi again,
could you give me the result of typing
gsl-config --version
in your terminal window??
thanks,
robert.
On Mon, 2011-11-07 at 12:35 -0500, Lapointe, David wrote:
> Hi Robert,
>
> I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine.
>
> David
>
> -----Original Message-----
> From: Robert Castelo [mailto:robert.castelo at upf.edu]
> Sent: Monday, November 07, 2011 12:24 PM
> To: Lapointe, David
> Cc: bioconductor at r-project.org
> Subject: RE: [BioC] problem with using GSVA package
>
> 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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