On Wed, Mar 30, 2011 at 12:44 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote:

> X11 is there, and I just found this online:
>
> So presumably there is not an X11.  But when I put in "capabilities",
> > it seems to be there.
>
>  R will have X11 capabilities if you have the X11 _binary_ library
> installed. To compile a package from source that needs to link with
> the X11 library you need the development headers. They come in another
> package.
>
>  From the command line, do:
>
>  sudo apt-get install libx11-dev
>
> and that should pull them from the Ubuntu repository. You'll need the
> root password for this.
>
>
Hi Ina,
This is correct. Does your error go away after installing libx11-dev?
Dan



> Ina
>
>
>
>
> ----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> To: "Ina Hoeschele" <inah@vbi.vt.edu>
> Cc: bioconductor@stat.math.ethz.ch, "Pan Du" <du4pan1@gmail.com>
> Sent: Wednesday, March 30, 2011 3:41:13 PM
> Subject: Re: [BioC] problems installing lumi
>
> On Wed, Mar 30, 2011 at 12:36 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote:
>
> > thanks much for your response, Dan. In the meantime I tried installing
> rgl
> > and I now seem to be getting a different error message:
> >
> > ...
> > configure: error: X11 not found but required, configure aborted.
> > ERROR: configuration failed for package ‘rgl’
> > * removing ‘/home/inah/R/x86_64-unknown-linux-gnu-library/2.12/rgl’
> > * installing *source* package ‘rgl’ ...
> > ...
> >
> >
> What does capabilities() say? Does it say you have X11?
> If not, then you need to build R with:
> --with-x
> in your "configure" command.
>
> Did you build R from source? If you got it from an OS package manager, it
> probably should already have been built with X11.
>
> Dan
>
>
>
> > Thanks for any comments. Ina
> >
> > ----- Original Message -----
> > From: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> > To: "Ina Hoeschele" <inah@vbi.vt.edu>
> > Cc: bioconductor@stat.math.ethz.ch, "Pan Du" <du4pan1@gmail.com>
> > Sent: Monday, March 28, 2011 5:47:33 PM
> > Subject: Re: [BioC] problems installing lumi
> >
> > On Mon, Mar 28, 2011 at 2:32 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote:
> >
> > > Hi all,
> > >  I am having trouble installing the lumi package (using biocLite) - can
> > > someone please give me a hint, please see below for error message.
> > > Thanks, Ina
> > >
> > > weight.c:249: warning: call to function ‘Rf_lgammafn’ without a real
> > > prototype
> > > local.h:89: note: ‘Rf_lgammafn’ was declared here
> > > weight.c:250: warning: call to function ‘Rf_lgammafn’ without a real
> > > prototype
> > > local.h:89: note: ‘Rf_lgammafn’ was declared here
> > > gcc -std=gnu99 -shared -L/usr/local/lib64 -o locfit.so S_enter.o band.o
> > > dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o
> > ev_interp.o
> > > ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o
> > > lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o
> > lf_wdiag.o
> > > lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o
> > m_isphr.o
> > > m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o
> > > pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o
> scb_iface.o
> > > simul.o smisc.o startlf.o weight.o -L/usr/lib64/R/lib -lR
> > > installing to
> > > /home/inah/R/x86_64-unknown-linux-gnu-library/2.12/locfit/libs
> > > ** R
> > > ** data
> > > ** preparing package for lazy loading
> > > ** help
> > > *** installing help indices
> > > ** building package indices ...
> > > ** testing if installed package can be loaded
> > > locfit 1.5-6     2010-01-20
> > >
> > > * DONE (locfit)
> > > ERROR: dependency ‘rgl’ is not available for package ‘ks’
> > > * removing ‘/home/inah/R/x86_64-unknown-linux-gnu-library/2.12/ks’
> > > ERROR: dependency ‘ks’ is not available for package ‘hdrcde’
> > > * removing ‘/home/inah/R/x86_64-unknown-linux-gnu-library/2.12/hdrcde’
> > > ERROR: dependency ‘hdrcde’ is not available for package ‘lumi’
> > > * removing ‘/home/inah/R/x86_64-unknown-linux-gnu-library/2.12/lumi’
> > >
> > > The downloaded packages are in
> > >        ‘/tmp/Rtmp2ppFf6/downloaded_packages’
> > > Warning messages:
> > > 1: In install.packages(pkgs = pkgs, repos = repos, ...) :
> > >  installation of package 'rgl' had non-zero exit status
> > > 2: In install.packages(pkgs = pkgs, repos = repos, ...) :
> > >  installation of package 'ks' had non-zero exit status
> > > 3: In install.packages(pkgs = pkgs, repos = repos, ...) :
> > >  installation of package 'hdrcde' had non-zero exit status
> > > 4: In install.packages(pkgs = pkgs, repos = repos, ...) :
> > >  installation of package 'lumi' had non-zero exit status
> > >
> > >
> > Hi Ina,
> >
> > It looks like rgl requires that you have the following installed (this is
> > from the README for the rgl package):
> >
> > OpenGL Library
> > OpenGL Utility Library (GLU)
> >
> > Also, please see the section of that README entitled
> > "BUILDING ON UNIX-STYLE OS (MacOS X, Linux, FreeBSD, ... )"
> > for some other tips on how to build rgl which is required for lumi.
> >
> > Dan
> >
> >
> >
> >
> >
> > > > sessionInfo()
> > > R version 2.12.2 (2011-02-25)
> > > Platform: x86_64-unknown-linux-gnu (64-bit)
> > >
> > > locale:
> > >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> > >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> > >  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> > >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> > >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > >
> > > attached base packages:
> > > [1] stats     graphics  grDevices utils     datasets  methods   base
> > >
> > > loaded via a namespa
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>

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