[BioC] problems installing lumi

Wed Mar 30 21:44:17 CEST 2011

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.

Ina

----- Original Message -----
From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
To: "Ina Hoeschele" <inah at vbi.vt.edu>
Cc: bioconductor at stat.math.ethz.ch, "Pan Du" <du4pan1 at 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 at 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 at fhcrc.org>
> To: "Ina Hoeschele" <inah at vbi.vt.edu>
> Cc: bioconductor at stat.math.ethz.ch, "Pan Du" <du4pan1 at 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 at 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
> >
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