[BioC] problems installing lumi

[Ina Hoeschele]

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’ ...
...

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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