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 > > > [[alternative HTML version deleted]]