[Bioc-devel] GLX extension missing on petty
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Ji?? Hon <xhonji01 at stud.fit.vutbr.cz> wrote:
Hi, the latest bioc build of my new package 'triplex' on petty ended with this error message: Warning in rgl.init(initValue) : RGL: GLX extension missing on server Warning in fun(libname, pkgname) : error in rgl_init For full report see http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html And I am wondering if there is anything I could do to fix this. Probably it's a build system problem, but other packages that depends on rgl and plots in 3D have no such build error (i.e. RDRToolbox) and that makes me sligthly nervous, so I would really appreciate any advice.
This is a build system problem, and I am looking into it. The build system runs under Xvfb, but I have no problem building your package when logged into the console of petty. However, do get a segfault when running R CMD check on the triplex source tarball: $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz [...] * checking examples ...sh: line 1: 41089 Segmentation fault LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R ERROR Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed The error most likely occurred in:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: triplex-package
### Title: Triplex search and visualization package
### Aliases: triplex-package triplex
### Keywords: package
### ** Examples
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq)
Searching for triplex type 0... Searching for triplex type 1... Searching for triplex type 2... Searching for triplex type 3... Searching for triplex type 4... Searching for triplex type 5... Searching for triplex type 6... Searching for triplex type 7...
triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
triplex.3D(t[1])
*** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: .C(rgl_material, success = FALSE, idata, cdata, ddata) 2: rgl.material(color = color, back = back, ...) 3: rgl.bg(color = bgr.col) 4: triplex.3D(t[1]) aborting ... Dan
Thank you a lot for your time and patience, Jirka
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