[Bioc-devel] GLX extension missing on petty

[Dan Tenenbaum]

Hi Jirka,


On Wed, Apr 3, 2013 at 9:06 AM, Jiří 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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