[Bioc-devel] GLX extension missing on petty

Dne Fri, 05 Apr 2013 19:07:12 +0200 Dan Tenenbaum <dtenenba at fhcrc.org>
napsal(a):

On Fri, Apr 5, 2013 at 2:11 AM, Ji?? Hon <xhonji01 at stud.fit.vutbr.cz>
wrote:

In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).

Thank you a lot for tracking that down. Unfortunately all vignette code
chunks that use rgl have been always disabled with eval=FALSE. That
probably
means we have no way to workaround this problem on petty.

Turns out the real problem was unescaped accented characters in the
vignette. Fixing that  along with two dontrun tags in example sections
allows the package to build and check on Mac. I've made the changes in
release and devel.

Thanks a lot for that, still it didn't pass check on Mac. So I removed the
work around of rgl segfault on Mac that is probably unnecessary and I hope
it helps. With dontrun tags around triplex.3D call no other rgl code should
be executed during check.

Jirka

Dan

Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum <dtenenba at fhcrc.org>
napsal(a):

On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum <dtenenba at fhcrc.org>
wrote:

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.

A little more info on this.

There are two problems. The first is that as mentioned before, our
builds do not run physically logged into the console; they use a
virtual frame buffer (Xvfb).

We could look into changing this, but at present triplex seems to be
the only package having this problem.

Xvfb apparently does not have the OpenGL extensions compiled in. I
will check with the XQuartz people. They have been responsive before.

The second problem is if I do log into the actual physical console of
the machine, I am able to build triplex but I get the following
segfault when trying to run R CMD check on triplex:

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 ...

This turns out to be reproducible simply like this:

library(rgl)
example(rgl.material)

And it's caused by the following line (Material.cpp:39) in the rgl
package:

  const char* version = (const char*)glGetString(GL_VERSION);

glGetString() is a function in the OpenGL library and it is segfaulting.


Obviously that should not be happening. I'll try to track that down.

In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).

The problem as far as I can tell is just on Snow Leopard which is what
we use on our build systems.
The package builds, checks, installs and runs OK on my Mountain Lion
laptop.

Dan

Dan

Thank you a lot for your time and patience,
Jirka