[Bioc-devel] GLX extension missing on petty

[Jiří Hon]

> 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.

Thank you a lot for your immediate reaction and please let me know if I  
could help with anything.

Jirka

Dne Wed, 03 Apr 2013 18:45:31 +0200 Dan Tenenbaum <dtenenba at fhcrc.org>  
napsal(a):

> 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.
>
>
> 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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