On Sat, Apr 6, 2013 at 10:39 AM, Jiří Hon <xhonj...@stud.fit.vutbr.cz> wrote:
> Dne Fri, 05 Apr 2013 19:07:12 +0200 Dan Tenenbaum <dtene...@fhcrc.org>
> napsal(a):
>
>
>> On Fri, Apr 5, 2013 at 2:11 AM, Jiří Hon <xhonj...@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.
>
Thank you. I did not mean to check that in. I can confirm that the
latest version passes check on petty.
Dan
> Jirka
>
>
>>
>> Dan
>>
>>
>>> Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum <dtene...@fhcrc.org>
>>> napsal(a):
>>>
>>>
>>>> On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum <dtene...@fhcrc.org>
>>>> wrote:
>>>>>
>>>>>
>>>>> Hi Jirka,
>>>>>
>>>>>
>>>>> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon <xhonj...@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
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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