[R-SIG-Mac] [R-sig-mac] trouble with point in polyhedron computation
David Winsemius
dwinsemius at comcast.net
Sun Apr 6 18:50:04 CEST 2014
On Apr 3, 2014, at 7:29 AM, Don McKenzie wrote:
> Just to complicate things :-(
>
> If I load alphashape3d, I get a crash with the following error
>
> “To open “R”, you need to install X11. Would you like to install X11
> now?”
>
> I have been running R 3.0.3. in a vanilla quartz window in Mavericks
> (OSX 10.9) on an iMac.
>
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>> library("alphashape3d”)
>
> CRASH AND ERROR POPUP
That didn't look like an error message but rather an opportunity. Do
you have XQuartz installed in your Mac? (I haven't upgraded to
Mavericks so do not know if XQuartz ships with that version.)
https://xquartz.macosforge.org/landing/
--
David.
> On Apr 3, 2014, at 2:25 AM, Agustin Angel Diez Castillo <agustin.diez at uv.es
> > wrote:
>
>> Hi,
>> If i got it right, the original question can be addressed somewhat
>> with inashape3d (alphashape3d package), something like:
>> library(alphashape3d)
>> set1 <- matrix(rnorm(333)/2,ncol=3)
>> plot3d(set1)
>> ashape3d.obj <- ashape3d(set1, alpha = 2)
>> set2 <- matrix(rnorm(33)/2,ncol=3)
>> in3d <- inashape3d(ashape3d.obj, points = set2)
>> plot(ashape3d.obj, transparency = 0.2)
>> rgl.points(points[in3d,], col ="blue")
>>
>> On Thursday, April 3, 2014 07:38 CEST, Don McKenzie <dmck at u.washington.edu
>> > wrote:
>>
>>> Thank you for the pointer. That’s quite a list, and I expect I
>>> will have to concede defeat, lacking the skill set to adapt my use
>>> of the package.
>>>
>>> On Apr 2, 2014, at 9:11 PM, Prof Brian Ripley
>>> <ripley at stats.ox.ac.uk> wrote:
>>>
>>>> Package ptinpoly has generated hangs/segfaults in its checks for
>>>> years, across platforms. That is why there are all the
>>>> exclusions at http://cran.r-project.org/web/checks/check_results_ptinpoly.html
>>>> .
>>>>
>>>> On 03/04/2014 01:48, Don McKenzie wrote:
>>>>> I have a 3D ordination with two groups, and want to identify the
>>>>> points in one group that lie within the 3D convex hull of the
>>>>> other. I would appreciate any enlightenment about why the
>>>>> command at the end (below in a toy example) crashes R when I try
>>>>> to ID the points in the hull using pip3d(), from package
>>>>> ptinpoly. convhulln() is from package geometry. Have I not
>>>>> supplied the right “Faces” argument to pip3d()?
>>>>>
>>>>> The objects are not large and are reproduced at the bottom of
>>>>> this message.
>>>>>
>>>>> Thanks
>>>>>
>>>>> ------------------------
>>>>>> sessionInfo()
>>>>> R version 3.0.3 (2014-03-06)
>>>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>
>>>>> locale:
>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods
>>>>> base
>>>>>
>>>>> other attached packages:
>>>>> [1] ptinpoly_2.0 misc3d_0.8-4 geometry_0.3-4 magic_1.5-6
>>>>> abind_1.4-0
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] tools_3.0.3
>>>>>
>>>>> ——
>>>>>
>>>>>> set1 <- matrix(rnorm(99),ncol=3)
>>>>>> ch1 <- convhulln(set1)
>>>>>
>>>>> Output completed. Verifying that all points are below outer
>>>>> planes of
>>>>> all facets. Will make 594 distance computations.
>>>>>
>>>>>> set2 <- matrix(rnorm(33)/2,ncol=3)
>>>>>
>>>>>> temp.out <- pip3d(set1,ch1,set2)
>>>>>
>>>>> R CRASHES HERE
>>>>>
>>>>> ----------------------------------
>>>>>
>>>>>
>>>>> Don McKenzie
>>>>> Research Ecologist
>>>>> Pacific Wildland Fire Sciences Lab
>>>>> US Forest Service
>>>>>
>>>>> Affiliate Professor
>>>>> School of Environmental and Forest Sciences
>>>>> University of Washington
>>>>> dmck at uw.edu
>>>>>
>>>>>
>>>>>
>>>>> ————————————————
>>>>>
>>>>> set1
>>>>> [,1] [,2] [,3]
>>>>> [1,] -0.36381788 0.96624676 -1.09251167
>>>>> [2,] -1.09242946 -0.82002293 0.42005666
>>>>> [3,] 0.93852498 1.18059117 -0.34816811
>>>>> [4,] -0.77413132 1.06018374 -0.37589340
>>>>> [5,] -1.67759103 -1.52469985 0.85310979
>>>>> [6,] 0.81729494 -0.18900503 0.83172169
>>>>> [7,] 0.30546957 0.97549183 -1.30815121
>>>>> [8,] 0.22201517 -0.38260850 -0.05412764
>>>>> [9,] 0.48817331 1.30314678 0.19143994
>>>>> [10,] 1.89836307 -0.34575059 0.55599170
>>>>> [11,] 0.20776401 0.04977816 -0.78034565
>>>>> [12,] -0.76819740 0.24554574 0.40398017
>>>>> [13,] 0.38369531 1.07688341 -0.22686023
>>>>> [14,] 0.31806928 1.15482656 -0.99259846
>>>>> [15,] 1.07142182 -1.03495199 -0.15650968
>>>>> [16,] -1.24667302 -0.35217160 0.71090188
>>>>> [17,] -0.92079326 -1.44075490 -0.42838857
>>>>> [18,] 0.16907840 0.37587569 1.34994069
>>>>> [19,] 0.50947015 1.81852997 -1.83315646
>>>>> [20,] 0.52015187 1.56904146 0.90679914
>>>>> [21,] -0.04261864 -1.22145642 0.51953397
>>>>> [22,] -0.86611946 -1.21106313 -0.86571463
>>>>> [23,] -0.13147715 0.07893287 0.83513033
>>>>> [24,] -0.63488792 -0.89396994 0.70103420
>>>>> [25,] -0.11370015 2.00351619 -0.17652412
>>>>> [26,] -1.04527261 -0.14570830 1.64893662
>>>>> [27,] 0.46238598 -0.07990767 0.16431874
>>>>> [28,] -0.72396505 1.45081393 -0.91068823
>>>>> [29,] -0.48892499 -1.05289633 1.36531224
>>>>> [30,] 1.83781721 1.50964339 1.85100986
>>>>> [31,] 1.00023790 -0.92779325 -2.16783507
>>>>> [32,] -0.51429532 -1.44766548 -1.41456589
>>>>> [33,] -0.93249545 -0.21845332 0.75023990
>>>>>
>>>>>> ch1
>>>>> [,1] [,2] [,3]
>>>>> [1,] 15 31 10
>>>>> [2,] 29 30 10
>>>>> [3,] 29 15 10
>>>>> [4,] 26 28 25
>>>>> [5,] 26 29 5
>>>>> [6,] 26 29 30
>>>>> [7,] 32 15 31
>>>>> [8,] 19 28 25
>>>>> [9,] 19 32 31
>>>>> [10,] 19 32 28
>>>>> [11,] 19 30 25
>>>>> [12,] 19 31 10
>>>>> [13,] 19 30 10
>>>>> [14,] 21 29 5
>>>>> [15,] 21 29 15
>>>>> [16,] 21 32 5
>>>>> [17,] 21 32 15
>>>>> [18,] 20 30 25
>>>>> [19,] 20 26 25
>>>>> [20,] 20 26 30
>>>>> [21,] 16 28 5
>>>>> [22,] 16 26 5
>>>>> [23,] 16 26 28
>>>>> [24,] 22 28 5
>>>>> [25,] 22 32 5
>>>>> [26,] 22 32 28
>>>>>
>>>>>> set2
>>>>> [,1] [,2] [,3]
>>>>> [1,] 0.061298933 0.561676607 -0.29029312
>>>>> [2,] -0.227292687 0.980185118 0.21751216
>>>>> [3,] 0.182482967 0.913803801 -0.08308208
>>>>> [4,] -0.143596376 -0.007469921 -0.33050543
>>>>> [5,] -0.354096826 0.023132113 0.45463150
>>>>> [6,] 0.006247011 0.183155253 0.97496500
>>>>> [7,] 0.128600720 -0.249603537 -0.24710206
>>>>> [8,] -0.418782299 -0.325201099 0.28908138
>>>>> [9,] 0.231829464 0.343250895 0.65134735
>>>>> [10,] -0.392597726 0.126741875 0.21411363
>>>>> [11,] -0.051290704 -1.007826669 0.92808143
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>>>
>>>> --
>>>> Brian D. Ripley, ripley at stats.ox.ac.uk
>>>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/
>>>> ~ripley/
>>>> University of Oxford, Tel: +44 1865 272861 (self)
>>>> 1 South Parks Road, +44 1865 272866 (PA)
>>>> Oxford OX1 3TG, UK Fax: +44 1865 272595
>>>
>>> Don McKenzie
>>> Research Ecologist
>>> Pacific Wildland Fire Sciences Lab
>>> US Forest Service
>>>
>>> Affiliate Professor
>>> School of Environmental and Forest Sciences
>>> University of Washington
>>> dmck at uw.edu
>>>
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> Don McKenzie
> Research Ecologist
> Pacific Wildland Fire Sciences Lab
> US Forest Service
>
> Affiliate Professor
> School of Environmental and Forest Sciences
> University of Washington
>
> dmck at uw.edu
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius, MD
Alameda, CA, USA
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