[R-SIG-Mac] [R-sig-mac] trouble with point in polyhedron computation
Don McKenzie
dmck at u.washington.edu
Thu Apr 3 16:29:03 CEST 2014
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
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]]
>>
>
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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
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