
On Apr 6, 2014, at 9:50 AM, David Winsemius <dwinsemius@comcast.net> wrote:

> 
> 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/

I think it’s just the vanilla quartz that ships with Mavericks, so that would be what I have, but I do need to check that.  Thanks for the tip.

Don

> 
> -- 
> David.
> 
>> On Apr 3, 2014, at 2:25 AM, Agustin Angel Diez Castillo <agustin.diez@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@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@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@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@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Brian D. Ripley,                  ripley@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@uw.edu
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 	[[alternative HTML version deleted]]
>>>> 
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@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@uw.edu
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius, MD
> Alameda, CA, USA
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@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@uw.edu





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