On Apr 6, 2014, at 9:50 AM, David Winsemius <[email protected]> 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 its 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 <[email protected]>
>> 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 <[email protected]>
>>> wrote:
>>>
>>>> Thank you for the pointer. Thats 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 <[email protected]>
>>>> 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
>>>>>> [email protected]
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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
>>>>>> [email protected]
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Brian D. Ripley, [email protected]
>>>>> 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
>>>> [email protected]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
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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
>>
>> [email protected]
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> [email protected]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> David Winsemius, MD
> Alameda, CA, USA
>
> _______________________________________________
> R-SIG-Mac mailing list
> [email protected]
> 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
[email protected]
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