On 02/01/2016 5:47 PM, David Winsemius wrote:
On Jan 2, 2016, at 10:34 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
On 02/01/2016 12:47 PM, Joseph Kunkel wrote:
Duncan, The rgl (binary) download says it, ver 0.95.1201, is as up to date as
binaries are for my MacBook Pro retina early 2013 with OS X El Capitan w. 16 GB
ram.
That version is just over a year old. We are getting closer to tracking down the problem
with newer ones that has prevented them from being distributed as binaries on OSX, so you
will likely find at some point that an "update.packages()" call causes you to
jump ahead a lot of versions. You can read the change list here:
https://r-forge.r-project.org/scm/viewvc.php/pkg/rgl/inst/NEWS?view=markup&root=rgl
(This goes a little newer than the CRAN version.)
Duncan Murdoch
Dear Joseph;
Since I started this thread and am a *NIX noob and not an experienced package developer,
I thought I would recount my stumbling efforts (at least the successful portions of them)
toward moving to the development version of `rgl` as opposed to the current CRAN version,
1435. I had earlier reported success in compiling from source and loading the version
1435 source, so I will assume that you are able to do that. If you don't have XCode and
XQuartz, you should start there.. I think this is an effective test of having the needed
XCode (mine is Version 7.2 (7C68) ) and XQuartz 2.7.8 (xorg-server 1.16.4) packages,
since I'm pretty sure something would fail if either of them are not paired to the El Cap
OS. I first tried the recommended checkout of the source from R-Forge. I was at at a
Terminal prompt and at the "user-root" which is `~/` in Unix-speak:
The way you describe below works, but there are easier ways: install
Xcode and Xquartz, then from within the R.app GUI, use the package
installer menu to install it from "CRAN (sources)" (for the latest CRAN
version), or "Other Repository", "http://r-forge.r-project.org";, with
"Binary format packages" unchecked. This will get the latest build from
R-forge.
The main reason you'd want to use svn is if you (think you) find a bug,
and want to play around with the source in order to isolate it. Or if
you just want to play around with the source for fun.
Duncan Murdoch
svn checkout svn://svn.r-forge.r-project.org/svnroot/rgl/
#----
# ... a really large number of files were downloaded ...
# That created a directory at the "user-root" named rgl which had in it a sub
directory named ~/rgl/pkg/ with a further subdirectory named ~/rgl/pkg/rgl/ , which was
where all the good stuff was sitting.
# So after some flailing around and reading some manuals, I got this to
succeed (at a Terminal prompt):
R CMD build -l ~/rgl/pkg/rgl rgl > rgl.log 2>&1
#-----------
# contents of log file
#-------------
Warning: unknown option ‘-l’
* checking for file ‘/Users/davidwinsemius/rgl/pkg/rgl/DESCRIPTION’ ... OK
* preparing ‘rgl’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘rgl/src/ext/GLsdk/GL/codegen’
* building ‘rgl_0.95.1438.tar.gz’
* checking for file ‘rgl/DESCRIPTION’ ... NO
#end contents------
# So I would drop that "-l" from that "CMD build"-call
# It was a hangover from a failed call to INSTALL
# However, since there were no errors
# ... and I could see rgl_0.95.1438.tar.gz in ~/
# I then tried this for an R console session:
install.packages("/Users/davidwinsemius/rgl_0.95.1438.tar.gz", repo=NULL,
dependencies=TRUE, type="source")
# Success.
Duncan is exhibiting an abundance of caution in not recommending that people
use the current version if it fails the automatic compilation checks. The
alternative for me was not having any version of 'rgl' that would work. The
version on CRAN will compile and load, but it does so with a warnign about some
difficulty with initialization and then fails to display any graphs ... at all.
--
David.
Thanks for the quick view of the error codes.
Joe Kunkel
On Jan 2, 2016, at 11:47 AM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
On 02/01/2016 10:23 AM, Joseph Kunkel wrote:
What is the recomendation about upgrading to R 3.2.3 for someone who is now
working on a project that is highly invested in using rgl? I am a bit
reluctant to fall far behind in upgrades but using the MacGUI and R 3.2.2 is
working reasonably well for me.
You didn't say what version of rgl you're using.
I have gotten some error complaints during/after rgl use which might be an
indication that I should upgrade?
Error 1 in MacGUI window:
2016-01-01 21:52:05.063 R[2942:183303] -deltaZ is deprecated for
NSEventTypeMagnify. Please use -magnification.
I don't think this is present in the current rgl. I don't remember if it was
there in earlier versions, but your verbose error message doesn't show any rgl
activity as far as I can see.
Duncan Murdoch
Verbose error 2 in MacGUI window:
2016-01-01 21:33:36.342 R[2942:183303] -[GLView delegate]: unrecognized
selector sent to instance 0x7f9690b73a70
2016-01-01 21:33:36.342 R[2942:183303] An uncaught exception was raised
2016-01-01 21:33:36.343 R[2942:183303] -[GLView delegate]: unrecognized
selector sent to instance 0x7f9690b73a70
2016-01-01 21:33:36.349 R[2942:183303] (
0 CoreFoundation 0x00007fff92e77ae2
__exceptionPreprocess + 178
1 libobjc.A.dylib 0x00007fff91c7d73c
objc_exception_throw + 48
2 CoreFoundation 0x00007fff92e7ab9d
-[NSObject(NSObject) doesNotRecognizeSelector:] + 205
3 CoreFoundation 0x00007fff92db3601
___forwarding___ + 1009
4 CoreFoundation 0x00007fff92db3188
_CF_forwarding_prep_0 + 120
5 R 0x000000010f78f1aa
-[RController validateMenuItem:] + 1002
6 AppKit 0x00007fff8c9a66f6 -[NSMenu
_enableItem:] + 706
7 AppKit 0x00007fff8c9b8152
-[NSCarbonMenuImpl _carbonUpdateStatusEvent:handlerCallRef:] + 517
8 AppKit 0x00007fff8c9aaea1
NSSLMMenuEventHandler + 708
9 HIToolbox 0x00007fff9456b7be
_ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec
+ 1231
10 HIToolbox 0x00007fff9456ac48
_ZL30SendEventToEventTargetInternalP14OpaqueEventRefP20OpaqueEventTargetRefP14HandlerCallRec
+ 404
11 HIToolbox 0x00007fff945809e6
SendEventToEventTarget + 40
12 HIToolbox 0x00007fff945ca99a
_ZL18SendHICommandEventjPK9HICommandjjhPKvP20OpaqueEventTargetRefS5_PP14OpaqueEventRef
+ 411
13 HIToolbox 0x00007fff945dcc2f
UpdateHICommandStatusWithCachedEvent + 47
14 HIToolbox 0x00007fff94566deb
_ZN13HIApplication12EventHandlerEP25OpaqueEventHandlerCallRefP14OpaqueEventRefPv
+ 2787
15 HIToolbox 0x00007fff9456b7be
_ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec
+ 1231
16 HIToolbox 0x00007fff9456ac48
_ZL30SendEventToEventTargetInternalP14OpaqueEventRefP20OpaqueEventTargetRefP14HandlerCallRec
+ 404
17 HIToolbox 0x00007fff945809e6
SendEventToEventTarget + 40
18 HIToolbox 0x00007fff945dc852
_ZL15SendMenuOpeningP14MenuSelectDataP8MenuDatadjjP14__CFDictionaryhPh + 716
19 HIToolbox 0x00007fff945f6d24
_ZL11DrawTheMenuP14MenuSelectDataPP9__CFArrayhPh + 280
20 HIToolbox 0x00007fff945f6a21
_ZL11MenuChangedP14MenuSelectDatahh + 316
21 HIToolbox 0x00007fff94711207
_ZL15TrackMenuCommonR14MenuSelectDataPhP13SelectionDataP10MenuResultS5_ + 1175
22 HIToolbox 0x00007fff945f64fa
_ZL14MenuSelectCoreP8MenuData5PointdjPP13OpaqueMenuRefPt + 555
23 HIToolbox 0x00007fff945f6230
_HandleMenuSelection2 + 460
24 AppKit 0x00007fff8c8d575e
_NSHandleCarbonMenuEvent + 277
25 AppKit 0x00007fff8c815435
_DPSNextEvent + 1906
26 AppKit 0x00007fff8cbe1943
-[NSApplication _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 454
27 R 0x000000010f79031c
-[RController doProcessEvents:] + 204
28 R 0x000000010f78a72a
-[RController handleReadConsole:] + 186
29 R 0x000000010f793f99
Re_ReadConsole + 185
30 libR.dylib 0x000000010f9c071f R_ReplDLLdo1
+ 143
31 R 0x000000010f7a2367
run_REngineRmainloop + 295
32 R 0x000000010f79673a -[REngine
runREPL] + 138
33 R 0x000000010f78574f main + 815
34 libdyld.dylib 0x00007fff8e5e65ad start + 1
35 ??? 0x0000000000000001 0x0 + 1
)
The prior error did not seem to affect the visual output of rgl but is
troublesome.
Joe Kunkel
-·. .· ·. .><((((º>·. .· ·. .><((((º>·. .· ·. .><((((º> .··.· >=-
=º}}}}}><
Joseph G. Kunkel, Emeritus Professor
Biology Department
UMass Amherst
Amherst MA 01003
j...@bio.umass.edu
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David Winsemius
Alameda, CA, USA
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