[R-SIG-Mac] R crashes with OSX 10.9 ?
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Vincent Philion
Jun 26, 2013, 12:42:40 PM6/26/13
to r-si...@r-project.org
Hi! I had a working R installation before I got carried away and installed the OSX “Maverick” developer preview.
Now, any error in R results in a crash.
ex:
> 1+1
[1] 2
> ()
Error: unexpected ')' in "()"
*** caught segfault ***
address 0x7c0, cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Help?
Vincent Philion, agr., M.Sc.
Microbiologiste/Phytopathologiste (pomiculture)
Institut de recherche et de développement en agro-environnement
Research and Development Institute for the Agri-Environment
www.irda.qc.ca<http://www.irda.qc.ca>
Centre de recherche
335, chemin des Vingt-Cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 0G7
vincent...@irda.qc.ca<mailto:vincent...@irda.qc.ca>
Bureau: 450 653-7368 #350
Cellulaire: 514-623-8275
Skype: VENTURIA
Télécopie: 450 653-1927
Verger expérimental
330, Rang des vingt-cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 4P6
Téléphone et télécopieur : 450 653-8375
Pour nous trouver, cliquer sur le lien:
Laboratoire<http://maps.google.ca/maps/place?cid=9609486867104665866&q=irda+pfi&hl=fr&sll=45.557814,-73.360476&sspn=8.87586,1.961403&ie=UTF8&ll=45.557814,-73.360476&spn=0,0&z=16>
Verger<http://maps.google.ca/maps/place?cid=11405391288824931904&q=verger+irda&hl=fr&sll=45.54961,-73.350585&sspn=0.012504,0.018389&ie=UTF8&ll=45.54961,-73.350585&spn=0,0&z=16>
[[alternative HTML version deleted]]
Now, any error in R results in a crash.
ex:
> 1+1
[1] 2
> ()
Error: unexpected ')' in "()"
*** caught segfault ***
address 0x7c0, cause 'memory not mapped'
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Help?
Vincent Philion, agr., M.Sc.
Microbiologiste/Phytopathologiste (pomiculture)
Institut de recherche et de développement en agro-environnement
Research and Development Institute for the Agri-Environment
www.irda.qc.ca<http://www.irda.qc.ca>
Centre de recherche
335, chemin des Vingt-Cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 0G7
vincent...@irda.qc.ca<mailto:vincent...@irda.qc.ca>
Bureau: 450 653-7368 #350
Cellulaire: 514-623-8275
Skype: VENTURIA
Télécopie: 450 653-1927
Verger expérimental
330, Rang des vingt-cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 4P6
Téléphone et télécopieur : 450 653-8375
Pour nous trouver, cliquer sur le lien:
Laboratoire<http://maps.google.ca/maps/place?cid=9609486867104665866&q=irda+pfi&hl=fr&sll=45.557814,-73.360476&sspn=8.87586,1.961403&ie=UTF8&ll=45.557814,-73.360476&spn=0,0&z=16>
Verger<http://maps.google.ca/maps/place?cid=11405391288824931904&q=verger+irda&hl=fr&sll=45.54961,-73.350585&sspn=0.012504,0.018389&ie=UTF8&ll=45.54961,-73.350585&spn=0,0&z=16>
[[alternative HTML version deleted]]
Vincent Philion
Jun 26, 2013, 12:47:20 PM6/26/13
to r-si...@r-project.org
Hello again, to further document = if I select to “abort”, the following report is sent to Apple (portion of report)
Process: R [2150]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 3.0.1 GUI 1.61 Snow Leopard build (6492)
Code Type: X86-64 (Native)
Parent Process: launchd [252]
Responsible: R [2150]
User ID: 503
Date/Time: 2013-06-26 12:44:57.496 -0400
OS Version: Mac OS X 10.9 (13A497d)
Report Version: 11
Anonymous UUID: FDE00247-F8B3-25C1-B799-942C4823E9B2
Sleep/Wake UUID: 190054C0-34B5-4355-B717-91749ECB2FDE
Crashed Thread: 1
Exception Type: EXC_CRASH (SIGSEGV)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Thread 0:: Dispatch queue: com.apple.main-thread
0 libsystem_c.dylib 0x00007fff84f378f2 strlen + 18
1 libobjc.A.dylib 0x00007fff8d89612d objc_opt::objc_stringhash_t::getIndex(char const*) const + 25
Thread 1 Crashed:
0 libsystem_kernel.dylib 0x00007fff85bbde9a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8c384f4e _pthread_wqthread + 324
2 libsystem_pthread.dylib 0x00007fff8c387fd9 start_wqthread + 13
> _______________________________________________
> R-SIG-Mac mailing list
> R-SI...@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Vincent Philion, agr., M.Sc.
Microbiologiste/Phytopathologiste (pomiculture)
Institut de recherche et de développement en agro-environnement
Research and Development Institute for the Agri-Environment
www.irda.qc.ca
_______________________________________________
R-SIG-Mac mailing list
R-SI...@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Process: R [2150]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 3.0.1 GUI 1.61 Snow Leopard build (6492)
Code Type: X86-64 (Native)
Parent Process: launchd [252]
Responsible: R [2150]
User ID: 503
Date/Time: 2013-06-26 12:44:57.496 -0400
OS Version: Mac OS X 10.9 (13A497d)
Report Version: 11
Anonymous UUID: FDE00247-F8B3-25C1-B799-942C4823E9B2
Sleep/Wake UUID: 190054C0-34B5-4355-B717-91749ECB2FDE
Crashed Thread: 1
Exception Type: EXC_CRASH (SIGSEGV)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Thread 0:: Dispatch queue: com.apple.main-thread
0 libsystem_c.dylib 0x00007fff84f378f2 strlen + 18
1 libobjc.A.dylib 0x00007fff8d89612d objc_opt::objc_stringhash_t::getIndex(char const*) const + 25
Thread 1 Crashed:
0 libsystem_kernel.dylib 0x00007fff85bbde9a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff8c384f4e _pthread_wqthread + 324
2 libsystem_pthread.dylib 0x00007fff8c387fd9 start_wqthread + 13
> R-SIG-Mac mailing list
> R-SI...@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Vincent Philion, agr., M.Sc.
Microbiologiste/Phytopathologiste (pomiculture)
Institut de recherche et de développement en agro-environnement
Research and Development Institute for the Agri-Environment
www.irda.qc.ca
Centre de recherche
335, chemin des Vingt-Cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 0G7
vincent...@irda.qc.ca
335, chemin des Vingt-Cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 0G7
vincent...@irda.qc.ca
Bureau: 450 653-7368 #350
Cellulaire: 514-623-8275
Skype: VENTURIA
Télécopie: 450 653-1927
Verger expérimental
330, Rang des vingt-cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 4P6
Téléphone et télécopieur : 450 653-8375
Pour nous trouver, cliquer sur le lien:
Laboratoire
Verger
Cellulaire: 514-623-8275
Skype: VENTURIA
Télécopie: 450 653-1927
Verger expérimental
330, Rang des vingt-cinq Est
Saint-Bruno-de-Montarville (Québec) J3V 4P6
Téléphone et télécopieur : 450 653-8375
Pour nous trouver, cliquer sur le lien:
Laboratoire
_______________________________________________
R-SIG-Mac mailing list
R-SI...@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Vincent Philion
Jun 26, 2013, 12:55:50 PM6/26/13
to r-si...@r-project.org
Hi!
Sorry for the multiple emails: I think this can help knowledgeable people solve this issue:
If I use Rstudio on the same computer, all is good.
> 1+1
[1] 2
> ()
Error: unexpected ‘)' in "()"
My conclusion: it’s really R 3.0.1 GUI 1.61 Snow Leopard build (6492) that is not happy with 10.9 (developer version #2)
Take home lesson: I should stay away of development software when I have work to do!
;-)
Vincent
Sorry for the multiple emails: I think this can help knowledgeable people solve this issue:
If I use Rstudio on the same computer, all is good.
> 1+1
[1] 2
> ()
Error: unexpected ‘)' in "()"
Take home lesson: I should stay away of development software when I have work to do!
;-)
Vincent
Simon Urbanek
Jun 26, 2013, 1:22:19 PM6/26/13
to Vincent Philion, r-si...@r-project.org
On Jun 26, 2013, at 12:42 PM, Vincent Philion wrote:
> Hi! I had a working R installation before I got carried away and installed the OSX „Maverick‰ developer preview.
>
> Now, any error in R results in a crash.
>
> ex:
>
>> 1+1
> [1] 2
>
>> ()
> Error: unexpected ')' in "()"
>
> *** caught segfault ***
> address 0x7c0, cause 'memory not mapped'
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Help?
>
Wait for a stable 10.9 ;) It's a DP after all.
> Hi! I had a working R installation before I got carried away and installed the OSX „Maverick‰ developer preview.
>
> Now, any error in R results in a crash.
>
> ex:
>
>> 1+1
> [1] 2
>
>> ()
> Error: unexpected ')' in "()"
>
> *** caught segfault ***
> address 0x7c0, cause 'memory not mapped'
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Help?
>
You can also build the GUI yourself for 10.9 - this works for me (10.9 DP2 + Xcode 5 DP2):
svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
cd Mac-GUI
xcodebuild -configuration Debug
open build/Debug/R.app
Cheers,
Simon
>
> Vincent Philion, agr., M.Sc.
> Microbiologiste/Phytopathologiste (pomiculture)
>
> Institut de recherche et de développement en agro-environnement
> Research and Development Institute for the Agri-Environment
>
> www.irda.qc.ca<http://www.irda.qc.ca>
>
> Centre de recherche
> 335, chemin des Vingt-Cinq Est
> Saint-Bruno-de-Montarville (Québec) J3V 0G7
>
> vincent...@irda.qc.ca<mailto:vincent...@irda.qc.ca>
>
> Bureau: 450 653-7368 #350
> Cellulaire: 514-623-8275
> Skype: VENTURIA
> Télécopie: 450 653-1927
>
> Verger expérimental
> 330, Rang des vingt-cinq Est
> Saint-Bruno-de-Montarville (Québec) J3V 4P6
> Téléphone et télécopieur : 450 653-8375
>
> Pour nous trouver, cliquer sur le lien:
> Laboratoire<http://maps.google.ca/maps/place?cid=9609486867104665866&q=irda+pfi&hl=fr&sll=45.557814,-73.360476&sspn=8.87586,1.961403&ie=UTF8&ll=45.557814,-73.360476&spn=0,0&z=16>
> Verger<http://maps.google.ca/maps/place?cid=11405391288824931904&q=verger+irda&hl=fr&sll=45.54961,-73.350585&sspn=0.012504,0.018389&ie=UTF8&ll=45.54961,-73.350585&spn=0,0&z=16>
>
>
>
>
> [[alternative HTML version deleted]]
>
Simon Urbanek
Jun 27, 2013, 8:50:03 AM6/27/13
to Vincent Philion, r-si...@r-project.org
The most recent nightlies (from r.research.att.com ) now work on 10.9. The issue is probably in the 10.9 OS, related to autorelease pools (Apple has broken things there before), but disabling optimization for one file seems to work around it ...
Cheers,
Simon
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