Bug 16706 - Interfacing with Finder on OS X 10.11 causes crashes
Summary: Interfacing with Finder on OS X 10.11 causes crashes
Status: UNCONFIRMED
Alias: None
Product: R
Classification: Unclassified
Component: Mac GUI / Mac specific (show other bugs)
Version: R 3.2.3
Hardware: x86_64/x64/amd64 (64-bit) Other
: P5 critical
Assignee: Simon Urbanek
URL:
Depends on:
Blocks:
 
Reported: 2016-02-09 22:59 UTC by E Lusczek
Modified: 2016-05-18 17:22 UTC (History)
4 users (show)

See Also:


Attachments
crash report from most recent instance (994.78 KB, text/rtf)
2016-02-09 22:59 UTC, E Lusczek
Details
Crash report from Feb. 25, 2016 (961.61 KB, text/rtf)
2016-02-25 18:42 UTC, E Lusczek
Details

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Description E Lusczek 2016-02-09 22:59:56 UTC
Created attachment 2021 [details]
crash report from most recent instance

R version 3.2.3
OS X version 10.11.3

Using Finder commands consistently causes R to crash.  It happens often (several times a day), but does not happen every time I interface with Finder through R.  The two operations that will cause a crash are opening a .R file, and saving quartz output as a .pdf.  Crash report attached. This is driving me mad and making work very difficult to do.  I have not been able to find anything in forums or FAQs that point to others experiencing this issue.  The IT helpdesk at my University has also been no help.

Output from Sys.getenv()

__CF_USER_TEXT_ENCODING      0x1F5:0:0
Apple_PubSub_Socket_Render   /private/tmp/com.apple.launchd.xvxc9Qxp1T/Render
DISPLAY                      /private/tmp/com.apple.launchd.nrdAkZuiMY/org.macosforge.xquartz:0
EDITOR                       vi
HOME                         /Users/lusc0006
LANG                         en_US.UTF-8
LN_S                         ln -s
LOGNAME                      lusc0006
MAKE                         make
PAGER                        /usr/bin/less
PATH                         /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
R_BROWSER                    /usr/bin/open
R_BZIPCMD                    /usr/bin/bzip2
R_DOC_DIR                    /Library/Frameworks/R.framework/Resources/doc
R_GUI_APP_REVISION           7060
R_GUI_APP_VERSION            1.66
R_GZIPCMD                    /usr/bin/gzip
R_HOME                       /Library/Frameworks/R.framework/Resources
R_INCLUDE_DIR                /Library/Frameworks/R.framework/Resources/include
R_LIBS_SITE                  
R_LIBS_USER                  ~/Library/R/3.2/library
R_PAPERSIZE                  a4
R_PDFVIEWER                  /usr/bin/open
R_PLATFORM                   x86_64-apple-darwin13.4.0
R_PRINTCMD                   lpr
R_QPDF                       /Library/Frameworks/R.framework/Resources/bin/qpdf
R_RD4PDF                     times,inconsolata,hyper
R_SESSION_TMPDIR             /var/folders/m2/2c80w28d51b2rbvsr6lxf1cr0000gn/T//Rtmp9fEO67
R_SHARE_DIR                  /Library/Frameworks/R.framework/Resources/share
R_SYSTEM_ABI                 osx,gcc,gxx,gfortran,?
R_TEXI2DVICMD                /usr/local/bin/texi2dvi
R_UNZIPCMD                   /usr/bin/unzip
R_ZIPCMD                     /usr/bin/zip
SED                          /usr/bin/sed
SHELL                        /bin/bash
SSH_AUTH_SOCK                /private/tmp/com.apple.launchd.eDATTMJAph/Listeners
TAR                          /usr/bin/tar
TMPDIR                       /var/folders/m2/2c80w28d51b2rbvsr6lxf1cr0000gn/T/
USER                         lusc0006
XPC_FLAGS                    0x0
XPC_SERVICE_NAME             org.R-project.R.118112
Comment 1 E Lusczek 2016-02-11 14:55:48 UTC
One other comment:

If I want to rewrite a figure from Quartz, I would just click on the existing file when I save.  This always causes R to crash.  

Thanks, and hope you can provide some guidance.
Elizabeth
Comment 3 Duncan Murdoch 2016-02-12 12:19:24 UTC
(Sorry, I posted the wrong URL; my previous message should now be hidden).

You are using R.app version 7060.  Some bugs like yours have been fixed since then in the nightly builds.  Could you try one of them, for example today's latest is

http://r.research.att.com/mavericks/R-3.2-branch/R-GUI-7128-3.2-mavericks-Release.dmg

If you see this later, look through the list of Mac OS X GUI builds at r.research.att.com.  You want one labelled 3.2-mavericks-Release for your OS and R version.
Comment 4 E Lusczek 2016-02-25 18:42:47 UTC
Created attachment 2030 [details]
Crash report from Feb. 25, 2016

Hi again,

I had installed the most recent build as you advised a few weeks ago and everything had been fine up until today.

Today R has crashed two times for me. Both crashes have occurred when opening a new .R file via the File menu (File->Open Document->Crash).

Immediately after the first crash today, I updated to the most recent build, 7135.  However, it just crashed again....and here we are.

Thanks very much for your help!
Comment 5 Simon Urbanek 2016-02-26 02:34:18 UTC
Thanks. However, the attachment here is not a crash log - it doesn't show any crashes. Are you sure you have attached the right file? Thanks.
Comment 6 E Lusczek 2016-02-26 17:10:36 UTC
Hmm, That file is what shows up in the Console record of the event.
Comment 7 E Lusczek 2016-03-01 21:12:47 UTC
Hi Simon, is this information helpful? I am still having issues with R crashing when I open files.

Thanks.
______________________________________________________________



Process:               R [55127]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               ???
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [55127]
User ID:               501

Date/Time:             2016-02-25 10:38:03.614 -0600
OS Version:            Mac OS X 10.11.3 (15D21)
Report Version:        11
Anonymous UUID:        A8CB1119-A3EA-923E-F8BC-F525FAAE9B8C

Sleep/Wake UUID:       0B3EB8A9-601F-4917-86C8-C60905C1620D

Time Awake Since Boot: 240000 seconds
Time Since Wake:       12000 seconds

System Integrity Protection: enabled

Crashed Thread:        0

Exception Type:        EXC_BREAKPOINT (SIGTRAP)
Exception Codes:       0x0000000000000002, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Application Specific Information:
dyld: launch, loading dependent libraries

Dyld Error Message:
  Library not loaded: /Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libR.dylib
  Referenced from: /Applications/R.app/Contents/MacOS/R
  Reason: image not found

Binary Images:
    0x7fff602de000 -     0x7fff60315007  dyld (360.19) <9D05FDF4-65CE-3B53-86D4-ABE1A5BF35F3> /usr/lib/dyld


System Profile:
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x111), Broadcom BCM43xx 1.0 (7.21.94.136.1a1)
Bluetooth: Version 4.4.3f4 16616, 3 services, 27 devices, 1 incoming serial ports
Thunderbolt Bus: iMac, Apple Inc., 23.10
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
USB Device: USB 3.0 Bus
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: FaceTime HD Camera (Built-in)
Serial ATA Device: APPLE HDD ST1000LM024, 1 TB
Model: iMac14,1, BootROM IM141.0118.B11, 4 processors, Intel Core i5, 2.7 GHz, 16 GB, SMC 2.14f24
Network Service: Ethernet, Ethernet, en0
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
Comment 8 Peter Dalgaard 2016-03-02 07:29:58 UTC
Umm, 

Dyld Error Message:
  Library not loaded: /Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libR.dylib
  Referenced from: /Applications/R.app/Contents/MacOS/R
  Reason: image not found

Note 3.3, i.e. this is for R-devel. Are you somehow mixing versions?
Comment 9 E Lusczek 2016-03-02 12:55:10 UTC
My bad--I downloaded the wrong package from r.research.att.com and accidentally included that error.  

I am at my wit's end with solving the issue I'm having with R and thus making dumb mistakes.

Plan is to clear out all error messages in Console, upgrade to the newest nightly build for 3.2, and go from there. 

Thanks for your patience.
Comment 10 Erik Wright 2016-05-18 14:59:32 UTC
I just want to chime in here to say that I also experience a permanent hang whenever I press the "Open document in editor" button on the R Mac GUI.  Using R.app GUI 1.68 (7202) x86_64-apple-darwin13.4.0
Comment 11 E Lusczek 2016-05-18 15:28:26 UTC
Erik, I found that opening R from the terminal goes a long way toward solving this issue. It happens far less frequently than it used to.  

Just open up a Terminal and enter
 /Applications/R.app/Contents/MacOS/R
Comment 12 Erik Wright 2016-05-18 17:22:43 UTC
Sorry, that did not fix the issue.