[R-SIG-Mac] R 3.2.2 Hangs Reading Files in El Capitan

[boB Rudis]

Agreed that I cannot reproduce with generated data sets on el capitan
either but would be glad to test with any real data you have.

On Fri, Dec 4, 2015 at 11:23 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
> Can you include a reproducible example? This seems to work for me as expected:
>
>   x <- rnorm(1e8)
>   saveRDS(x, tmp <- tempfile())
>   file.info(tmp)$size
>   y <- readRDS(tmp)
>   identical(x,y)
>
> Could be a hw issue with your disk.
>
>
>
>
> On Sun, Nov 29, 2015 at 4:34 PM, Charles DiMaggio
> <charles.dimaggio at gmail.com> wrote:
>> Hi. After upgrading to el capitan R hangs on readRDS() and load()  for largish (say 500MB or larger) files, requiring a Force Quit of R.  I am working on a 64 GB Mac Pro machine and had no problem loading these size files prior to upgrade.  Reading and loading smaller files (1MB or less) seems to work fine. I re-installed R 3.2.2 GUI 1.66 Mavericks, XQuartz and CLT after the upgrade. Turned off SIP but experienced the same problem.
>>
>> I've looked over recent list posting about R behavior after upgrade to el capitan, and have not seen anything about this.  Am hoping soon-to-be-released R version 3.2.3 (Wooden Christmas-Tree) will address this weirdness, but wondering if anyone else has experienced anything similar?
>>
>> First few of lines of Mac Error Report below:
>>
>> Date/Time:       2015-11-28 15:45:00 -0500
>> OS Version:      Mac OS X 10.11.1 (Build 15B42)
>> Architecture:    x86_64
>> Report Version:  22
>>
>> Command:         R
>> Path:            /Applications/R.app/Contents/MacOS/R
>> Version:         R 3.2.2 GUI 1.66 Mavericks build (6996)
>> Parent:          launchd [1]
>> PID:             563
>>
>> Event:           hang
>> Duration:        1.70s (process was unresponsive for 25 seconds before sampling)
>> Steps:           17 (100ms sampling interval)
>>
>> Hardware model:  MacPro6,1
>> Active cpus:     8
>>
>> ...
>>
>> Heaviest stack for the main thread of the target process:
>>   17  start + 1 (libdyld.dylib + 13741) [0x7fff88f2f5ad]
>>   17  main + 815 (R + 5967) [0x1053e374f]
>>   17  -[REngine runREPL] + 138 (R + 75578) [0x1053f473a]
>>   17  run_REngineRmainloop + 295 (R + 123751) [0x105400367]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1243228) [0x10561d85c]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 675070) [0x105592cfe]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1044002) [0x1055ece22]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 674823) [0x105592c07]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1029000) [0x1055e9388]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 673910) [0x105592876]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 750621) [0x1055a541d]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1601435) [0x105674f9b]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1592422) [0x105672c66]
>>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1594038) [0x1056732b6]
>>   14  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1596619) [0x105673ccb]
>>   7   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1595584) [0x1056738c0]
>>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1592773) [0x105672dc5]
>>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1600194) [0x105674ac2]
>>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 383889) [0x10554bb91]
>>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 316653) [0x10553b4ed]
>>   1   inflate + 258 (libz.1.dylib + 20735) [0x7fff9e4e30ff] (running)
>>
>>
>> Process:         R [563]
>> Path:            /Applications/R.app/Contents/MacOS/R
>> Architecture:    x86_64
>> Parent:          launchd [1]
>> UID:             501
>> Task size:       350330 pages (+14553)
>> CPU Time:        1.604s
>> Note:            Unresponsive for 25 seconds before sampling
>> Note:            2 idle work queue threads omitted
>>
>>
>> Cheers
>>
>> Charles
>>
>>
>> Charles DiMaggio, PhD, MPH
>> Director of Injury Research
>> Department of Surgery
>> New York University School of Medicine
>> Division of Trauma, Emergency Surgery and Critical Care Surgery
>> Bellevue Hosptial Center
>> 462 First Avenue, NBV 15
>> New York, NY 10016-9196
>> Charles.Dimaggio at nyumc.org
>> Office: 212.263.3202
>> Mobile: 516.308.6426
>>
>>
>>
>>
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
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