date:20151204

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

2015-12-04 Thread Jeroen Ooms

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
 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.dimag...@nyumc.org
> Office: 212.263.3202
> Mobile: 516.308.6426
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2015-12-04 Thread 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  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
>  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.dimag...@nyumc.org
>> Office: 212.263.3202
>> Mobile: 516.308.6426
>>
>>
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

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

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