[R-SIG-Mac] R 3.2.2 Hangs Reading Files in El Capitan
Charles DiMaggio
charles.dimaggio at gmail.com
Mon Dec 7 15:59:56 CET 2015
Thanks very much for that, Simon. I will do that and get back to the group.
Charles
Charles DiMaggio, PhD, MPH
Director of Injury Research
Department of Surgery
New York University School of Medicine
550 First Avenue
New York, NY 10016
Direct Line: 1.516.308.6426
Office: 1.212.263.3202
charles.dimaggio at nyumc.org
> On Dec 5, 2015, at 4:51 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
>
>
> On Dec 5, 2015, at 11:24 AM, Charles DiMaggio <charles.dimaggio at gmail.com <mailto:charles.dimaggio at gmail.com>> wrote:
>
>> Bob and Jeroen, many thanks for your follow up. Unfortunately the files I was working with are under a data use agreement. But I couldn’t find any reference to similar issues online, so agree it may be an idiosyncrasy of my system. I ended up rolling back to Mavericks. I’ll wait for the official release of 3.2.3 in a few days and try again.
>>
>
> You don't need to wait - you can always try the latest build from http://r.research.att.com <http://r.research.att.com/> but since there were no changes in the area it would be surprising if it behaved any differently.
>
> If you really want to dig into it, you could run R using
> R -d lldb
> then
> r
> and do whatever you need to replicate it. Once it seems stuck, hit <Ctrl><C> and then
> bt
> to list the back trace of where it got stuck. That would help us to find out if it's getting stuck in the system itself or if it may have something to do with R.
>
> Thanks,
> Simon
>
>
>> Cheers
>>
>> Charles
>>
>>
>>> On Dec 4, 2015, at 11:39 AM, boB Rudis <bob at rudis.net> wrote:
>>>
>>> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
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>>
>> Charles DiMaggio, PhD, MPH
>> Director of Injury Research
>> Department of Surgery
>> New York University School of Medicine
>> Division of Trauma, Emergency Surgery and Surgical Critical Care
>> Bellevue Hospital Center
>> 462 First Avenue, NBV 15
>> New York, NY 10016-9196
>> Charles.Dimaggio at nyumc.org
>> Office: 212.263.3202
>> Direct: 516.308.6426
>>
>>
>>
>>
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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