R 3.2.2 Hangs Reading Files in El Capitan

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]]