On 12/16/2013 02:34 PM, Ryan C. Thompson wrote:
Indeed, loading rJava and calling .jinit() also triggers the bug. I have updated
my script (same URL as before) to demonstrate this. I run the bad code before
and after calling .jinit(), and it only crashes the second time.
The following simplified example segfaults for me.
library(locfit)
library(rJava)
.jinit()
load("Xy.rda")
weights = 1; span = 0.278355438187155; degree = 0
locfit.raw(X, y, weights = weights, alpha = span, deg = degree)
FWIW
> .jinit()
[New Thread 0x7fffee204700 (LWP 19818)]
[New Thread 0x7fffee103700 (LWP 19819)]
[New Thread 0x7fffee002700 (LWP 19820)]
[New Thread 0x7fffedf01700 (LWP 19821)]
[New Thread 0x7fffede00700 (LWP 19822)]
[New Thread 0x7fffedcff700 (LWP 19823)]
[New Thread 0x7fffedbfe700 (LWP 19824)]
[New Thread 0x7fffedafd700 (LWP 19825)]
[New Thread 0x7fffecf04700 (LWP 19826)]
[New Thread 0x7fffece03700 (LWP 19827)]
[New Thread 0x7fffecd02700 (LWP 19828)]
[New Thread 0x7fffecc01700 (LWP 19829)]
[New Thread 0x7fffecb00700 (LWP 19830)]
[New Thread 0x7fffec9ff700 (LWP 19831)]
[New Thread 0x7fffec8fe700 (LWP 19832)]
[New Thread 0x7fffec7fd700 (LWP 19833)]
and at the time of the segfault
(gdb) thread
[Current thread is 1 (Thread 0x7ffff7fd4780 (LWP 19815))]
Martin
On Mon 16 Dec 2013 02:30:34 PM PST, Simon Urbanek wrote:
On Dec 16, 2013, at 5:20 PM, Ryan <r...@thompsonclan.org> wrote:
On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:
On Mon, Dec 16, 2013 at 2:03 PM, Ryan <r...@thompsonclan.org> wrote:
I'm quite sure that it is an interaction between something that xlsxjars
does and edgeR's C code. The example I gave is a reduction from my actual
script, and I finally figured out that loading the xlsxjars package is what
triggers the crash. If I comment out the line that loads xlsxjars, then
everything runs just fine for me.
My current solution is to use the parallel package to load and use the xlsx
package only in subprocesses, so the main R process never uses java.
Out of curiosity, are you saying that if you simply load rJava instead
of xlsxjars in the same place (or perhaps load another package that
depends on rJava), is the crash avoided, too?
Yes, that's right, if I load rJava instead of xlsxjars, there is no crash.
Perhaps loading rJava does not actually launch a Java subprocess, but loading
xlxsjars does?
JVM is not started until you call
.jinit()
so try that ..
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