I'm forwarding a bug report from Jeff Gove that didn't make it to the list.
-Deepayan
------- Original Message --------
Subject: alpha transparency crashes R
Date: Fri, 07 Nov 2008 14:32:27 -0500
From: jeff gove <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
I ran into a problem with R crashing when a certain number of
transparent objects (e.g., symbols) are sent to a PDF output device.
This has happened on R 2.71, 2.7.2 (Fedora 8 and Ububtu 8.04
platforms) and now 2.8.0 (I've only tried Fedora 8). The current
pertinent R system stats are...
R.version
_
platform x86_64-redhat-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 8.0
year 2008
month 10
day 20
svn rev 46754
language R
version.string R version 2.8.0 (2008-10-20)
The following small example program when run with n large enough
(e.g., n=1000) and transparency will crash R...
alphaBomb.r = function(n=100, wantAlpha=T) {
df = data.frame(a=rnorm(n),b=runif(n))
if(wantAlpha)
alpha=runif(n)
else
alpha = 1
j = xyplot(b~a, df, alpha=alpha, pch=19)
print(j)
trellis.device('pdf',file='alphaBomb.pdf',version='1.4')
print(j)
dev.off()
}
Please note that the crash seems to occur in the dev.off() component,
and that the file actually seems to get written out correctly. The
trace of the bomb is found below, excluding the memory map. Please
also note that it may be somehow related to grid, as the following
code (supplied by Deepayan Sarkar) using base graphics does not crash
R, even with n=100000...
pdf()
n = 1000
plot(rnorm(n), rnorm(n), col = rgb(0, 0, 0, alpha = runif(n)), pch = 16)
dev.off()
The error trace from the above alphaBomb.r() code is...
R> alphaBomb.r(100) #this is fine
X11cairo
2
R> alphaBomb.r(1000,F) #also fine
R> alphaBomb.r(1000)
*** glibc detected *** /usr/lib64/R/bin/exec/R: double free or
corruption (!prev): 0x00000000032c1d90 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3ee8c72832]
/lib64/libc.so.6(cfree+0x8c)[0x3ee8c75f2c]
/usr/lib64/R/library/grDevices/libs/grDevices.so[0x2aaab000b0fc]
/usr/lib64/R/lib/libR.so[0x3d1f48ddd3]
/usr/lib64/R/lib/libR.so[0x3d1f48e2dc]
/usr/lib64/R/lib/libR.so[0x3d1f4ec81c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x42e)[0x3d1f4be8ae]
/usr/lib64/R/lib/libR.so[0x3d1f4bf572]
/usr/lib64/R/lib/libR.so(Rf_eval+0x42e)[0x3d1f4be8ae]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x291)[0x3d1f4c0bf1]
/usr/lib64/R/lib/libR.so(Rf_eval+0x303)[0x3d1f4be783]
/usr/lib64/R/lib/libR.so[0x3d1f4bf572]
/usr/lib64/R/lib/libR.so(Rf_eval+0x42e)[0x3d1f4be8ae]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x291)[0x3d1f4c0bf1]
/usr/lib64/R/lib/libR.so(Rf_eval+0x303)[0x3d1f4be783]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x188)[0x3d1f4dc878]
/usr/lib64/R/lib/libR.so[0x3d1f4dcb90]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0x50)[0x3d1f4dcec0]
/usr/lib64/R/bin/exec/R(main+0x1b)[0x40082b]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3ee8c1e074]
/usr/lib64/R/bin/exec/R[0x400729]
======= Memory map: ========
etc...
Please note that R only crashes with PDF output; tiff, png and eps
(even though it doesn't accept transparency) all exit cleanly.
My version of glibc is 2.7.
Thanks, I hope that the problem is already resolved!
Jeff
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