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[BUGZILLA #13264] alpha transparency crashes R #3483

Closed MichaelChirico closed 4 years ago

MichaelChirico commented 4 years ago

From: jeff gove <jhgove@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">

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(∼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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MichaelChirico commented 4 years ago

NOTES: Fixed in 2.8.1 we believe

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MichaelChirico commented 4 years ago

Audit (from Jitterbug): Fri Nov 7 20:48:08 2008 ripley moved from incoming to Graphics Fri Dec 12 15:18:20 2008 ripley changed notes Fri Dec 12 14:18:20 2008 ripley moved from Graphics to Graphics-fixed

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