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MichaelChirico / r-bugs

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[BUGZILLA #17191] Bug in reporting error opening a PDF output file in temp directory #6366

Closed MichaelChirico closed 4 years ago

MichaelChirico commented 4 years ago

It's hard to reproduce this problem, but looking at the code it's pretty clear what the problem is.

In R-3.3.2/src/library/grDevices/src/devPS.c, function PDF_NewPage, around line 7221:

pd->pdffp = fopen(tmp, "w+b");
free(tmp);
if(! pd->pdffp) error("cannot open file '%s', reason %s", 
              tmp, strerror(errno));

Note that tmp is freed before the error message is created. On my system, the memory manager appears to write a null byte at the beginning of the buffer when free() is called, resulting in this error message:

Error in plot.new() : cannot open file '', reason No such file or directory

The original problem is not R's bug -- I think the file system TMPDIR is pointing to gets unmounted by a long-running R job. However, the fact that the error message is broken made it harder for me to diagnose the problem. I don't know what kind of try/catch/finally mechanism R uses, but ideally free(tmp) would happen after error() is called.

Note also that R eventually dumps core, which I care about less than the broken error message.

0 0x00000037ff467934 in fwrite () from /lib64/libc.so.6

1 0x00002ae33b8c10e2 in PDF_endpage () at devPS.c:6509

2 0x00002ae33b8c284b in PDF_Close () at devPS.c:7257

3 0x00002ae338dbf05e in removeDevice.part.0 ()

from /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.3.0/lib64/R/lib/libR.so

4 0x00002ae338dbf4c9 in Rf_KillAllDevices ()

from /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.3.0/lib64/R/lib/libR.so

5 0x00002ae338ee42e4 in Rstd_CleanUp ()

from /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.3.0/lib64/R/lib/libR.so

6 0x00002ae338e21947 in run_Rmainloop ()

from /broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.3.0/lib64/R/lib/libR.so

7 0x00000000004007bb in main () at Rmain.c:29

Thanks!

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MichaelChirico commented 4 years ago

Here's how I could reliably trigger the problem (on Ubuntu 14.04) ...

## Make tempdir() unwritable system(paste("chmod a-w", tempdir()))

## compression is on by default pdf() ## Incorrect error message is in PDF_NewPage() plot.new() ## This triggers a segfault (for me at least) dev.off()

I have committed a fix to r-devel (r71752) so that, in addition to giving a better message (and not segfaulting), the error is now a warning and compression is turned off for the PDF device.

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MichaelChirico commented 4 years ago

Thanks!

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