From mtmorgan at fhcrc.org  Thu Jun 21 23:23:37 2007
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 21 Jun 2007 14:23:37 -0700
Subject: [Rd] segfault during cbind
In-Reply-To: <Pine.LNX.4.64.0706212206280.27147@gannet.stats.ox.ac.uk> (Brian
	Ripley's message of "Thu, 21 Jun 2007 22:10:51 +0100 (BST)")
References: <6phd4zpm3x3.fsf@gopher4.fhcrc.org>
	<Pine.LNX.4.64.0706212206280.27147@gannet.stats.ox.ac.uk>
Message-ID: <6ph4pl1m27a.fsf@gopher4.fhcrc.org>

Yes, that seems to do the trick, for both seg fault and valgrind!
Thanks very much.

Martin

Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:

> I think it needs to be
>
>  		case LISTSXP:
>  		    PROTECT(u = coerceVector(u, mode));
>  		    k = LENGTH(u);
>  		    idx = (!isMatrix(u)) ? rows : k;
>  		    for (i = 0; i < idx; i++)
>  			SET_VECTOR_ELT(result, n++,
>  				       duplicate(VECTOR_ELT(u, i % k)));
>  		    UNPROTECT(1);
>  		    break;
>
> around 1258 in bind.c.  Can you test that please?
>
>
> On Thu, 21 Jun 2007, Martin Morgan wrote:
>
>> The following code results in a seg fault.
>>
>>> sessionInfo()
>> R version 2.6.0 Under development (unstable) (2007-06-21 r42013)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> csvFile <- read.csv("Barley1.na22.annot.csv", as.is=TRUE, na.strings="---")
>>> probe <- csvFile[,1]
>>> gb <- csvFile[, 9]
>>> rm(csvFile)
>>> gb <- lapply(unlist(gb),
>> +              function(x) toupper(strsplit(x,"\\.")[[1]][1]))
>>> id_file <- cbind(probe,gb)
>>
>> *** caught segfault ***
>> address 0x2c9f0, cause 'memory not mapped'
>>
>> Traceback:
>> 1: cbind(probe, gb)
>> 2: makeBasefiles("Barley1.na22.annot.csv")
>> aborting ...
>> Segmentation fault
>>
>> valgrind says
>>
>> ==25398== Invalid read of size 8
>> ==25398==    at 0x4E7BB2D: cbind (bind.c:1258)
>> ==25398==    by 0x4E7B430: do_bind (bind.c:1113)
>> ==25398==    by 0x4F42A1B: do_internal (names.c:1116)
>> ==25398==    by 0x4EF959B: Rf_eval (eval.c:463)
>> ==25398==    by 0x4EF9F91: Rf_applyClosure (eval.c:666)
>> ==25398==    by 0x4EF988D: Rf_eval (eval.c:507)
>> ==25398==    by 0x4EFC3E0: do_set (eval.c:1404)
>> ==25398==    by 0x4EF959B: Rf_eval (eval.c:463)
>> ==25398==    by 0x4EFB866: do_begin (eval.c:1156)
>> ==25398==    by 0x4EF959B: Rf_eval (eval.c:463)
>> ==25398==    by 0x4EF9F91: Rf_applyClosure (eval.c:666)
>> ==25398==    by 0x4EF988D: Rf_eval (eval.c:507)
>> ==25398==  Address 0x8F46010 is 72,976 bytes inside a block of size 182,760 free'd
>> ==25398==    at 0x4C226DB: free (in /usr/lib64/valgrind/amd64-linux/vgpreload_memcheck.so)
>> ==25398==    by 0x4F2D848: ReleaseLargeFreeVectors (memory.c:760)
>> ==25398==    by 0x4F359E9: RunGenCollect (memory.c:1378)
>> ==25398==    by 0x4F38938: R_gc_internal (memory.c:2171)
>> ==25398==    by 0x4F38046: Rf_allocVector (memory.c:1961)
>> ==25398==    by 0x4EDE779: duplicate1 (duplicate.c:221)
>> ==25398==    by 0x4EDD698: Rf_duplicate (duplicate.c:115)
>> ==25398==    by 0x4E7BB34: cbind (bind.c:1258)
>> ==25398==    by 0x4E7B430: do_bind (bind.c:1113)
>> ==25398==    by 0x4F42A1B: do_internal (names.c:1116)
>> ==25398==    by 0x4EF959B: Rf_eval (eval.c:463)
>> ==25398==    by 0x4EF9F91: Rf_applyClosure (eval.c:666)
>>
>> gdb says
>>
>> (gdb) backtrace
>> #0  0x00002b2dfe6940c9 in duplicate1 (s=0x2c9f0)
>>    at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134
>> #1  0x00002b2dfe694035 in Rf_duplicate (s=0x2c9f0)
>>    at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115
>> #2  0x00002b2dfe632555 in cbind (call=0xaaba48, args=0xb6abf0, mode=19,
>>    rho=0xb6ba40, deparse_level=1)
>>    at /home/mtmorgan/src/R-devel/src/main/bind.c:1263
>> #3  0x00002b2dfe631e51 in do_bind (call=0xaaba48, op=0x62f950, args=0xb6abf0,
>>    env=0xb6ba40) at /home/mtmorgan/src/R-devel/src/main/bind.c:1113
>> #4  0x00002b2dfe6f93d4 in do_internal (call=0xaabab8, op=0x62d028,
>>    args=0xaaba10, env=0xb6ba40)
>>    at /home/mtmorgan/src/R-devel/src/main/names.c:1115
>>
>> and
>>
>> (gdb) up
>> #2  0x00002b2dfe632555 in cbind (call=0xaaba48, args=0xb6abf0, mode=19,
>>    rho=0xb6ba40, deparse_level=1)
>>    at /home/mtmorgan/src/R-devel/src/main/bind.c:1263
>> (gdb) p i
>> $7 = 22839
>> (gdb) p idx
>> $8 = 22840
>>
>> Both rm and lapply are needed to trigger the fault; an R level gc()
>> before the final line 'cures' the fault (and the valgind complaint).
>>
>> The data file is available (with free registration) at
>>
>> https://www.affymetrix.com/support/file_download.affx?onloadforward=/analysis/downloads/na22/ivt/Barley1.na22.annot.csv.zip
>>
>> Martin
>>
>
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org



[Rd] segfault during cbind
Martin Morgan