From ripley at stats.ox.ac.uk  Thu Jun 21 23:10:51 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Thu, 21 Jun 2007 22:10:51 +0100 (BST)
Subject: [Rd] segfault during cbind
In-Reply-To: <6phd4zpm3x3.fsf@gopher4.fhcrc.org>
References: <6phd4zpm3x3.fsf@gopher4.fhcrc.org>
Message-ID: <Pine.LNX.4.64.0706212206280.27147@gannet.stats.ox.ac.uk>

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



[Rd] segfault during cbind
Prof Brian Ripley