From mtmorgan at fhcrc.org  Thu Jun 21 22:46:32 2007
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 21 Jun 2007 13:46:32 -0700
Subject: [Rd] segfault during cbind
Message-ID: <6phd4zpm3x3.fsf@gopher4.fhcrc.org>

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



[Rd] segfault during cbind
Martin Morgan