[Rd] segfault during cbind

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Thu, 21 Jun 2007 13:46:32 -0700


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)

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

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Received on Thu 21 Jun 2007 - 20:51:04 GMT

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