[Rd] segfault during cbind

[Martin Morgan]

To amend, the traceback is only

> Traceback:
>  1: cbind(probe, gb)
> aborting ...

Oops. Martin

Martin Morgan <mtmorgan at fhcrc.org> writes:

> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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