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.
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