On Thu, 21 Jun 2007, Martin Morgan wrote: > Yes, that seems to do the trick, for both seg fault and valgrind! > Thanks very much.
Thanks: this and a similar one elsewhere seem long-standing bugs in bind.c Will commit shortly. > > Martin > > Prof Brian Ripley <[EMAIL PROTECTED]> writes: > >> 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, [EMAIL PROTECTED] >> 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 > > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel