Yes, that seems to do the trick, for both seg fault and valgrind! Thanks very much.
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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel