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
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
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, 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