Re: [Rd] segfault during cbind
To amend, the traceback is only Traceback: 1: cbind(probe, gb) aborting ... Oops. Martin Martin Morgan [EMAIL PROTECTED] 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 0x2b2dfe6940c9 in duplicate1 (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134 #1 0x2b2dfe694035 in Rf_duplicate (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115 #2 0x2b2dfe632555 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 0x2b2dfe631e51 in do_bind (call=0xaaba48, op=0x62f950, args=0xb6abf0, env=0xb6ba40) at /home/mtmorgan/src/R-devel/src/main/bind.c:1113 #4 0x2b2dfe6f93d4 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 0x2b2dfe632555 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault during cbind
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 0x2b2dfe6940c9 in duplicate1 (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134 #1 0x2b2dfe694035 in Rf_duplicate (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115 #2 0x2b2dfe632555 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 0x2b2dfe631e51 in do_bind (call=0xaaba48, op=0x62f950, args=0xb6abf0, env=0xb6ba40) at /home/mtmorgan/src/R-devel/src/main/bind.c:1113 #4 0x2b2dfe6f93d4 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 0x2b2dfe632555 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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault during cbind
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 0x2b2dfe6940c9 in duplicate1 (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134 #1 0x2b2dfe694035 in Rf_duplicate (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115 #2 0x2b2dfe632555 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 0x2b2dfe631e51 in do_bind (call=0xaaba48, op=0x62f950, args=0xb6abf0, env=0xb6ba40) at /home/mtmorgan/src/R-devel/src/main/bind.c:1113 #4 0x2b2dfe6f93d4 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 0x2b2dfe632555 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, UKFax: +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
Re: [Rd] segfault during cbind
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 0x2b2dfe6940c9 in duplicate1 (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:134 #1 0x2b2dfe694035 in Rf_duplicate (s=0x2c9f0) at /home/mtmorgan/src/R-devel/src/main/duplicate.c:115 #2 0x2b2dfe632555 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 0x2b2dfe631e51 in do_bind (call=0xaaba48, op=0x62f950, args=0xb6abf0, env=0xb6ba40) at /home/mtmorgan/src/R-devel/src/main/bind.c:1113 #4 0x2b2dfe6f93d4 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 0x2b2dfe632555 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, UKFax: +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
