Re: [Rd] segfault with format.POSIXct()
Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. Uwe Ligges On 23.04.2010 01:32, Sebastian P. Luque wrote: Hi, I'm getting a segmentation fault as follows: ---cut here---start-- R begt- as.POSIXct(strptime(10/01/2009 06:00:00, format=%d/%m/%Y %H:%M:%S), +tz=GMT) R tser- seq(begt, by=5, length.out=91000) R tser.trunc- format(tser) Error: segfault from C stack overflow ---cut here---end With the following set up: ---cut here---start-- R sessionInfo() R version 2.11.0 RC (2010-04-19 r51778) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] slmisc_0.7.3 lattice_0.18-3 loaded via a namespace (and not attached): [1] grid_2.11.0 ---cut here---end Reducing the size of the sequence in seq.POSIXct() to 9 doesn't cause a segfault, so it seems to be a memory issue. Is this a bug? Thanks, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On 23/04/2010 7:31 AM, Uwe Ligges wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. I've just found that the bug 14267 is related to a POSIXlt formatting bug, so this is likely to be the same thing. Duncan Murdoch Uwe Ligges On 23.04.2010 01:32, Sebastian P. Luque wrote: Hi, I'm getting a segmentation fault as follows: ---cut here---start-- R begt- as.POSIXct(strptime(10/01/2009 06:00:00, format=%d/%m/%Y %H:%M:%S), +tz=GMT) R tser- seq(begt, by=5, length.out=91000) R tser.trunc- format(tser) Error: segfault from C stack overflow ---cut here---end With the following set up: ---cut here---start-- R sessionInfo() R version 2.11.0 RC (2010-04-19 r51778) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] slmisc_0.7.3 lattice_0.18-3 loaded via a namespace (and not attached): [1] grid_2.11.0 ---cut here---end Reducing the size of the sequence in seq.POSIXct() to 9 doesn't cause a segfault, so it seems to be a memory issue. Is this a bug? Thanks, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On Fri, 23 Apr 2010 07:46:10 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 23/04/2010 7:31 AM, Uwe Ligges wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. I've just found that the bug 14267 is related to a POSIXlt formatting bug, so this is likely to be the same thing. I just tried with: ---cut here---start-- R sessionInfo() R version 2.12.0 Under development (unstable) (2010-04-23 r51810) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base ---cut here---end and using a sequence of 20 worked without problems. It doesn't seem as if bug 14267 has been fixed in the 2.12.0 devel version above, but something else might have fixed the C stack overflow I'm getting. Thanks for the pointers! -- Seb __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On Fri, 23 Apr 2010 13:31:14 +0200, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. Is this with 2.11.0 ? Thanks. -- Seb __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On Apr 23, 2010, at 2:50 PM, Sebastian P. Luque wrote: On Fri, 23 Apr 2010 13:31:14 +0200, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. Is this with 2.11.0 ? Thanks. I'm getting a bit further with bug 14267: On OSX I am NOT seeing it with R-devel, although it is there with 2.11.0 Patched. Running with a non-optimized compile, I can get some more information It is happening on the i-th iteration of the loop in do_formatPOSIXlt with (gdb) p i $4 = 86870 Unfortunately, it looks like a bigger exercise to get valgrind running on Snow Leopard -- too big for Friday afternoon anyway. However, the alloca() call on line 774 of src/main/datetime.c does look suspect to me. I can see that it was introduced with r51353 and has since disappeared in R-devel (r51398). -- Seb __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On 23/04/2010 10:03 AM, peter dalgaard wrote: On Apr 23, 2010, at 2:50 PM, Sebastian P. Luque wrote: On Fri, 23 Apr 2010 13:31:14 +0200, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. Is this with 2.11.0 ? Thanks. I'm getting a bit further with bug 14267: On OSX I am NOT seeing it with R-devel, although it is there with 2.11.0 Patched. Running with a non-optimized compile, I can get some more information It is happening on the i-th iteration of the loop in do_formatPOSIXlt with (gdb) p i $4 = 86870 Unfortunately, it looks like a bigger exercise to get valgrind running on Snow Leopard -- too big for Friday afternoon anyway. However, the alloca() call on line 774 of src/main/datetime.c does look suspect to me. I can see that it was introduced with r51353 and has since disappeared in R-devel (r51398). I've just committed a patch for this on R-2-11-branch. The problem was that the alloca() was within a loop, so it kept allocating more and more space until the end of the function call, and blew the stack. In R-devel, this was changed to the C99 construct of defining a variable sized array within a block, and that was fine, because it was released at the end of the block, not at the end of the function call. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On Fri, 23 Apr 2010 16:03:15 +0200, peter dalgaard pda...@gmail.com wrote: I'm getting a bit further with bug 14267: On OSX I am NOT seeing it with R-devel, although it is there with 2.11.0 Patched. Running with a non-optimized compile, I can get some more information It is happening on the i-th iteration of the loop in do_formatPOSIXlt with (gdb) p i $4 = 86870 Unfortunately, it looks like a bigger exercise to get valgrind running on Snow Leopard -- too big for Friday afternoon anyway. However, the alloca() call on line 774 of src/main/datetime.c does look suspect to me. I can see that it was introduced with r51353 and has since disappeared in R-devel (r51398). So it does seems as if this is all related to that bug, which somehow got fixed in R-devel. Thanks everyone, -- Seb __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault with format.POSIXct()
On Apr 23, 2010, at 4:17 PM, Duncan Murdoch wrote: On 23/04/2010 10:03 AM, peter dalgaard wrote: On Apr 23, 2010, at 2:50 PM, Sebastian P. Luque wrote: On Fri, 23 Apr 2010 13:31:14 +0200, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. Is this with 2.11.0 ? Thanks. I'm getting a bit further with bug 14267: On OSX I am NOT seeing it with R-devel, although it is there with 2.11.0 Patched. Running with a non-optimized compile, I can get some more information It is happening on the i-th iteration of the loop in do_formatPOSIXlt with (gdb) p i $4 = 86870 Unfortunately, it looks like a bigger exercise to get valgrind running on Snow Leopard -- too big for Friday afternoon anyway. However, the alloca() call on line 774 of src/main/datetime.c does look suspect to me. I can see that it was introduced with r51353 and has since disappeared in R-devel (r51398). I've just committed a patch for this on R-2-11-branch. The problem was that the alloca() was within a loop, so it kept allocating more and more space until the end of the function call, and blew the stack. In R-devel, this was changed to the C99 construct of defining a variable sized array within a block, and that was fine, because it was released at the end of the block, not at the end of the function call. Yes, that's what I suspected. Thanks for the fix! -p Duncan Murdoch -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] segfault with format.POSIXct()
Hi, I'm getting a segmentation fault as follows: ---cut here---start-- R begt - as.POSIXct(strptime(10/01/2009 06:00:00, format=%d/%m/%Y %H:%M:%S), +tz=GMT) R tser - seq(begt, by=5, length.out=91000) R tser.trunc - format(tser) Error: segfault from C stack overflow ---cut here---end With the following set up: ---cut here---start-- R sessionInfo() R version 2.11.0 RC (2010-04-19 r51778) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] slmisc_0.7.3 lattice_0.18-3 loaded via a namespace (and not attached): [1] grid_2.11.0 ---cut here---end Reducing the size of the sequence in seq.POSIXct() to 9 doesn't cause a segfault, so it seems to be a memory issue. Is this a bug? Thanks, -- Seb __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
