edd at debian.org
2007-Dec-07 03:20 UTC
[Rd] Bug#454678: r-base-core: Crash when calling edit.matrix with edit.row.names = TRUE when there are no rownames (PR#10500)
Ben,
Thanks for the bug report. I am off two minds about it as discussed below.
But as it does indeed create a crash / segfault, I am passing this on to the
R bug tracker. A suggested two-line patch is below; I tested the patch
against a 'vanilla' 2.6.1 source tree.
On 6 December 2007 at 19:32, Ben Goodrich wrote:
| -----BEGIN PGP SIGNED MESSAGE-----
| Hash: SHA1
|
| Package: r-base-core
| Version: 2.6.1-1
| Severity: important
|
| Hi Dirk,
|
| My strong hunch is that this bug should just be forwarded upstream but
| it might have something to do with libc6 on Debian. To reproduce it, do
|
| args(utils:::edit.matrix)
| mat <- matrix(rnorm(30), nrow = 10, ncol = 3)
| edit(mat, edit.row.names = TRUE) #crash
I can confirm that it crashes 2.6.0 and 2.6.1. I also spent the last little
while building a (non-stripped) debug version that reveals:
(gdb) where
#0 0xb7b2ef2c in __gconv_transform_utf8_internal () from
/lib/i686/cmov/libc.so.6
#1 0xb7b89f75 in mbrtowc () from /lib/i686/cmov/libc.so.6
#2 0xb7db05e3 in Rstrwid (str=0x8052010 "\020!\005\b\002",
slen=134595712,
quote=0) at printutils.c:284
#3 0xb7db0888 in Rstrlen (s=0x8051ff8, quote=0) at printutils.c:377
#4 0xb7d2de24 in Rf_formatString (x=0x873bbb8, n=1, fieldwidth=0xbfd0fc04,
quote=0) at format.c:62
#5 0xb7db12b5 in Rf_EncodeElement (x=0x873ba10, indx=100, quote=0, dec=46
'.')
at printutils.c:576
#6 0xb754ae0d in get_col_width (DE=0xbfd100b0, col=1) at dataentry.c:804
#7 0xb754edb4 in initwin (DE=0xbfd100b0, title=0xb755eed9 "R Data
Editor")
at dataentry.c:1986
#8 0xb7549319 in RX11_dataentry (call=0x89b3fe8, op=0x806c970, args=0x8ba40c8,
rho=0x89b4bd0) at dataentry.c:382
#9 0xb7e52771 in do_dataentry (call=0x89b3fe8, op=0x806c970, args=0x8ba40c8,
rho=0x89b4bd0) at X11.c:91
#10 0xb7d6045e in do_internal (call=0x89b4020, op=0x8061fa4, args=0x8ba40c8,
env=0x89b4bd0) at names.c:1120
#11 0xb7d1f352 in Rf_eval (e=0x89b4020, rho=0x89b4bd0) at eval.c:463
#12 0xb7d21d5d in do_set (call=0x89b4074, op=0x8060df0, args=0x89b4058,
rho=0x89b4bd0) at eval.c:1407
#13 0xb7d1f352 in Rf_eval (e=0x89b4074, rho=0x89b4bd0) at eval.c:463
#14 0xb7d212b4 in do_begin (call=0x89b2798, op=0x8062458, args=0x89b4090,
rho=0x89b4bd0) at eval.c:1159
#15 0xb7d1f352 in Rf_eval (e=0x89b2798, rho=0x89b4bd0) at eval.c:463
#16 0xb7d1fb67 in Rf_applyClosure (call=0x89b1c9c, op=0x89b1ba0,
arglist=0x89b1e24, rho=0x89b1d7c, suppliedenv=0x89b1cd4) at eval.c:669
#17 0xb7d60a32 in applyMethod (call=0x89b1c9c, op=0x89b1ba0, args=0x89b1e24,
rho=0x89b1d7c, newrho=0x89b1cd4) at objects.c:126
#18 0xb7d61223 in Rf_usemethod (generic=0x8069af8 "edit",
obj=0x8a87868,
call=0x89b1e94, args=0x8052110, rho=0x89b1d7c, callrho=0x8073f9c,
defrho=0x828f2fc, ans=0xbfd10d00) at objects.c:291
#19 0xb7d61776 in do_usemethod (call=0x89b1e94, op=0x80711b8, args=0x89b1e78,
env=0x89b1d7c) at objects.c:399
#20 0xb7d1f352 in Rf_eval (e=0x89b1e94, rho=0x89b1d7c) at eval.c:463
#21 0xb7d1fb67 in Rf_applyClosure (call=0x89b2230, op=0x89b2150,
arglist=0x89b1e24, rho=0x8073f9c, suppliedenv=0x8073fb8) at eval.c:669
#22 0xb7d1f601 in Rf_eval (e=0x89b2230, rho=0x8073f9c) at eval.c:507
#23 0xb7d4a879 in Rf_ReplIteration (rho=0x8073f9c, savestack=0, browselevel=0,
state=0xbfd1116c) at main.c:263
#24 0xb7d4aa61 in R_ReplConsole (rho=0x8073f9c, savestack=0, browselevel=0)
at main.c:312
#25 0xb7d4bec7 in run_Rmainloop () at main.c:975
#26 0xb7d4beee in Rf_mainloop () at main.c:982
#27 0x08048733 in main (ac=0, av=0x0) at Rmain.c:35
#28 0xb7b27450 in __libc_start_main () from /lib/i686/cmov/libc.so.6
#29 0x08048691 in _start ()
(gdb) up
Now, two comments.
Firstly, we all prefer if R would not crash. So this may need some fixing.
Secondly, I think you are rather close to bordering on user error. As your
snippet shows, you need to invoke args on the non-exported edit.matrix to
learn about the edit.row.names argument. Moreover, you also know full well
from looking at this that this will only be true when there actually are
names set --- and you then proceed to call it when there are none. Guess
what: it blows up.
So we could fix this in a number of places. Here is one which I tested; R
Core may opt to apply this, or a better version, or to drop the issue:
edd at ron:~/src/debian/R> diff -u R-2.6.1/src/library/utils/R/edit.R{.orig,}
--- R-2.6.1/src/library/utils/R/edit.R.orig 2007-09-04 17:12:32.000000000
-0500
+++ R-2.6.1/src/library/utils/R/edit.R 2007-12-06 21:12:32.000000000 -0600
@@ -166,6 +166,8 @@
else names(datalist) <- paste("col", 1:ncol(name), sep =
"")
modes <- as.list(rep.int(mode(name), ncol(name)))
if (edit.row.names) {
+ if (is.null(dn[[1]])) ## true if forced edit.row.names as TRUE on null
+ dn[[1]] <- paste("row", 1:dim(name)[1],
sep="")
datalist <- c(list(row.names = dn[[1]]), datalist)
modes <- c(list(row.names = "character"), modes)
}
This results in:> mat <- matrix(rnorm(30), nrow = 10, ncol = 3); edit(mat, edit.row.names
= TRUE)
col1 col2 col3
row1 0.6185206 0.32911907 -0.12263839
row2 0.4553981 -1.77532265 2.06745757
row3 0.4676557 0.58817426 -0.30507048
row4 1.1898153 -1.24888167 1.02240513
row5 -1.4809138 0.05212133 0.25272844
row6 1.5709981 -1.87496256 -0.05699266
row7 0.3770318 -0.43538598 -1.28299648
row8 1.3900096 0.15139637 -1.01168270
row9 -0.3973376 0.05933193 0.34420058
row10 -1.4248380 0.86637712 -1.25193470> q()
when the matrix is simply saved from the editor -- ie no segfault.
Hope this helps, and best regards, Dirk
| The only other version of R I can get my hands on at the moment (2.5.1,
| not Debian) does not crash but throws an uninformative error. This crash
| also occurs when calling fix(), which calls edit(). It does not occur if
| the matrix being edited has rownames already. A little gdb output is
| pasted below. -- Thanks, Ben
|
| R version 2.6.1 (2007-11-26)
| Copyright (C) 2007 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
|
| R is free software and comes with ABSOLUTELY NO WARRANTY.
| You are welcome to redistribute it under certain conditions.
| Type 'license()' or 'licence()' for distribution details.
|
| (no debugging symbols found)
| (no debugging symbols found)
| Natural language support but running in an English locale
|
| R is a collaborative project with many contributors.
| Type 'contributors()' for more information and
| 'citation()' on how to cite R or R packages in publications.
|
| Type 'demo()' for some demos, 'help()' for on-line help, or
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| Type 'q()' to quit R.
|
| (no debugging symbols found)
| (no debugging symbols found)
| > mat <- matrix(rnorm(30), nrow = 10, ncol = 3)
| > edit(mat, edit.row.names = TRUE)
| (no debugging symbols found)
| - ---Type <return> to continue, or q <return> to quit---
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
| (no debugging symbols found)
|
| Program received signal SIGSEGV, Segmentation fault.
| 0xb7b48f2c in __gconv_transform_utf8_internal () from
| /lib/i686/cmov/libc.so.6
|
|
| - -- System Information:
| Debian Release: lenny/sid
| APT prefers unstable
| APT policy: (500, 'unstable')
| Architecture: i386 (i686)
|
| Kernel: Linux 2.6.23.9-slh-smp-1 (SMP w/1 CPU core; PREEMPT)
| Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
| Shell: /bin/sh linked to /bin/bash
|
| Versions of packages r-base-core depends on:
| ii libbz2-1.0 1.0.3-7 high-quality block-sorting
| file co
| ii libc6 2.7-3 GNU C Library: Shared libraries
| ii libgcc1 1:4.2.2-4 GCC support library
| ii libgfortran2 4.2.2-4 Runtime library for GNU
| Fortran ap
| ii libice6 2:1.0.4-1 X11 Inter-Client Exchange
| library
| ii libjpeg62 6b-14 The Independent JPEG
| Group's JPEG
| ii libpaper-utils 1.1.23 library for handling paper
| charact
| ii libpcre3 7.3-2 Perl 5 Compatible Regular
| Expressi
| ii libpng12-0 1.2.15~beta5-3 PNG library - runtime
| ii libreadline5 5.2-3 GNU readline and history
| libraries
| ii libsm6 2:1.0.3-1+b1 X11 Session Management library
| ii libx11-6 2:1.0.3-7 X11 client-side library
| ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library
| ii perl 5.8.8-12 Larry Wall's Practical
| Extraction
| ii refblas3 [libblas.so.3] 1.2-8 Basic Linear Algebra
| Subroutines 3
| ii tcl8.4 8.4.16-4 Tcl (the Tool Command
| Language) v8
| ii tk8.4 8.4.16-2 Tk toolkit for Tcl and X11,
| v8.4 -
| ii unzip 5.52-10 De-archiver for .zip files
| ii zip 2.32-1 Archiver for .zip files
| ii zlib1g 1:1.2.3.3.dfsg-7 compression library - runtime
|
| Versions of packages r-base-core recommends:
| ii r-base-dev 2.6.1-1 GNU R installation of
| auxiliary GN
| ii r-recommended 2.6.1-1 GNU R collection of
| recommended pa
|
| - -- no debconf information
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|
--
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