[Rd] Segmentation violation in eval.c (R 2.1.0) (PR#7893)
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Hi,
I get a segmentation fault in eval.c:
do_set (call=0x8ce166c, op=0x82b43b8, args=0x8ce1650, rho=0x8acf218)
at eval.c:1309
1309switch (NAMED(s)) {
The instruction is
0x080becf1 do_set+177:movzbl (%eax),%edx
and %eax contains a non-accessible address
(gdb) x/x $eax
0x4a5bf008: Cannot access memory at address 0x4a5bf008
in another try it was
(gdb) x/x $eax
0x59a5a008: Cannot access memory at address 0x59a5a008
This segmentation fault occurs reproducible in a long simulation script.
However, I don't know the place in the .R file. I would like to isolate
the bug but don't know how. I attached the gdb session. I use R 2.1.0 on
a Linux machine (Athlon64). Maybe a package that I wrote and use for the
simulation clobbers some memory (although I already added some sanity
checks). But please let me know when you hear about this bug another
time (or have an idea how to debug this or have a solution).
Thank you,
Andreas
--
Andreas Westfeld, 0432 01CC F511 9E2B 0B57 5993 0B22 98F8 4AD8 EEEA
[EMAIL PROTECTED] http://www.inf.tu-dresden.de/~aw4
TU Dresden Fakultät Informatik, Institut für Systemarchitektur
Datenschutz und Datensicherheit, Tel. +49-351-463-37918
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source(ber3.R)
Program received signal SIGSEGV, Segmentation fault.
do_set (call=0x86c8770, op=0x82b43b8, args=0x86c878c, rho=0x8626404)
at eval.c:1309
1309switch (NAMED(s)) {
# PRIMVAL(op): is 1 (code = 1)
(gdb) p R_FunTab[op-u.primsxp.offset]
$14 = {name = 0x81d99e8 -, cfun = 0x80bec40 do_set, code = 1,
Rf_eval = 100, arity = -1, gram = {kind = PP_ASSIGN, precedence = PREC_LEFT,
rightassoc = 1}}
# isSymbol(CAR(args)):
(gdb) p Rf_isSymbol(CAR(args))
$16 = TRUE
# NAMED(s):
(gdb) p s-sxpinfo.named
$20 = 0
# (s =) eval(CADR(args), rho):
(gdb) p *Rf_eval(CADR(args), rho)
$27 = {sxpinfo = {type = 13, obj = 0, named = 0, gp = 0, mark = 0, debug = 0,
trace = 0, fin = 0, gcgen = 0, gccls = 7}, attrib = 0x82a5588,
gengc_next_node = 0x1ee60648, gengc_prev_node = 0x4b1cb008, u = {primsxp = {
offset = 985600}, symsxp = {pname = 0xf0a00, value = 0x0,
internal = 0x0}, listsxp = {carval = 0xf0a00, cdrval = 0x0,
tagval = 0x0}, envsxp = {frame = 0xf0a00, enclos = 0x0, hashtab = 0x0},
closxp = {formals = 0xf0a00, body = 0x0, env = 0x0}, promsxp = {
value = 0xf0a00, expr = 0x0, env = 0x0}}}
# s:
(gdb) p *s
$28 = {sxpinfo = {type = 7, obj = 0, named = 0, gp = 0, mark = 1, debug = 0,
trace = 0, fin = 0, gcgen = 1, gccls = 0}, attrib = 0x82a5588,
gengc_next_node = 0x85ba270, gengc_prev_node = 0x85bb5c8, u = {primsxp = {
offset = 25}, symsxp = {pname = 0x19, value = 0x82a5588,
internal = 0x82a5588}, listsxp = {carval = 0x19, cdrval = 0x82a5588,
tagval = 0x82a5588}, envsxp = {frame = 0x19, enclos = 0x82a5588,
hashtab = 0x82a5588}, closxp = {formals = 0x19, body = 0x82a5588,
env = 0x82a5588}, promsxp = {value = 0x19, expr = 0x82a5588,
env = 0x82a5588}}}
0x080becd6 do_set+150:call 0x815a720 Rf_isSymbol
---Type return to continue, or q return to quit---
0x080becdb do_set+155:test %eax,%eax
0x080becdd do_set+157:je 0x80bed36 do_set+246
0x080becdf do_set+159:mov%edi,0x4(%esp)
0x080bece3 do_set+163:mov0x14(%ebx),%eax
0x080bece6 do_set+166:mov0x10(%eax),%eax
0x080bece9 do_set+169:mov%eax,(%esp)
0x080becec do_set+172:call 0x80bc530 Rf_eval
# here the SIGSEGV occurs:
0x080becf1 do_set+177:movzbl (%eax),%edx
# %eax:
(gdb) x/x $eax
0x4a5bf008: Cannot access memory at address 0x4a5bf008
SECOND TRY:
Program received signal SIGSEGV, Segmentation fault.
do_set (call=0x8ce166c, op=0x82b43b8, args=0x8ce1650, rho=0x8acf218)
at eval.c:1309
1309switch (NAMED(s)) {
(gdb) x/x $eax
0x59a5a008: Cannot access memory at address 0x59a5a008
(gdb) p *s
$2 = {sxpinfo = {type = 7, obj = 0, named = 0, gp = 0, mark = 1, debug = 0,
trace = 0, fin = 0, gcgen = 1, gccls = 0}, attrib = 0x82a5588,
gengc_next_node = 0x85ba270, gengc_prev_node = 0x85bb5c8, u = {primsxp = {
offset = 25}, symsxp = {pname = 0x19, value = 0x82a5588,
internal = 0x82a5588}, listsxp = {carval = 0x19, cdrval = 0x82a5588,
tagval = 0x82a5588}, envsxp = {frame = 0x19, enclos = 0x82a5588,
hashtab = 0x82a5588}, closxp = {formals = 0x19, body = 0x82a5588,
env = 0x82a5588}, promsxp = {value = 0x19, expr = 0x82a5588,
env = 0x82a5588}}}
(gdb)
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[Rd] R OS X
Hi, with newest R.app (1.11) / R2.1.0a if a package is installed for the current user, it is not installed properly (does not get an installed version entry and is not loadable). If installed system wide it works. The package I installed is xgobi. MAC OS X 10.4.1 Volker - - - - - - - - - - - -- -- --- -- - - - - - - - - - - - -- - - Dipl.-Biol. Volker Runkel Lehrstuhl f. Zoologie II www.biologie.uni- erlangen.de/zoo2 Staudtstr. 5 Telefon: 09131-85 28788 91058 Erlangen [EMAIL PROTECTED] erlangen.de - - - - - - - - - - - -- -- --- -- - - - - - - - - - - - -- - - __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R OS X
Hi Volker, Just tried this with 1 of the few packages I had not installed yet systemwide. In the Startup preferences I selected to add $Home/R/Library and restarted R. Then installed package its and loaded the library and ran the example. Can you try if that sequence works for you? A better alias for Mac questions is R-SIG-Mac. Regards, Rob On May 24, 2005, at 6:11 AM, Volker Runkel wrote: Hi, with newest R.app (1.11) / R2.1.0a if a package is installed for the current user, it is not installed properly (does not get an installed version entry and is not loadable). If installed system wide it works. The package I installed is xgobi. MAC OS X 10.4.1 Volker - - - - - - - - - - - -- -- --- -- - - - - - - - - - - - -- - - Dipl.-Biol. Volker Runkel Lehrstuhl f. Zoologie II www.biologie.uni- erlangen.de/zoo2 Staudtstr. 5 Telefon: 09131-85 28788 91058 Erlangen [EMAIL PROTECTED] erlangen.de - - - - - - - - - - - -- -- --- -- - - - - - - - - - - - -- - - __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Reversing axis in a log plot (PR#7894)
Full_Name: Christian Marquardt
Version: 2.1.0
OS: Linux (Redhat 9)
Submission from: (NULL) (151.170.240.10)
Following the advice of a reader of R-help, I would now like to submit this as a
bug report:
Say we have
x = seq(1,3, by = 0.01)
y = exp(x)
Plotting and reversing linear axis is fine
plot(x,y)
plot(x,y, ylim = c(30,1))
as is a usual log-plot:
plot(x,y, log = y, ylim = c(1,30))
However,
plot(x,y, log = y, ylim = c(30,1))
fails with
Error in axis(2, ...) : log - axis(), 'at' creation, _SMALL_ range:
invalid {xy}axp or par;
axp[0]= 10, usr[0:1]=(34.3721,0.872801)
In addition: Warning message:
CreateAtVector log(from axis()): usr[0] = 34.3721 0.872801 = usr[1] !
According to Petr Pikal petr.pikal -at- precheza.cz, replacing the ylim
argument by ylim = c(30,1.2) helps in the above example; but in my real world
applications, it's actually difficult to find a working value for ylim.
I hope this is useful,
Christian.
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[Rd] Non-nested testing and anova.lm()
I'd like to elicit comments on what I am sure is an ancient topic, but one for which I can't seem to google up a satisfactory reference. I'm curious about the laissez-faire attitude adopted in anova.lm and friends regarding non-nested hypothesis tests. I was under the misapprehension until yesterday that attempts to test non-nested hypotheses, i.e. compare lm objects with non-nested design matrices, produced an error. On the contrary, not even a warning is generated. The Ur text on this sort of thing (aka The White Book) seems to suggest (p 210) that test statistics are computed only when models are nested, but ?anova.lm is quite clear: For all but the first model, the change in degrees of freedom and sum of squares is also given. (This only make statistical sense if the models are nested.) It is conventional to list the models from smallest to largest, but this is up to the user. My motivation for the question is that I'm considering reworking the code for anova.rq in my quantreg package. Currently, I have a rather half-hearted attempt to check nesting using variable names, and was considering implementing something more algebraic based on explicitly looking at subspace inclusions, but now I'm wondering if R's caveat emptor policy might be a viable alternative. Any comments would be welcome. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
