bolker@zoo.ufl.edu
2005-Dec-22 18:23 UTC
[Rd] Windows crash in confint() with nls fit (PR#8428)
Full_Name: Ben Bolker
Version: 2.2.1
OS: Windows XP and 2000
Submission from: (NULL) (128.227.60.124)
The following code, using confint() to try
to get confidence intervals on an nls object
that has been fitted with algorithm="port"
reliably crashes R 2.2.0 and 2.2.1 with the
latest version of MASS on a Windows 2000 and
a Windows XP machine here. I *think* earlier
versions of MASS may not have crashed, but
I have now updated the versions on most of
my machines and don't have a test version handy.
On XP, I get an error-report-do-you-want-
to-send-this-to-Microsoft dialog box. On 2000
I get a "Rgui has generated errors ..." dialog box.
I can get this far:
debug: profiledModel <- .Call("nls_iter", fittedModel, ctrl, trace,
PACKAGE = "stats")
Browse[1]> where
where 1: prof$getProfile()
where 2: profile.nls(object, which = parm, alphamax = (1 - level)/4)
where 3: profile(object, which = parm, alphamax = (1 - level)/4)
where 4: confint.nls(n1)
where 5: confint(n1)
I'm not set up to debug compiled code on Windows, and I haven't
been able to reproduce the problem on Linux.
set.seed(1001)
x = runif(200)
a =1
b = 1
c = -0.1
y = a+b*x+c*x^2+rnorm(200,sd=0.05)
plot(x,y)
curve(a+b*x+c*x^2,add=TRUE)
n1 = nls(y~a+b*x+c*I(x^2),start=c(a=1,b=1,c=0.1),algorithm="port")
confint(n1) ## boom
N.B.: It only crashes if algorithm="port" is specified.
## [1] "Windows 2000 Professional (build 2195) Service Pack 4.0"
##
## > R.version
## _
## platform i386-pc-mingw32
## arch i386
## os mingw32
## system i386, mingw32
## status
## major 2
## minor 2.0
## year 2005
## month 10
## day 06
## svn rev 35749
## language R
##
## MASS
##
## Version: 7.2-23
## Date: 2005-12-08
##
##
## "Windows XP Professional (build 2600) Service Pack 2.0"
## _
##platform i386-pc-mingw32
##arch i386
##os mingw32
##system i386, mingw32
##status
##major 2
##minor 2.0
##year 2005
##month 10
##day 06
##svn rev 35749
##language R
##
##Version: 7.2-23
##Date: 2005-12-08 ## CRASH
##> R.version
## _
##platform i386-pc-mingw32
##arch i386
##os mingw32
##system i386, mingw32
##status
##major 2
##minor 2.1
##year 2005
##month 12
##day 20
##svn rev 36812
##language R
## CRASH
murdoch@stats.uwo.ca
2005-Dec-22 19:19 UTC
[Rd] Windows crash in confint() with nls fit (PR#8428)
On 12/22/2005 1:23 PM, bolker at zoo.ufl.edu wrote:> Full_Name: Ben Bolker > Version: 2.2.1 > OS: Windows XP and 2000 > Submission from: (NULL) (128.227.60.124) > > > The following code, using confint() to try > to get confidence intervals on an nls object > that has been fitted with algorithm="port" > reliably crashes R 2.2.0 and 2.2.1 with the > latest version of MASS on a Windows 2000 and > a Windows XP machine here. I *think* earlier > versions of MASS may not have crashed, but > I have now updated the versions on most of > my machines and don't have a test version handy. > > On XP, I get an error-report-do-you-want- > to-send-this-to-Microsoft dialog box. On 2000 > I get a "Rgui has generated errors ..." dialog box. > > I can get this far: > > debug: profiledModel <- .Call("nls_iter", fittedModel, ctrl, trace, > PACKAGE = "stats") > > Browse[1]> where > where 1: prof$getProfile() > where 2: profile.nls(object, which = parm, alphamax = (1 - level)/4) > where 3: profile(object, which = parm, alphamax = (1 - level)/4) > where 4: confint.nls(n1) > where 5: confint(n1) > > I'm not set up to debug compiled code on Windows, and I haven't > been able to reproduce the problem on Linux.I see it in R-devel too. It's in a strcmp; I'll see if I can track down the cause. Duncan Murdoch> > set.seed(1001) > x = runif(200) > a =1 > b = 1 > c = -0.1 > y = a+b*x+c*x^2+rnorm(200,sd=0.05) > plot(x,y) > curve(a+b*x+c*x^2,add=TRUE) > n1 = nls(y~a+b*x+c*I(x^2),start=c(a=1,b=1,c=0.1),algorithm="port") > confint(n1) ## boom > > N.B.: It only crashes if algorithm="port" is specified. > > ## [1] "Windows 2000 Professional (build 2195) Service Pack 4.0" > ## > ## > R.version > ## _ > ## platform i386-pc-mingw32 > ## arch i386 > ## os mingw32 > ## system i386, mingw32 > ## status > ## major 2 > ## minor 2.0 > ## year 2005 > ## month 10 > ## day 06 > ## svn rev 35749 > ## language R > ## > ## MASS > ## > ## Version: 7.2-23 > ## Date: 2005-12-08 > ## > ## > > ## "Windows XP Professional (build 2600) Service Pack 2.0" > ## _ > ##platform i386-pc-mingw32 > ##arch i386 > ##os mingw32 > ##system i386, mingw32 > ##status > ##major 2 > ##minor 2.0 > ##year 2005 > ##month 10 > ##day 06 > ##svn rev 35749 > ##language R > > ## > ##Version: 7.2-23 > ##Date: 2005-12-08 ## CRASH > > ##> R.version > ## _ > ##platform i386-pc-mingw32 > ##arch i386 > ##os mingw32 > ##system i386, mingw32 > ##status > ##major 2 > ##minor 2.1 > ##year 2005 > ##month 12 > ##day 20 > ##svn rev 36812 > ##language R > ## CRASH > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
murdoch@stats.uwo.ca
2005-Dec-22 19:51 UTC
[Rd] Windows crash in confint() with nls fit (PR#8428)
I've found the problem, but someone who knows more about nls() will have to fix it. The problem is that in the demo code below, n1 ends up being an nls object, but n1$call$control is NULL. profiler.nls() assumed that the nls object passed to it has a non-NULL element there, and doesn't check. I've fixed the code so now it doesn't crash, but it now dies with this error instead: > confint(n1) ## boom Waiting for profiling to be done... Error in prof$getProfile() : 'control$maxiter' absent I'll commmit my change to R-devel and R-patched shortly. Duncan Murdoch On 12/22/2005 1:23 PM, bolker at zoo.ufl.edu wrote:> Full_Name: Ben Bolker > Version: 2.2.1 > OS: Windows XP and 2000 > Submission from: (NULL) (128.227.60.124) > > > The following code, using confint() to try > to get confidence intervals on an nls object > that has been fitted with algorithm="port" > reliably crashes R 2.2.0 and 2.2.1 with the > latest version of MASS on a Windows 2000 and > a Windows XP machine here. I *think* earlier > versions of MASS may not have crashed, but > I have now updated the versions on most of > my machines and don't have a test version handy. > > On XP, I get an error-report-do-you-want- > to-send-this-to-Microsoft dialog box. On 2000 > I get a "Rgui has generated errors ..." dialog box. > > I can get this far: > > debug: profiledModel <- .Call("nls_iter", fittedModel, ctrl, trace, > PACKAGE = "stats") > > Browse[1]> where > where 1: prof$getProfile() > where 2: profile.nls(object, which = parm, alphamax = (1 - level)/4) > where 3: profile(object, which = parm, alphamax = (1 - level)/4) > where 4: confint.nls(n1) > where 5: confint(n1) > > I'm not set up to debug compiled code on Windows, and I haven't > been able to reproduce the problem on Linux. > > set.seed(1001) > x = runif(200) > a =1 > b = 1 > c = -0.1 > y = a+b*x+c*x^2+rnorm(200,sd=0.05) > plot(x,y) > curve(a+b*x+c*x^2,add=TRUE) > n1 = nls(y~a+b*x+c*I(x^2),start=c(a=1,b=1,c=0.1),algorithm="port") > confint(n1) ## boom > > N.B.: It only crashes if algorithm="port" is specified. > > ## [1] "Windows 2000 Professional (build 2195) Service Pack 4.0" > ## > ## > R.version > ## _ > ## platform i386-pc-mingw32 > ## arch i386 > ## os mingw32 > ## system i386, mingw32 > ## status > ## major 2 > ## minor 2.0 > ## year 2005 > ## month 10 > ## day 06 > ## svn rev 35749 > ## language R > ## > ## MASS > ## > ## Version: 7.2-23 > ## Date: 2005-12-08 > ## > ## > > ## "Windows XP Professional (build 2600) Service Pack 2.0" > ## _ > ##platform i386-pc-mingw32 > ##arch i386 > ##os mingw32 > ##system i386, mingw32 > ##status > ##major 2 > ##minor 2.0 > ##year 2005 > ##month 10 > ##day 06 > ##svn rev 35749 > ##language R > > ## > ##Version: 7.2-23 > ##Date: 2005-12-08 ## CRASH > > ##> R.version > ## _ > ##platform i386-pc-mingw32 > ##arch i386 > ##os mingw32 > ##system i386, mingw32 > ##status > ##major 2 > ##minor 2.1 > ##year 2005 > ##month 12 > ##day 20 > ##svn rev 36812 > ##language R > ## CRASH > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
bolker@zoo.ufl.edu
2005-Dec-22 20:24 UTC
[Rd] Windows crash in confint() with nls fit (PR#8428)
Duncan Murdoch wrote:> I've found the problem, but someone who knows more about nls() will have > to fix it. > > The problem is that in the demo code below, n1 ends up being an nls > object, but n1$call$control is NULL. profiler.nls() assumed that the > nls object passed to it has a non-NULL element there, and doesn't check. > > I've fixed the code so now it doesn't crash, but it now dies with this > error instead: > > > confint(n1) ## boom > Waiting for profiling to be done... > Error in prof$getProfile() : 'control$maxiter' absent > > I'll commmit my change to R-devel and R-patched shortly. > > Duncan Murdoch >thank you for the quick response! actually, I discovered I'm wrong -- bug affects Linux as well, gives a segmentation fault (I must have tried it without the algorithm="port" argument by accident.) I've looked at the code but I regretfully concur that someone else will have to work on this -- I can hack nls so it reinserts a "control" element in n1$call, but $tol and $minFactor are explicitly deleted from the control list, and so we only get one step farther. I don't know what assumptions nls_iter is really making and whether it's safe to make them when the port algorithm is being used or not ... My best guess at this point, poking around, is that profiler.nls in src/library/stats/R/nls-profile.R has to be changed in parallel with nls to call port_nlsb instead of nls_iter when the port algorithm is being used, but this is all getting a bit deep for me ... Ben