Re: [Rd] strange error with rw2010dev
Kjetil == Kjetil Brinchmann Halvorsen [EMAIL PROTECTED] on Sun, 10 Apr 2005 14:00:52 -0400 writes: Kjetil The error reported below still occurs in todays Kjetil (2005-04-08) rw2010beta, should I file a formal bug Kjetil report? Thank you, Kjetil. It seems nobody has found time to look at this in the mean time. However, I can confirm the bug on quite a different platform (Linux Redhat 64-bit on AMD 64). The problem is infinite recursion which you see more easily, when you set something like options(expressions=500). Further note that the bug is not new, it also happens in previous versions of R ( - i.e. no reason to stop using R 2.1.0 beta!) Here's a ``pure script'' testmat - matrix(1:80, 20,4) dim(testmat) # testframe - data.frame(testmat=I(testmat), x=rnorm(20), y=rnorm(20), z=sample(1:20)) str(testframe) options(expressions=100) summary(testframe) ## Error: evaluation nested too deeply: infinite recursion / options(expression=)? ## -- or -- ## Error: protect(): protection stack overflow ### In the second case, I at least get a useful trace back: traceback() ## longish output, shows the infinite recursion: .. ... 17: summary.data.frame(data.frame(object), ...) 16: summary.matrix(object, digits = digits, ...) 15: summary.default(X[[1]], ...) 14: FUN(X[[1]], ...) 13: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 12: summary.data.frame(data.frame(object), ...) 11: summary.matrix(object, digits = digits, ...) 10: summary.default(X[[1]], ...) 9: FUN(X[[1]], ...) 8: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 7: summary.data.frame(data.frame(object), ...) 6: summary.matrix(object, digits = digits, ...) 5: summary.default(X[[1]], ...) 4: FUN(X[[1]], ...) 3: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 2: summary.data.frame(testframe) 1: summary(testframe) Thanks again for the report; this should be fixable before release. Martin __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange error with rw2010dev
Martin Maechler [EMAIL PROTECTED] writes: Kjetil == Kjetil Brinchmann Halvorsen [EMAIL PROTECTED] on Sun, 10 Apr 2005 14:00:52 -0400 writes: Kjetil The error reported below still occurs in todays Kjetil (2005-04-08) rw2010beta, should I file a formal bug Kjetil report? Thank you, Kjetil. It seems nobody has found time to look at this in the mean time. However, I can confirm the bug on quite a different platform (Linux Redhat 64-bit on AMD 64). The problem is infinite recursion which you see more easily, when you set something like options(expressions=500). Further note that the bug is not new, it also happens in previous versions of R ( - i.e. no reason to stop using R 2.1.0 beta!) Here's a ``pure script'' testmat - matrix(1:80, 20,4) dim(testmat) # testframe - data.frame(testmat=I(testmat), x=rnorm(20), y=rnorm(20), z=sample(1:20)) str(testframe) options(expressions=100) summary(testframe) ## Error: evaluation nested too deeply: infinite recursion / options(expression=)? ## -- or -- ## Error: protect(): protection stack overflow ### In the second case, I at least get a useful trace back: traceback() ## longish output, shows the infinite recursion: .. ... 17: summary.data.frame(data.frame(object), ...) 16: summary.matrix(object, digits = digits, ...) 15: summary.default(X[[1]], ...) 14: FUN(X[[1]], ...) 13: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 12: summary.data.frame(data.frame(object), ...) 11: summary.matrix(object, digits = digits, ...) 10: summary.default(X[[1]], ...) 9: FUN(X[[1]], ...) 8: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 7: summary.data.frame(data.frame(object), ...) 6: summary.matrix(object, digits = digits, ...) 5: summary.default(X[[1]], ...) 4: FUN(X[[1]], ...) 3: lapply(as.list(object), summary, maxsum = maxsum, digits = 12, ...) 2: summary.data.frame(testframe) 1: summary(testframe) Thanks again for the report; this should be fixable before release. Preferably before code freeze! (today) I think we (Thomas L.?) got it analysed once before: The issue is that summary.matrix is passing data.frame(object) back to summary.data.frame without removing the AsIs class. I don't a simple unclass() will do here. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange error with rw2010dev
PD == Peter Dalgaard [EMAIL PROTECTED] on 11 Apr 2005 09:46:11 +0200 writes: . MM Thanks again for the report; this should be fixable MM before release. PD Preferably before code freeze! (today) PD I think we (Thomas L.?) got it analysed once before: The PD issue is that summary.matrix is passing PD data.frame(object) back to summary.data.frame without PD removing the AsIs class. PD I don't a simple unclass() will do here. or, a bit more cautiously, summary.matrix - function(object, ...) summary.data.frame(data.frame(if(inherits(object,AsIs)) unclass(object) else object), ...) That does cure the problem in the Kjetil's example and the equivalent ## short 1-liner: summary(df - data.frame(mat = I(matrix(1:8, 2 I'm currently make-checking the above. Martin __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange error with rw2010dev
On Mon, 11 Apr 2005, Martin Maechler wrote: PD == Peter Dalgaard [EMAIL PROTECTED] on 11 Apr 2005 09:46:11 +0200 writes: . MM Thanks again for the report; this should be fixable MM before release. PD Preferably before code freeze! (today) PD I think we (Thomas L.?) got it analysed once before: The PD issue is that summary.matrix is passing PD data.frame(object) back to summary.data.frame without PD removing the AsIs class. PD I don't a simple unclass() will do here. or, a bit more cautiously, summary.matrix - function(object, ...) summary.data.frame(data.frame(if(inherits(object,AsIs)) unclass(object) else object), ...) I do not think that is correct. You need either to remove the AsIs class and leave any other classes, or unclass all objects. Otherwise adding an AsIs class will change the behaviour. I would suggest that if you get to the summary.matrix method you want the summary as a matrix and so should always unclass, but that is debatable (think for example of an object of class c(mts, ts), which is a classed matrix, and there is an as.data.frame.ts method but no summary.ts). -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange error with rw2010dev
The error reported below still occurs in todays (2005-04-08) rw2010beta, should I file a formal bug report? Kjetil. Kjetil Brinchmann Halvorsen wrote: With rw2010dev I get a strange protect(): protection stack overflow error with a small data frame which otherwise is usable: If anybody wants to have a look I can provide an RData file with the problematic data frame. Doesn't seem to be necessary, the following simulated example generates the error: testmat - matrix(1:80, 20,4) dim(testmat) [1] 20 4 str(testmat) int [1:20, 1:4] 1 2 3 4 5 6 7 8 9 10 ... testframe - data.frame(testmat=I(testmat), x=rnorm(20), y=rnorm(20), z=sample(1:20)) str(testframe) `data.frame': 20 obs. of 4 variables: $ testmat: int [1:20, 1:4] 1 2 3 4 5 6 7 8 9 10 ... ..- attr(*, class)= chr AsIs $ x : num 0.768 -0.462 0.450 0.476 -1.077 ... $ y : num 0.453 1.227 -1.514 -0.904 -0.129 ... $ z : int 10 4 15 19 14 3 9 17 18 5 ... summary(testframe) Error: protect(): protection stack overflow Kjetil -- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange error with rw2010dev
On Mon, 28 Mar 2005, Kjetil Brinchmann Halvorsen wrote: testmat - matrix(1:80, 20,4) dim(testmat) [1] 20 4 str(testmat) int [1:20, 1:4] 1 2 3 4 5 6 7 8 9 10 ... testframe - data.frame(testmat=I(testmat), x=rnorm(20), y=rnorm(20), z=sample(1:20)) str(testframe) `data.frame': 20 obs. of 4 variables: $ testmat: int [1:20, 1:4] 1 2 3 4 5 6 7 8 9 10 ... ..- attr(*, class)= chr AsIs $ x : num 0.768 -0.462 0.450 0.476 -1.077 ... $ y : num 0.453 1.227 -1.514 -0.904 -0.129 ... $ z : int 10 4 15 19 14 3 9 17 18 5 ... summary(testframe) Error: protect(): protection stack overflow Yes, you're getting infinite recursion. summary.data.frame calls summary.matrix to handle the first column, and this then calls summary.data.frame on data.frame(testframe[[1]]), but str(data.frame(testframe[[1]])) `data.frame': 20 obs. of 1 variable: $ testframe..1..: int [1:20, 1:4] 1 2 3 4 5 6 7 8 9 10 ... ..- attr(*, class)= chr AsIs so round and round we go. Perhaps summary.matrix should do something to remove the AsIs attribute? -thomas __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
