search for: rcont2

...ritten by Peter Hurd. See: https://stat.ethz.ch/pipermail/r-sig-ecology/2008-July/000275.html Peter Hurd's implementation of g.test() looks very much like the implementation of stats::chisq.test(), and is clearly based on it. In particular, the 2 functions are based on the same C function, rcont2, that used to belong to the R C API. However, in recent revisions of R-devel, rcont2 was moved to the stats package and not registered as a "C callable". So it's not accessible anymore and that breaks Biostrings. Anyway, g.test() does not belong to Biostrings in the first place. So m...

...I mean, the function call never returns (running > 10 hours > so far), the process is unresponsive to SIGINT (but I call kill it with > TERM), and the process still consumes cycles on the CPU. > This is due to calling `exp' with a very small value leading to a zero return value in rcont2 (src/appl/rcont.c) line 70: x = exp(fact[iap - 1] + fact[ib] + fact[ic] + fact[idp - 1] - fact[ie] - fact[nlmp - 1] - fact[igp - 1] - fact[ihp - 1] - fact[iip - 1]); if (x >= dummy) { goto L160; }...

...hours so far), the process is unresponsive >> to SIGINT (but I call kill it with TERM), and the process >> still consumes cycles on the CPU. >> Torsten> This is due to calling `exp' with a very small Torsten> value leading to a zero return value in rcont2 Torsten> (src/appl/rcont.c) line 70: yes, that's correct. Please, before anyone starts changing the code: I have had an version of rcont.c in my own code tree which uses much less goto's than the current official code. I'd like to commit it (with an error message for the m...

...r), the process is unresponsive >>> to SIGINT (but I call kill it with TERM), and the >>> process still consumes cycles on the CPU. >>> Torsten> This is due to calling `exp' with a very small Torsten> value leading to a zero return value in rcont2 Torsten> (src/appl/rcont.c) line 70: MM> yes, that's correct. However, as I have found out now, the real reason *is* integer overflow (in multiplication), as I had guessed originally (but didn't believe anymore for a while after your exp() underflow diagnosis). Note that thi...

Hello everybody, I'm running R 1.8.1 on both Linux and OS X compiled with gcc 3.2.2 and 3.3, respectively. The following call seems to freeze the interpreter on both systems: > chisq.test(matrix(c(233, 580104, 3776, 5786104), 2, 2), simulate.p.value=TRUE) By freeze, I mean, the function call never returns (running > 10 hours so far), the process is unresponsive to SIGINT (but I

...registration.o machar platform.o ptr_R_loadhistory ../unix/libunix.a(stubs.o) Rf_pnchisq arithmetic.o Rf_pnbinom arithmetic.o optif9 optimize.o rcont2 random.o R_pretty0 engine.o setulb optim.o Rf_qcauchy arithmetic.o UsingReadline platform.o Rf_pwilcox arithmetic.o find_interv_vec...

...registration.o machar platform.o ptr_R_loadhistory ../unix/libunix.a(stubs.o) Rf_pnchisq arithmetic.o Rf_pnbinom arithmetic.o optif9 optimize.o rcont2 random.o R_pretty0 engine.o setulb optim.o Rf_qcauchy arithmetic.o UsingReadline platform.o Rf_pwilcox arithmetic.o find_interv_vec...

...gztell connections.o BZ2_bzReadOpen connections.o R_zeroin optimize.o ptr_R_savehistory ../unix/libunix.a(stubs.o) loglin registration.o lowess registration.o machar platform.o ptr_R_loadhistory ../unix/libunix.a(stubs.o) Rf_pnchisq arithmetic.o Rf_pnbinom arithmetic.o optif9 optimize.o rcont2 random.o R_pretty0 engine.o setulb optim.o Rf_qcauchy arithmetic.o UsingReadline platform.o Rf_pwilcox arithmetic.o find_interv_vec registration.o Rf_qnchisq arithmetic.o Rf_qnbinom arithmetic.o Rf_rcauchy random.o Rf_trigamma arithmetic.o massdist registration.o pcre_info pcre.o pcre_...

...registration.o machar platform.o ptr_R_loadhistory ../unix/libunix.a(stubs.o) Rf_pnchisq arithmetic.o Rf_pnbinom arithmetic.o optif9 optimize.o rcont2 random.o R_pretty0 engine.o setulb optim.o Rf_qcauchy arithmetic.o UsingReadline platform.o Rf_pwilcox arithmetic.o find_interv_vec...

...(9410, 76167) > cc <- c(25000, 60577) > r2dtable(3, rr, cc) [[1]] [,1] [,2] [1,] 2721 6689 [2,] 22279 53888 [[2]] [,1] [,2] [1,] 2834 6576 [2,] 22166 54001 [[3]] [,1] [,2] [1,] 2778 6632 [2,] 22222 53945 I have looked inside the C code for the C_r2dtable() and rcont2() functions, but I cannot do much more than guess where this behaviour could originate, so I would like to ask for help from anybody more experienced in the R implementation. Guess there is some kind of inflection point depending on the total sample size of the table, or maybe the generation algori...

...INDEX list is deprecated with a warning. o Translation packages are deprecated. o Calling rep() or rep.int() on a pairlist is deprecated and will give a warning. In any case, rep() converted a pairlist to a list so you may as well do that explicitly. o Entry point rcont2 is no longer part of the API, and will move to package stats in R 2.16.0. o The 'internal' graphics device invoked by .Call("R_GD_nullDevice", package = "grDevices") is about to be removed: use pdf(file = NULL) instead. o eigen(EISPACK = TRUE)...

...INDEX list is deprecated with a warning. o Translation packages are deprecated. o Calling rep() or rep.int() on a pairlist is deprecated and will give a warning. In any case, rep() converted a pairlist to a list so you may as well do that explicitly. o Entry point rcont2 is no longer part of the API, and will move to package stats in R 2.16.0. o The 'internal' graphics device invoked by .Call("R_GD_nullDevice", package = "grDevices") is about to be removed: use pdf(file = NULL) instead. o eigen(EISPACK = TRUE)...

...INDEX list is deprecated with a warning. o Translation packages are deprecated. o Calling rep() or rep.int() on a pairlist is deprecated and will give a warning. In any case, rep() converted a pairlist to a list so you may as well do that explicitly. o Entry point rcont2 is no longer part of the API, and will move to package stats in R 2.16.0. o The 'internal' graphics device invoked by .Call("R_GD_nullDevice", package = "grDevices") is about to be removed: use pdf(file = NULL) instead. o eigen(EISPACK = TRUE)...

...interface pointers formerly available only to R.app are now available to front-ends on all Unix-alikes: one has been added for the interface to View(). o PACKAGE = "" is now an error in .C() etc calls: it was always contrary to the documentation. o Entry point rcont2 has been migrated to package stats and so is no longer available. o R_SVN_REVISION in Rversion.h is now an integer (rather than a string) and hence usable as e.g. #if R_SVN_REVISION < 70000. o The entry points rgb2hsv and hsv2rgb have been migrated to package grDevic...

...interface pointers formerly available only to R.app are now available to front-ends on all Unix-alikes: one has been added for the interface to View(). o PACKAGE = "" is now an error in .C() etc calls: it was always contrary to the documentation. o Entry point rcont2 has been migrated to package stats and so is no longer available. o R_SVN_REVISION in Rversion.h is now an integer (rather than a string) and hence usable as e.g. #if R_SVN_REVISION < 70000. o The entry points rgb2hsv and hsv2rgb have been migrated to package grDevic...