Sorry, but I lost this thread, so I sending this as a new message. This is really a follow-up to a post from a couple days ago saying that fisher.test from the ctest library crashed on the following data set:> T[,1] [,2] [1,] 2 1 [2,] 2 1 [3,] 4 0 [4,] 8 0 [5,] 6 0 [6,] 0 0 [7,] 1 0 [8,] 1 1 [9,] 7 1 [10,] 8 2 [11,] 1 0 [12,] 3 1 [13,] 1 1 [14,] 3 0 [15,] 7 2 [16,] 4 1 [17,] 2 0 [18,] 2 0 [19,] 2 0 Then Professor Ripley responded that the problem was not related to the Windows port (as the original author implied) but to the amount of memory R was started with. I just ran some tests on this I have to report that I am getting crashes every time I try this problem. (1) On my WinNT machine I got up to Rgui.exe --vsize=220M --nsize=4000k which produces> gc()free total (Mb) Ncells 3857498 4000000 76.3 Vcells 28790374 28835840 220.0 and it still crashes with the "referenced memory cannot be read" message. I also noticed that the error message comes immediately, no matter how large the memory allocation is. This machine is a Pentium Pro 200Mhz with 192Mb of memory (2) On my Linux box I can only go to about --vsize=120M --nsize=1000k. This is a Pentium MMX 266Mhz with 64Mb of memory. The machine crashes after "thinking" for about 3 seconds. It produces segmentation violation error and dumps core. It seems to me that, unless I have some unlucky machines, the problem is not just handling too small memory allocation ungracefully. Any comments will be appreciated, Andy -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
If I recall Ripley said something about workspace but it was an internal arg
to the function as in
fisher.test(x, y = NULL, workspace = 200000, hybrid = FALSE,
or = 1, alternative = "two.sided", conf.level = 0.95)
I think that it's this "workspace" argument he meant and should be
increased.
Regards.
----- Original Message -----
From: "Andy Jaworski" <apjaworski at mmm.com>
To: <r-help at stat.math.ethz.ch>
Sent: Friday, August 25, 2000 5:10 PM
Subject: [R] unexpected R crash - again
> Sorry, but I lost this thread, so I sending this as a new message.
>
> This is really a follow-up to a post from a couple days ago saying that
> fisher.test from the ctest library crashed on the following data set:
> > T
> [,1] [,2]
> [1,] 2 1
> [2,] 2 1
> [3,] 4 0
> [4,] 8 0
> [5,] 6 0
> [6,] 0 0
> [7,] 1 0
> [8,] 1 1
> [9,] 7 1
> [10,] 8 2
> [11,] 1 0
> [12,] 3 1
> [13,] 1 1
> [14,] 3 0
> [15,] 7 2
> [16,] 4 1
> [17,] 2 0
> [18,] 2 0
> [19,] 2 0
>
> Then Professor Ripley responded that the problem was not related to the
> Windows port (as the original author implied) but to the amount of memory
R> was started with.
>
> I just ran some tests on this I have to report that I am getting crashes
> every time I try this problem.
> (1) On my WinNT machine I got up to
> Rgui.exe --vsize=220M --nsize=4000k
> which produces
> > gc()
> free total (Mb)
> Ncells 3857498 4000000 76.3
> Vcells 28790374 28835840 220.0
>
> and it still crashes with the "referenced memory cannot be read"
message.
I> also noticed that the error message comes immediately, no matter how large
> the
> memory allocation is. This machine is a Pentium Pro 200Mhz with 192Mb of
> memory
>
> (2) On my Linux box I can only go to about --vsize=120M --nsize=1000k.
This> is a Pentium MMX 266Mhz with 64Mb of memory. The machine crashes
> after "thinking" for about 3 seconds. It produces
segmentation
> violation error and dumps core.
>
> It seems to me that, unless I have some unlucky machines, the problem is
not> just handling too small memory allocation ungracefully.
>
> Any comments will be appreciated,
>
> Andy
>
>
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
-.-.-> r-help mailing list -- Read
http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html> Send "info", "help", or "[un]subscribe"
> (in the "body", not the subject !) To: r-help-request at
stat.math.ethz.ch
>
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"Andy Jaworski" <apjaworski at mmm.com> writes:> Sorry, but I lost this thread, so I sending this as a new message. > > This is really a follow-up to a post from a couple days ago saying that > fisher.test from the ctest library crashed on the following data set: > > T > [,1] [,2] > [1,] 2 1 > [2,] 2 1 > [3,] 4 0 > [4,] 8 0 > [5,] 6 0 > [6,] 0 0 > [7,] 1 0 > [8,] 1 1 > [9,] 7 1 > [10,] 8 2 > [11,] 1 0 > [12,] 3 1 > [13,] 1 1 > [14,] 3 0 > [15,] 7 2 > [16,] 4 1 > [17,] 2 0 > [18,] 2 0 > [19,] 2 0...> (2) On my Linux box I can only go to about --vsize=120M --nsize=1000k. This > is a Pentium MMX 266Mhz with 64Mb of memory. The machine crashes > after "thinking" for about 3 seconds. It produces segmentation > violation error and dumps core. > > It seems to me that, unless I have some unlucky machines, the problem is not > just handling too small memory allocation ungracefully. > > Any comments will be appreciated,Aha. So it also happens on Linux. That should make debugging it quite a bit easier. Happens here as well, and the immediate cause is that Program received signal SIGSEGV, Segmentation fault. 0x40f9e9f0 in f2xact (nrow=0x40f9afd0, ncol=0x40f9afc8, table=0x40f9adf8, ldtabl=0x40f9ae90, expect=0x40f9ae88, percnt=0x40f9ae80, emin=0x40f9ae78, prt=0x40f9ae70, pre=0x40f9ae68, fact=0x40fa5008, ico=0x40fa5264, iro=0x40fa52b0, kyy=0x40fa52fc, idif=0x40fa5348, irn=0x40fa5350, key=0x40fa6f40, ldkey=0x40fa46a4, ipoin=0x40fa82b0, stp=0x40fa9618, ldstp=0x40fa46b0, ifrq=0x40ff2460, dlp=0x4105f9b8, dsp=0x41062098, tm=0x41064778, key2=0x41066e60, iwk=0x40fa5358, rwk=0x40fa6218) at ../../../../../R/src/library/ctest/src/fexact.c:690 690 pastp = stp[ipn + ikstp]; (gdb) p ipn $1 = -97902590 which in turn comes from 689 ipn = ipoin[ipo + ikkey]; with ipo & ikkey both at 622, seemingly sane. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Yudi Pawitan
2000-Aug-26 12:51 UTC
exact test for large tables. Was: [R] unexpected R crash - again
If you have an actual large table to analyse, rather than trying to solve the space problem, you may want to consider a MonteCarlo implementation of the exact test. Very easy to implement in R. See, for example, Lange's Numerical Analysis for Statisticians, Section 21.7. -Yudi- At 04:10 PM 8/25/00 -0500, Andy Jaworski <apjaworski at mmm.com> wrote:>Sorry, but I lost this thread, so I sending this as a new message. > >This is really a follow-up to a post from a couple days ago saying that >fisher.test from the ctest library crashed on the following data set: >> T > [,1] [,2] > [1,] 2 1 > [2,] 2 1 > [3,] 4 0 > [4,] 8 0 > [5,] 6 0 > [6,] 0 0 > [7,] 1 0 > [8,] 1 1 > [9,] 7 1 >[10,] 8 2 >[11,] 1 0 >[12,] 3 1 >[13,] 1 1 >[14,] 3 0 >[15,] 7 2 >[16,] 4 1 >[17,] 2 0 >[18,] 2 0 >[19,] 2 0 > >Then Professor Ripley responded that the problem was not related to the >Windows port (as the original author implied) but to the amount of memory R >was started with. > >I just ran some tests on this I have to report that I am getting crashes >every time I try this problem. >(1) On my WinNT machine I got up to > Rgui.exe --vsize=220M --nsize=4000k > which produces >> gc() > free total (Mb) >Ncells 3857498 4000000 76.3 >Vcells 28790374 28835840 220.0 > >and it still crashes with the "referenced memory cannot be read" message. I >also noticed that the error message comes immediately, no matter how large >the >memory allocation is. This machine is a Pentium Pro 200Mhz with 192Mb of >memory > >(2) On my Linux box I can only go to about --vsize=120M --nsize=1000k. This >is a Pentium MMX 266Mhz with 64Mb of memory. The machine crashes > after "thinking" for about 3 seconds. It produces segmentation >violation error and dumps core. > >It seems to me that, unless I have some unlucky machines, the problem is not >just handling too small memory allocation ungracefully. > >Any comments will be appreciated, > >Andy > > >-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.->r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html >Send "info", "help", or "[un]subscribe" >(in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch >_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._>Yudi Pawitan yudi at stat.ucc.ie Department of Statistics UCC Cork, Ireland Ph 353-21-490 2906 Fax 353-21-427 1040 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._