search for: fexact

...function (fisher.test) in my program for like a billion times! Though my program is in Python and I feel that using rpy2 to interface R to python doesn't give me satisfactory performance. So I looked into R code and found out that fisher.test is actually a wrapper around another function called fexact which is implemented in C. Using Cython I managed to directly call the function and get the desired results. But the weird problem is that after calling the function for like 4000 times (with same parameters) a segmentation fault occurs! Eliminating the possibility that my interfacing code has any...

This is a bad bug as reported by Robin Hankin, it is still in "R-patched" ... ##- From: Robin Hankin <r.hankin@auckland.ac.nz> ##- To: r-help@stat.math.ethz.ch ##- Subject: [R] possum sleeping: thanks and fisher.test() FEXACT error ##- Date: Thu, 13 Jun 2002 16:46:26 +1200 ## ..... ## Example slighlty modified (MM) d4 <- matrix(c(0, 0, 0, 0, 0, 0, 3, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 4, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,...

Dear All, I am using fexact.c on a C++ program I wrote. To minimize dependencies on other files (e.g., to not need to include R.h and ctest.h ---now I only include the R files Boolean.h, Constants.h, and Memory.h), I have re-written all declarations of Sints as ints and, what is potentially more serious, I have re-written...

...rancis -- > dat1 = matrix(c(0,1,0,1,0,0,1,0,0,0,1,0,1,0,0,1,0,0,0,1,0,1,0,0,1,0,0,0,0, 1,1,0,0,1,0,0,1,0,0,1,0,0,3,0,0,2,0,0,1,0,0,0,1,0,0,2,0,0, 2,0,0,1,0,1,0,0,3,0,0,2,0,0,0,1,0,5,0,0,0,1,0,1,0,0), nrow=3) > fisher.test( dat1 ) Error in fisher.test(dat1) : Bug in FEXACT: gave negative key

...tar'ed the package in the library directory. I have write permissions for those directories. Apparently the linker cannot find a "main" module file or a certain (shared?) library. Some -lxxx missing on compiler's command line? Installing package `ctest' ... libs make: `fexact.o' is up to date. ld: warning: cannot find entry symbol _start; defaulting to 08048280 fexact.o: In function `fexact': /usr/local/share/R/library/ctest/src/fexact.c:160: undefined reference to `calloc' /usr/local/share/R/library/ctest/src/fexact.c:290: undefined reference to `fr...

...similar number of (randomly generated) data points, and it worked then. There are 258 data points in two columns (i.e. 2 * 134), if that helps. Any advice would be very much appreciated, Many thanks, Ken Edwards. R script below: fisher.test(testData) Error in fisher.test(testData) : FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the workspace.

Dear all, I’m having an awkward problem in R. When I write the command Fisher.test(school.data,workspace=2e+07), where school.data is the matrix corresponding to the data set, I get the error message: FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the workspace. Increasing the workspace: Fisher.test(school.data,workspace=1e+10), I get a different message, but it still doesn’t work: NAs in foreign function call (arg 10) In addition: Warning message:...

...t on at least one occasion). The next step is to check whether the five animals have different preferences. I have an array called alldata which has 50 rows (one per tree) and five columns (one per animal). But, in R-1.5.0, R> fisher.test(alldata[,2:5]) Error in fisher.test(alldata[, 2:5]) : FEXACT error 30. Stack length exceeded in f3xact. This problem should not occur. what am I doing wrong here? R> dput (alldata) structure(c(0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 2, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0,...

The last line gets duplicated when a file is read like this: a <- scan(file=filename, what="", sep="\n", strip.white=c(TRUE), quiet=TRUE) (This error does not occur on Linux, the only other platform I tested.) Version: platform = hppa2.0-hp-hpux10.20 arch = hppa2.0 os = hpux10.20 system = hppa2.0, hpux10.20 Actually, all binaries are

...d libraries. It seems I am missing something to link. Before I spend my time hunting it down, maybe someone has an immediate idea. gs. == my output: make[4]: Entering directory `//local.src/R-1.0.0/src/library/ctest/src' gcc -shared -Xlsharedlibrary -Xlexpall -o ctest.so alnorm.o ansari.o fexact.o kendall.o ks.o prho.o swilk.o -L/usr/lib/gcc-lib/powerpc-apple-machten4/2.8.1 -lg2c -lm ansari.o: In function `errmsg': ansari.c:13: undefined reference to `Rf_error' ansari.o: In function `w_init': ansari.c:21: undefined reference to `R_chk_calloc' ... ansari.c:84: undefined re...

...o di Milano". For my master degree thesis I have to analyze some categorical data. My dataset is composed by 327 individuals and 16 variables. I am using Fisher exact test to test independence on IxJ contingency tables, but I have a problem with one variable. R gives me this error message: FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the workspace. or also this one: FEXACT error 6. LDKEY is too small for this problem. Try increasing the size of the workspace. Do you know what these error messages mean? What can I do? Thank you in advance f...

...tables greater than 2X2. It looks like I have an insane amount of factorials to be multiplied. Is that problem? Is it an overflow issue? Jeff Last night’s post: I just a ran a fisher.test on a 9x5 table and received the following message Error in fisher.test(apaslg.t) : FEXACT error 30. Stack length exceeded in f3xact. This problem should not occur. I agree. The problem should not occur. I did some searching but only found other reports of the problem. Does anyone know of a fix? Jeff Internal Virus Database is out-of-date. Checked by AVG Free Edi...

...disk4/hoffmann/Work/rwork/src/library/ctest/src' gcc -I../../../../include -I/usr/local/include -fPIC -g -O2 -c ../../../../../R-1.1.1/src/library/ctest/src/ansari.c -o ansari.o gcc -I../../../../include -I/usr/local/include -fPIC -g -O2 -c ../../../../../R-1.1.1/src/library/ctest/src/fexact.c -o fexact.o gcc -I../../../../include -I/usr/local/include -fPIC -g -O2 -c ../../../../../R-1.1.1/src/library/ctest/src/kendall.c -o kendall.o gcc -I../../../../include -I/usr/local/include -fPIC -g -O2 -c ../../../../../R-1.1.1/src/library/ctest/src/ks.c -o ks.o gcc -I../../../../inclu...

...ill be appreciated. JD ---------------------------------------------------------------------- R : Copyright 2006, The R Foundation for Statistical Computing Version 2.3.1 (2006-06-01) . . . > m = matrix(10*1:9, nc=3) > fisher.test(m, hybrid=TRUE) Error in fisher.test(m, hybrid = TRUE) : FEXACT error 6. LDKEY is too small for this problem. Try increasing the size of the workspace. In addition: Warning message: 'hybrid' is ignored for a 2 x 2 table in: fisher.test(m, hybrid = TRUE)

...gt; Like Uwe this works for me the first few times and I do BDR> then get a backtrace (in memory.c, so this is almost BDR> certainly an earlier overrun). >> MM> I see. This has been different for me. >> BDR> I think we've had problems before with FEXACT BDR> incorrectly specifying the required sizes of its BDR> workspaces. >> (I'm not so sure this is the problem here.) >> >> I found that >> >> fisher.test(d4[1:30,]) >> >> gives a direct segmentation fault (...

...obability calculated in (2), small values being discrepant; ... ) "?fisher.test" says only: In the one-sided 2 by 2 cases, p-values are obtained directly using the hypergeometric distribution. Otherwise, computations are based on a C version of the FORTRAN subroutine FEXACT which implements the network developed by Mehta and Patel (1986) and improved by Clarkson, Fan & Joe (1993). The FORTRAN code can be obtained from <URL: http://www.netlib.org/toms/643>. I have had a look at this FORTRAN code, and cannot ascertain it from the code itse...

...t; > Installing package `ctest' ... > > libs > > g77 -mieee -fPIC -O2 -c alnorm.f -o alnorm.o > > gcc -I/usr/lib/R/include -DHAVE_CONFIG_H -mieee -fPIC -O2 -c ansari.c -o > > ansari.o > > gcc -I/usr/lib/R/include -DHAVE_CONFIG_H -mieee -fPIC -O2 -c > > fexact.c -o fexact.o > > gcc -I/usr/lib/R/include -DHAVE_CONFIG_H -mieee -fPIC > > -O2 -c kendall.c -o kendall.o > > /tmp/ccYUoygd.s: Assembler messages: > > /tmp/ccYUoygd.s:123: Error: unknown opcode `sqrttsu' > > /tmp/ccYUoygd.s:132: Error: unknown opcode `sqrttsu...

...31 7 61 class24 7 6 55 5 49 71 93 90 1 18 16 79 class34 1 1 4 3 19 8 29 61 4 4 5 37 So in made a matrix and used >fisher.test(classtable4). But then this error occurs: Fehler in fisher.test(classtable4) : FEXACT error 7. LDSTP is too small for this problem. Try increasing the size of the workspace. Well I then increased the workspace: >fisher.test(classtable4, workspace=1e8) But then the same error occurs. Do someone knows an alternative to the fisher.test or the chisq.test? Thank you very much! A...

...is up to date. building package `base' ../../../library/base/R/base is unchanged building package `ctest' ../../../library/ctest/R/ctest is unchanged f90 -c alnorm.f -o alnorm.o alnorm.f external function ALNORM 53 Lines Compiled ld -b -o ctest.sl alnorm.o ansari.o fexact.o kendall.o ks.o prho.o swilk.o /opt/fortran90/lib/libF90.a -lcl /opt/fortran90/lib/libisamstub.a ld: DP relative code in file alnorm.o - shared library must be position independent. Use +z or +Z to recompile. *** Error exit code 1 Thanks, Marcus... -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-...

...ude -c stl.f -o stl.o f95 -PIC -O -I/mounts/devel/SUNWspro/prod/include -c portsrc.f -o portsrc.o cc -xtarget=generic64 -G -L/mounts/devel/SUNWspro/lib/amd64 -L/usr/sfw/lib/amd64 -L/mounts/devel/GNU/repoz/readline43/lib/amd64 -o stats.so init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o isoreg.o Srunmed.o Trunmed.o dblcen.o distance.o hclust-utils.o nls.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sbart.o sgram.o sin...