> On Mar 31, 2017, at 7:04 AM, Stefan Evert <stefa...@collocations.de> wrote: > > >> On 30 Mar 2017, at 11:51, Eshi Vaz <eshithasunit...@gmail.com> wrote: >> >> When trying to computer a fisher’s exact test using the fisher.test function >> from the gmodels() package, <---- > > The problem seems to be with a different fisher.test() function from the > gmodels package, not with stats::fisher.test. > > The usual recommendation is to contact the package authors for help. > > Best regards, > Stefan
There is no fisher.test() function in the gmodels package. The error message is being generated from compiled code in stats::fisher.test(). A Google search for the error message indicates that there are reports going back at least as far as 2002, suggesting that the underlying issue is an integer overflow: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=1662 with at least one example resolved back in 2005: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=6986 The former report has recent reports from 2014/2015 suggesting that the original 2002 issue is still present, at least in specific situations: 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, 0, 1, 0, 0, 2, 0, 0, 0, 2, 2, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 3, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 8, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, 0, 2, 0, 0, 0, 0, 2, 0, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 0, 0, 0), nr=50) > fisher.test(d4) Error in fisher.test(d4) : FEXACT error 30. Stack length exceeded in f3xact. This problem should not occur. tab <- structure(list(V1 = c(1, 0, 0, 0, 0, 0), V2 = c(323, 4, 1, 0, 0, 22), V3 = c(3, 0, 0, 0, 0, 1), V4 = c(2, 0, 1, 0, 1, 3), V5 = c(1, 0, 0, 0, 0, 4), V6 = c(1, 0, 0, 0, 0, 0), V7 = c(0, 0, 0, 1, 0, 1), V8 = c(96, 0, 0, 0, 0, 2)), .Names = c("V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8"), class = "data.frame", row.names = c(NA, -6L)) > fisher.test(tab) Error in fisher.test(tab) : Bug in FEXACT: gave negative key Note that in the second example, the data frame is coerced to a matrix inside fisher.test(). The above two examples were run using R version 3.3.3 on macOS 10.12.4 in a CLI console. Regards, Marc Schwartz ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
