[BioC] Ignore maanova warning messages?

[Loren Engrav]

Reposting with new subject line as suggested
And with more info as suggested
design file and short gene file attached
=======================

Am using maanova 1.14.0
Process runs to completion but ends with

> ftest.Breed.mix_100perm090709F1FsRerun <- matest
(BDeset_gcrma_WithAffyID090709, BGanova.Br_T.mix090709, term = "Breed", n.perm =
100, critical = .9, test.type = c("ftest"), shuffle.method = c("sample"),
MME.method = c("REML"), test.method = c(1,1), pval.pool = TRUE, verbose = TRUE)
Doing F-test on observed data ...
Doing permutation. This may take a long time ...
Finish permutation #  100
There were 50 or more warnings (use warnings() to see the first 50)

> warnings()
Warning messages:
1: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
2: In FUN(newX[, i], ...) : coercing argument of type 'double' to logical
3: In any(parsed.formula$random) : coercing argument of type 'double' to
logical
4: In any(parsed.formula$random) : coercing argument of type 'double' to
logical
5: In any(parsed.formula$random) : coercing argument of type 'double' to
logical
and on and on...

the three commands are

file2 <- read.madata("file1.txt", designfile="DesignV4LR081109.txt",
header=TRUE, spotflag=FALSE, intensity=2, probeid=1)

file3 <- fitmaanova(file2, formula=~Breed+Time, random= ~Time, covariate =
~1, verbose=TRUE)

file4 <- matest (file2, file3, term = "Breed", n.perm = 1000, critical = .9,
test.type = c("ftest"), shuffle.method = c("sample"), MME.method =
c("REML"), test.method = c(1,1), pval.pool = TRUE, verbose = TRUE)

> sessionInfo()

R version 2.9.0 (2009-04-17)
x86_64-apple-darwin9.6.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] maanova_1.14.0