| Detailed description |
from PeterD:
Dear maintainers of
BMA GenABEL SNPassoc cherry.
Your packages are currently failing the automatic CRAN checks under r-devel. This is due to a change in the labeling of columns in anova tables, which you have been using to extract p values.
E.g. (from "cherry")
anova(glm(form, data=birthwt, family=binomial), fullfit, test="Chisq")$"P(>|Chi|)"[2]
does no longer work because the column is now labeled "Pr(>Chi)".
Since you probably don't want to break compatibility with R 2.13.x, you can't just change the string. Instead, the straightforward workaround would seem to be
t1 <- glm(form, data=birthwt, family=binomial), fullfit, test="Chisq")
t2 <- t1$"P(>|Chi|)"
if (is.null(t2)) t2 <- t1$"Pr(>Chi)"
t2[2]
Or, at some loss of readability:
t1[2, grep("^P.*Chi",names(t1))]
Apologies for the inconvenience, but please adjust your packages and resubmit to CRAN.
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