I've been fighting a CMD check error for coxme this morning. I thought I had
it fixed,
but instead I had forgotton --as-cran on my last test run. So the version just
submitted
to CRAN has warning messages in the log.
I think it is an issue with CRAN. I've sent a message to R-devel asking for
help.
Since then, as a guess, I renamed my internal "ismat" function to something
else and the
error went away.
Here is the code block in coxme, it is part of the "check user arguments for
validity"
block at the start of the function. Run coxme in a terminal and all is well,
run R CMD
check without as-cran and all is well, but with --as-cran the ismat function
gives
warnings. Changing the name to something else fixes the issue. The function
exists only
to save some typing. (No need to really read the block, just notice the
multiple calls to
ismat()
ismat <- function (x) {
inherits(x, c("matrix", "bdsmatrix", "Matrix"), which=FALSE)
}
if (missing(varlist) || is.null(varlist)) {
varlist <- vector('list', nrandom)
for (i in 1:nrandom) varlist[[i]] <- coxmeFull() #default
}
else {
if (is.function(varlist)) varlist <- varlist()
if (inherits(varlist, 'coxmevar')) varlist <- list(varlist)
else if (ismat(varlist))
varlist <- list(coxmeMlist(list(varlist)))
else {
if (!is.list(varlist)) stop("Invalid varlist argument")
if (all(sapply(varlist, ismat))) {
# A list of matrices
if (nrandom >1)
stop(paste("An unlabeled list of matrices is",
"ambiguous when there are multiple random
terms"))
else varlist <- list(coxmeMlist(varlist))
}
else { #the user gave me a list, not all matrices
for (i in 1:length(varlist)) {
if (is.function(varlist[[i]]))
varlist[[i]] <-varlist[[i]]()
if (ismat(varlist[[i]]))
varlist[[i]] <- coxmeMlist(list(varlist[[i]]))
if (class(varlist[[i]]) != 'coxmevar') {
if (is.list(varlist[[i]])) {
if (all(sapply(varlist[[i]], ismat)))
varlist[[i]] <- coxmeMlist(varlist[[i]])
else stop("Invalid varlist element")
}
else stop("Invalid varlist element")
}
}
}
}
while(length(varlist) < nrandom) varlist <- c(varlist,
list(coxmeFull()))
}
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