> Martin Morgan
> on Wed, 10 Sep 2014 11:49:31 -0700 writes:
> In the context of installing a Bioconductor package using our biocLite()
> function, install.packages() warns
>> install.packages("RUVSeq",
repos="http://bioconductor.org/packages/2.14/bioc";)
> Installing package into
'/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14'
> (as 'lib' is unspecified)
> Warning message:
> package 'RUVSeq' is not available (for R version 3.1.1 Patched)
> but really the problem is that the package is not available at the
specified
> repository (it is available, for the same version of R, in the Bioc devel
> repository http://bioconductor.org/packages/3.0/bioc).
> I can see the value of identifying the R version, and see that mentioning
> something about 'specified repositories' would not necessarily be
helpful. Also,
> since the message is translated and our user base is international, it is
> difficult to catch and process by the biocLite() script.
> Is there a revised wording that could be employed to more accurately
convey the
> reason for the failure, or is this an opportunity to use the condition
system?
> Index: src/library/utils/R/packages2.R
> ===
> --- src/library/utils/R/packages2.R (revision 66562)
> +++ src/library/utils/R/packages2.R (working copy)
> @@ -46,12 +46,12 @@
> p0 <- unique(pkgs)
> miss <- !p0 %in% row.names(available)
> if(sum(miss)) {
> - warning(sprintf(ngettext(sum(miss),
> - "package %s is not available (for %s)",
> - "packages %s are not available (for %s)"),
> - paste(sQuote(p0[miss]), collapse=", "),
> - sub(" *\\(.*","", R.version.string)),
> -domain = NA, call. = FALSE)
> +txt <- ngettext(sum(miss), "package %s is not available (for
%s)",
> +"packages %s are not available (for %s)")
> +msg <- simpleWarning(sprintf(txt, paste(sQuote(p0[miss]),
collapse=", "),
> + sub(" *\\(.*","",
R.version.string)))
> +class(msg) <- c("packageNotAvailable", class(msg))
> + warning(msg)
> if (sum(miss) == 1L &&
> !is.na(w <- match(tolower(p0[miss]),
> tolower(row.names(available) {
Yes, I think this would be a fine example and the first one in
"base R" AFAIK of using the condition system by sub classing.
The fact that you cannot check for the warning/error message *text* in
your own tryCatch() or similar because of internationalization
and hence translation had bitten other people before... and I am
sure is still wrongly used also in package land.. where the bug
never triggers as long as testing is done in the C or an 'en' locale.
How would your biocLite() be adapted to use "packageNotAvailable" ?
Martin Maechler, ETH Zurich
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