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))))) {
--
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