[Bioc-devel] BioC 2.5: Broken interpackage man page links

Hello BioC-develers,
R-devel has recently begun surfacing long-time broken man interpackage 
man page links such as \link[base]{mget} (corrected link: 
\link[base:get]{mget} since mget is described in base's get.Rd file). Up 
until this point, broken interpackage man page links were not discovered 
through R CMD check. Now these broken links are assigned WARNINGs.

These broken links are widespread, with nearly 1 in 3 BioC packages 
containing at least one broken link. Please consult the BioC 2.5: 
Multiple platform build/check report to check on the status of your 
packages:

http://bioconductor.org/checkResults/2.5/bioc-LATEST/

To fix your package, update your version of R-devel and read Section 2.5 
of Writing R Extensions:

http://cran.fhcrc.org/doc/manuals/R-exts.html#Cross_002dreferences

The relevant paragraph for this issue is the following:

There are two other forms of optional argument specified as 
\link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to 
files foo.html and bar.html respectively. These are rarely needed, 
perhaps to refer to not-yet-installed packages (but there the HTML help 
system will resolve the link at run time) or in the normally undesirable 
event that more than one package offers help on a topic20 (in which case 
the present package has precedence so this is only needed to refer to 
other packages). They are only in used in (C)HTML help (and not for 
hyperlinks in LaTeX conversions of help pages), and link to the file 
rather than the topic (since there is no way to know which topics are in 
which files in an uninstalled package).


The sooner these broken links are fixed, the easier the BioC 2.5 release 
will be. If you have any questions, feel free to ask them to this board.


Cheers,
Patrick