On Mon, Mar 4, 2013 at 2:22 AM, Laurent Gatto <lg...@cam.ac.uk> wrote: > On 4 March 2013 09:57, Antti Honkela <antti.honk...@hiit.fi> wrote: >> According to the build logs my package (tigre) appears to have the same >> problem, but I cannot reproduce this on my own install of R-devel (r62117). >> >> Perhaps this is just an R bug that has since been fixed? > > I believe the warnings result from changes to R r62077 > > prefer loaded namepaces in find.package > deprecate .find.package and .path.package > > Biobase and affy (which our packages rely on) use .find.package. > > $ grep .find.package Biobase/R/* > Biobase/R/packages.R: pkgpath <- .find.package(package) > Biobase/R/vignettes.R: vigrds = file.path(.find.package(pkgs), > "Meta", "vignette.rds") > Biobase/R/vignettes.R: vigs = file.path(.find.package(pkgName), > "doc", vigMtrx[, "PDF"]) > > $ grep .find.package affy/R/* > affy/R/getCDFenv.R: if (length(.find.package(cdfname, lib.loc=lib, > quiet=TRUE)) == 0) > > I suspect that's were the warnings come from and were the fix should > be applied. > > Hope this helps. >
I've fixed all BioC packages that were calling .find.package(); they now call find.package(). Dan > Best wishes, > > Laurent > > >> Antti >> >> >> >> On 04/03/13 10:52, Andreas Heider wrote: >>> >>> Dear mailing list, >>> how can I solve the warning during the CHECK of the examples in my >>> virtualArray package that states: >>> >>> Warning: ‘.find.package’ is deprecated. >>> >>>> From what function call does it originate? >>> >>> >>> Thanks, >>> Andreas >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> -- >> Antti Honkela >> antti.honk...@hiit.fi - http://www.hiit.fi/u/ahonkela/ >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
