[Bioc-devel] avoiding call to ".find.package"
lg390 at cam.ac.uk
Mon Mar 4 11:22:36 CET 2013
On 4 March 2013 09:57, Antti Honkela <antti.honkela at 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),
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
Hope this helps.
> 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?
>> [[alternative HTML version deleted]]
>> Bioc-devel at r-project.org mailing list
> Antti Honkela
> antti.honkela at hiit.fi - http://www.hiit.fi/u/ahonkela/
> Bioc-devel at r-project.org mailing list
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