[Bioc-devel] avoiding call to ".find.package"

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.

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

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Antti Honkela
antti.honkela at hiit.fi   -   http://www.hiit.fi/u/ahonkela/

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