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

[Laurent Gatto]

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),
"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
>>
>>         [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Antti Honkela
> antti.honkela at hiit.fi   -   http://www.hiit.fi/u/ahonkela/
>
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