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

[Dan Tenenbaum]

On Mon, Mar 4, 2013 at 2:22 AM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
> 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.
>

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 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/
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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