[Bioc-devel] Biobase: Imports repeats Depends

[Henrik Bengtsson]

On Mon, Apr 27, 2015 at 6:45 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
>
> Hi Henrik,
>
> I know it's not necessary and I know that the WRE manual and
> 'R CMD check' don't like this but I like to list in Imports what
> I import and to list in Depends what I want to see attached to
> the search() path. For the same reason that I like to explicitly
> export the generic functions that I define in my packages even
> if exporting the methods defined on these generics is enough
> (because it has the side effect to automatically export the
> generic).
>
> More generally it's about expressing intentions directly versus
> expressing them in an indirect manner (e.g. by relying on side
> effects). I think the latter is wrong. Hope that makes sense.

Thanks for clarifying.  I simply thought it was a mistake/cut'n'paste typo.

H..

>
> Cheers,
> H.
>
>
>
> On 04/25/2015 01:12 PM, Henrik Bengtsson wrote:
>>
>> It seems unnecessary that BiocGenerics have the same package under
>> Imports as under Depends.  The former can be dropped.
>>
>>> packageDescription("BiocGenerics")
>>
>> Package: BiocGenerics
>> Title: S4 generic functions for Bioconductor
>> Description: S4 generic functions needed by many Bioconductor packages.
>> Version: 0.14.0
>> Author: The Bioconductor Dev Team
>> Maintainer: Bioconductor Package Maintainer
>>          <maintainer at bioconductor.org>
>> biocViews: Infrastructure
>> Depends: methods, utils, graphics, stats, parallel
>> Imports: methods, utils, graphics, stats, parallel
>> Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, AnnotationDbi,
>>          oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
>>          annotate, RUnit
>> License: Artistic-2.0
>> Collate: S3-classes-as-S4-classes.R normarg-utils.R update-utils.R
>>          .....
>> NeedsCompilation: no
>> Packaged: 2015-04-17 03:42:27 UTC; biocbuild
>> Built: R 3.3.0; ; 2015-04-25 20:08:25 UTC; windows
>>
>> /Henrik
>>
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>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>
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