Re: [Rd] advise on Depends

2013-10-25 Thread Michael Lawrence
On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search

Re: [Rd] advise on Depends

2013-10-25 Thread John Chambers
One additional point to Michael's summary: The methods package itself should stay in Depends:, to be safe. There are a number of function calls to the methods package that may be included in generated methods for user classes. These have not been revised to work when the methods package is

Re: [Rd] advise on Depends

2013-10-25 Thread Dirk Eddelbuettel
On 25 October 2013 at 13:39, John Chambers wrote: | One additional point to Michael's summary: | | The methods package itself should stay in Depends:, to be safe. | | There are a number of function calls to the methods package that may be included in generated methods for user classes. These

Re: [Rd] advise on Depends

2013-10-25 Thread Henrik Bengtsson
On Fri, Oct 25, 2013 at 1:39 PM, John Chambers j...@r-project.org wrote: One additional point to Michael's summary: The methods package itself should stay in Depends:, to be safe. There are a number of function calls to the methods package that may be included in generated methods for user

Re: [Rd] advise on Depends

2013-10-25 Thread Paul Gilbert
On 13-10-25 05:21 PM, Henrik Bengtsson wrote: On Fri, Oct 25, 2013 at 1:39 PM, John Chambers j...@r-project.org wrote: One additional point to Michael's summary: The methods package itself should stay in Depends:, to be safe. It would be nice to have more detail about when this is

Re: [Rd] advise on Depends

2013-10-25 Thread John Chambers
Software generated in methods for user classes calls functions in the methods package, as I said. I don't know the circumstances (if any) when such calls fail to find functions if the whole package is imported. Perhaps someone on this list may have examples. But for sure just importing

Re: [Rd] advise on Depends

2013-10-25 Thread Hervé Pagès
On 10/25/2013 11:26 AM, Michael Lawrence wrote: On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’

[Rd] advise on Depends

2013-10-23 Thread Kasper Daniel Hansen
This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search path is excessive and importing selectively is preferable. Let us say my package A either uses a