[Bioc-devel] Use Imports instead of Depends in the DESCRIPTION files of bioconductor packages

[Gordon K Smyth]

Hi Michael,

What aspect of the methods package causes the slowness?

There are many packages (limma for one) that depend on methods but load 
quickly.

Regards
Gordon


> Date: Wed, 31 Dec 2014 09:17:01 -0800
> From: Michael Lawrence <lawrence.michael at gene.com>
> To: Peng Yu <pengyu.ut at gmail.com>
> Cc: Bioconductor Package Maintainer <maintainer at bioconductor.org>,
> 	"bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] [devteam-bioc] Use Imports instead of
> 	Depends in the DESCRIPTION files of bioconductor packages.
>
> The slowness is due to the methods package. We're working on it.
>
> Michael
>
> On Wed, Dec 31, 2014 at 8:47 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
>
>> On Wed, Dec 31, 2014 at 9:41 AM, Martin Morgan <mtmorgan at fredhutch.org>
>> wrote:
>>> On 12/24/2014 07:31 PM, Maintainer wrote:
>>>>
>>>> Hi,
>>>>
>>>> Many bioconductor packages Depends on other packages but not Imports
>>>> other packages. (e.g., IRanges Depends on BiocGenerics.) Imports is
>>>> usually preferred to Depends.
>>>>
>>>>
>>>>
>> http://stackoverflow.com/questions/8637993/better-explanation-of-when-to-use-imports-depends
>>>> http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/
>>>>
>>>> Could the unnecessary Depends be forced to be replaced by Imports?
>>>> This should improve the package load time significantly.
>>>
>>>
>>> R package symbols and other objects are collated at build time into a
>> 'name
>>> space'. When used,
>>>
>>> - Import: loads the name space from disk.
>>> - Depends: loads the name space from disk, and attaches it to the
>> search()
>>> path.
>>>
>>> Attaching is very inexpensive compared to loading, so there is no speed
>>> improvement gained by Import'ing instead of Depend'ing.
>>
>> Yes. For example, changing Depends to Imports does not improve the
>> package load time much.
>>
>> But loading a package in 4 sec seems to be too long.
>>
>>>  system.time(suppressPackageStartupMessages(library(MBASED)))
>>    user  system elapsed
>>   4.404   0.100   4.553
>>
>> For example, it only takes 10% of the time to load ggplot2. It seems
>> that many bioconductor packages have similar problems.
>>
>>> system.time(suppressPackageStartupMessages(library(ggplot2)))
>>    user  system elapsed
>>   0.394   0.036   0.460
>>
>>> The main reason to Depend: on a package is because the symbols defined by
>>> the package are needed by the end-user. Import'ing a package is
>> appropriate
>>> when the package provides functionality only relevant to the package
>> author.
>>
>> What causes the load time to be too long? Is it because exporting too
>> many functions from all dependent packages to the global namespace?
>>
>>> There are likely to be specific packages that mis-use Depends; packages
>> such
>>> as IRanges, GenomicRanges, etc use Depends: as intended, to  provide
>>> functions that are useful to the end user.
>>>
>>> Maintainers are certainly encouraged to think carefully about adding
>>> packages providing functionality irrelevant to the end-user to the
>> Depends:
>>> field. The codetoolsBioC package (available from svn, see
>>> http://bioconductor.org/developers/how-to/source-control/) provides some
>>> mostly reliable hints to package authors about correctly formulating a
>>> NAMESPACE file to facilitate using Imports: instead of Depends:.
>>>
>>> General questions about Bioconductor packages should be addressed to the
>>> support forum https://support.bioconductor.org.
>>>
>>> Questions about Bioconductor development (such as this) should be
>> addressed
>>> to the bioc-devel mailing list (subscription required)
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel.
>>>
>>> I have cc'd the bioc-devel mailing list; I hope that is ok.
>>
>>
>>
>> --
>> Regards,
>> Peng

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