[Bioc-devel] limma Suggests:statmod vs Imports:statmod

Robert Castelo robert@c@@telo @ending from upf@edu
Fri May 11 09:39:04 CEST 2018

hi Ryan,

thanks for the clarification.


On 05/11/2018 09:08 AM, Ryan Thompson wrote:
> Hi Robert,
> My understanding is that the "requireNamespace" trick, combined with 
> listing the package in "Suggests" is the standard way to implement 
> optional dependencies. Users of limma that never use 
> duplicateCorrelation or other functions that require statmod will never 
> need to install it.
> For more info, see this old post about the same problem: 
> https://support.bioconductor.org/p/16932/
> Regards,
> Ryan
> On Thu, May 10, 2018 at 11:58 PM Robert Castelo <robert.castelo at upf.edu 
> <mailto:robert.castelo at upf.edu>> wrote:
>     hi,
>     this is a question for limma developers.
>     at every new fresh installation of BioC and limma i get this message
>     when i use 'duplicateCorrelation()':
>     "statmod package required but is not installed"
>     i just install 'statmod' and problem solved. this, however, triggers
>     questions from some of my students since they expect that BioC
>     dependencies within functions are automatically installed when the
>     desired package is installed for the first time.
>     i've observed within the limma source that the 'statmod' functionality
>     is used within other functions and in all cases this is dealt as in
>     'duplicateCorrelation()', where first it's checked whether the package
>     namespace can be loaded and the user is asked otherwise to install it:
>     if(!requireNamespace("statmod",quietly=TRUE)) stop("statmod package
>     required but is not installed")
>     and the 'statmod' package is listed in the 'Suggests:' field of the
>     DESCRIPTION file.
>     just out of curiosity, is there a particular reason to import the
>     functionality of 'statmod' in this way? wouldn't be possible to do it
>     via 'Imports:'?
>     thanks!
>     robert.
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Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550

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