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

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.

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.