hi Ryan,
thanks for the clarification.
robert.
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.cast...@upf.edu
<mailto:robert.cast...@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.
_______________________________________________
Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
