[Bioc-devel] Suggestion to use packageStartupMessage() instead of cat() in GLAD

[Henrik Bengtsson]

Hi,

maintainer CC:ed, but since this may apply to other
packages/developers too, I send it to the list.

In .onLoad() of GLAD the welcome message is outputted using cat().
Could you please update this to use packageStartupMessage() instead.
This way it is possible to load GLAD quietly.  Moreover, the message
will not be loaded if you access a function in GLAD using "::", e.g.
GLAD::as.profileCGH.  Right now/with cat() you get:

% R --vanilla

> fcn <- GLAD::as.profileCGH

######################################################################################

Have fun with GLAD

For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002)
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)

If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)

If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar,
Bioinformatics, 2008)

For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg

######################################################################################

New options are available in daglad: see help for details.


> print(fcn)
function (object, ...)
{
    UseMethod("as.profileCGH")
}
<environment: namespace:GLAD>


Thanks

Henrik

PS. Your "rulers" - ####....# - are longer than 80, which is the
typical terminal width, and therefore they will line wrap.  You might
want to shorten them to 80 or dynamically use getOption("width").