[Bioc-devel] Sweave changes (keep.source = TRUE or FALSE?)

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Thu Dec 7 18:00:44 CET 2006

> Note: I got only one serious email (the one by Deepayan I'll answer in
> a minute) that keep.source=FALSE produces better looking documents in
> some cases, and that's a discussion I like.  All other complaints
> where simply of the form "we can't change it because it has always
> been the way that it is". I thought that rule is not necessarily true
> in a research project like R.

I don't accept the caricature here.  People can disagree on what
a good default setting is, and, apparently, even what a bug is.
I would never have regarded the use of R deparse formatting by Sweave
as a bug -- that just tells you how messy my sources are.  I can pay
the price of setting an option if you want to remove the role of
deparse in code formatting.  But I wanted you alert you to an alternative
attitude about it, which includes reckoning with the possibility that
things may look a lot worse in a lot of default-processed documents, both
those written in the past and those to be written, when the default is changed.
That possibility may also be dismissed, but it is not a conservative
complaint, and it does provide a basis for thinking about the purpose
of a default setting.

No one challenged the introduction of the new functionality.  The initial
justification for the alteration of the default included the desire to get
more information on possible problems with the new keep.source functionality
in connection with Sweave.  I found that somewhat annoying -- yes, it will
generate data on possible problems, but at substantial cost to users, or
maybe just to our project.  So I think there was a basis for objection to
the altered default, but one that could be discussed.  I recognize that
R-devel is unstable and experimental, but there is still a role for some
pushback, and the core can choose to disregard it if the benefits of the
change outweigh the costs.

I was completely mystified by the transition from a
default setting for a code formatting process to considerations of
central configuration files or flavors of R.  But maybe that reflects
my limitations more than anything else.  I think this issue is very
local to a feature of a specific piece of software and should have no
broad ramifications for the general installation process or
distribution/installation of R.

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