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

Alberto Nettel-Aguirre nettela at telus.net
Thu Dec 7 17:19:21 CET 2006

Hello, I am not one of the developers, but I am surely one of the users of R and
Sweave in the academic world. I rarely reply to the thread as I have not much to
say, but I do read much of what is happening.

I agree with Friedrich. I think we (as users) have to appreciate the effort that
has gone into developing both R and Latex (Sweave) for using together. We have a
software that is free, that is reliable and very sound statistically speaking.

One of the great things about these softwares is the fact that changes can
happen and that everything is really transparent, the fact that there is help
available and that the developers are always kind enough to be answering
questions worth answering.

The fact that any change will be announced and that instructions on how to
implement or on how to go back to a previous version is way more than what any
commercial software does. Commercial software goes on, makes changes, tries to
keep that backwards comapatibility, but still there is a black box or a very
complex procedure for getting back to older defaults etc.

As a user with, by far not the same knowledge of the 'guts' of R and Latex as
the developers, I feel that any change the developers see fit, and that is
announced and that there is a way to 'evrride' such options, is perfect.

We can't (should not at least) expect the developers to keep track of our work
and our preferences for each user. As long as there is that freedom for each
user to adapt the siftware to his/her needs, I believe we are in a priviledged

Thanks to FL, DM and all.

Quoting Friedrich Leisch <friedrich.leisch at stat.uni-muenchen.de>:

> >>>>> On Wed, 06 Dec 2006 12:37:22 -0600,
> >>>>> Kevin R Coombes (KRC) wrote:
>   > Hi,
>   > I don't really think anyone believes that the parse&deparse behavior was
>   > exactly a "feature". Instead, I think the primary issue is one of 
>   > backwards compatibility.
>   > You are proposing to change the behavior of Sweave in a manner that will
>   > cause old code to break. Here "break" has two meanings. Some automatic 
>   > development tools will stop working on existing valid code.  In 
>   > addition, existing valid code will produce results that differ from what
>   > they produced previously.
>   > To deal with this, you are going to add an option that will allow users 
>   > to get the old behavior.  However, you propose to set the default value 
>   > of the option to require users to go back and modify all their old code 
>   > in order to prevent things from breaking. It seems obvious to me that 
>   > the default behavior should be the one that does not break old code or 
>   > require the editing of old code in order to get the old behavior.
>   > The reason I use Sweave (for virtually every analysis I do any more) is 
>   > that I can guarantee that when I can go back to the code six months from
>   > now, I can regenerate the analysis and I can regenerate the 
>   > documentation, and I know that I will get the same results. Changing the
>   > default behavior of Sweave violates that guarantee, since the 
>   > documentation will not be identical to what it was before. Personally, I
>   > am willing to pay the cost with NEW analyses to invoke the new behavior 
>   > explicitly (which I do agree is the preferred behavior) because I think 
>   > the goal of backwards compatibility is more important.
>   > In other words, I disagree with your characterization of the 
>   > parse&deparse behavior as a "bug".  It did not cause incorrect results 
>   > in the documentation or the code, and everyone using Sweave knew about 
>   > the behavior.
> Give me a break, that is simply nonsense. Sweave guarantees that you
> can reproduce your results USING THE VERSION OF R THAT WAS USED FOR
> THE ORIGINAL ANALYSIS, and that will still be true, because in R 2.4.x
> there is no option keep.source.  Running a new version of R means
> dozens of R functions will have changed, plotting functions may yield
> figures that look different etc. etc. ... what you propose is in
> essence that we are not allowed to change the default behaviour of ANY
> R FUNCTION. Is that what you are proposing?
> And note that the changes I propose will not change any numerical
> results or figures, nor will I "break code", the only thing that
> changes is that the formatting of input lines looks different (and in
> most cases better, that's why we want to do it).
> It's not like I am changing Sweave behavior every other week, actually
> it is the first one at all. I have thought a lot whether I want to do
> it or not, and I really think it is a good idea. What is great about R
> is that it is allowed to change (if changes are transparent and
> announced early enough). There is a certain operation system with a
> market share of about 90% where backwards compatibility is more
> important than development or security, and I don'tthink that should
> be our role model.
> Best,
> Fritz
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