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

Kevin R. Coombes krc at mdacc.tmc.edu
Wed Dec 6 19:37:22 CET 2006


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.


Friedrich Leisch wrote:
>>>>>> On Tue, 05 Dec 2006 15:27:02 +0000,
>>>>>> Wolfgang Huber (WH) wrote:
> [...]
> IMO R must be allowed to change, but if possible it should be easy to
> protect yourself against changes when possible. I always considered
> the parse&deparse behavior of Sweave a bug for which I had no simple
> solution (and am somewhat surprised that there are people who think it
> is a feature). So now that the bug is fixed, it would be natural for
> me to make that available as default.
> [...]

> Best,
> Fritz
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