John Maindonald email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473 fax : +61 2(6125)5549
Centre for Mathematics& Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm
On 22/12/2010, at 3:14 AM, Duncan Murdoch wrote:
On 21/12/2010 3:23 AM, John Maindonald wrote:
Although the specific behaviour that was reported has been fixed, bugs
remain in Sweave's processing of comment lines when keep.source=TRUE
This is in some senses a follow-up from earlier bugs. Hence the query --
what is the preferred procedure, to submit a new bug report? (Another option
might be to add a comment to the web page for bug 14459.)
Is there now a preference to submit via the web page, rather than send a message
to r-bugs at r-project.org? If so, the relevant paragraph in the FAQ surely requires
updating:
<<<
On Unix-like systems a bug report can be generated using the function bug.report(). This automatically includes the version information and sends the bug to the correct address. Alternatively the bug report can be emailed to R-bugs at R-project.org or submitted to the Web page at http://bugs.R-project.org/. Please try including results of sessionInfo() in your bug report.
I have posted files test10.Rnw, test11.Rnw, and test12.Rnw that demonstrate the bugs at
http://www.maths.anu.edu.au/~johnm/r/issues/
The output files test10.tex, test11.tex and test12.tex are from r53870 on
x86_64-apple-darwin9.8.0/x86_64 (64-bit)
test10.Rnw has a code chunk that begins and ends with a comment.
An NA appears following the final comment. This disappears if I
remove the initial comment line.
This is now fixed. It was a different bug than 14459.
test11.Rnw follows a comment line with a named code chunk. The
comment line does not appear in the output.
test12.Rnw places a line of code between the comment line and the
named code chunk. The comment line does now appear in the output.
These look like a different issue, and are still unfixed, and are unlikely to be fixed soon.
The problem is that the handling of source references in Sweave is messy, and needs a major cleanup, which takes time. Between now and at least mid-February I won't have the time it would take, and I don't know anyone else who would do it. So I would not bet on these fixes getting done before 2.13.0.
The problems I know about are these:
- if you use a named chunk<<chunkname>> in another, you won't get
leading and trailing comments on the named chunk.
- if you mix named chunks and \SweaveInput, you won't get the original source at all in the expanded chunks.
Your examples look like the first of these. I had thought the comments had to be in the chunk to get lost, but apparently not.
Just to make priorities clear: in the short term I will fix bugs where NAs show up inappropriately. I will not fix bugs involving dropping leading or trailing comments when there are simple workarounds. (The workaround in your case is not to use the named chunk.)
Duncan Murdoch
John Maindonald email: john.maindonald at anu.edu.au
phone : +61 2 (6125)3473 fax : +61 2(6125)5549
Centre for Mathematics& Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm