How do I identify which Sweave code chunk gives an error?

Question

When running Sweave from emacs-ess, errors are provided with a code chunk number. Is there an easy way to navigate among the code chunks by number? Otherwise, they are difficult to identify.

score 5 · Accepted Answer · answered Dec 21 '10 at 18:50

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I don't use emacs-ess (I use Eclipse/ StatEt) but this shows which code chunks are being processed by label (each code chunk starts with <<label="Some Text"... Does your code chunks include labels ?

answered Dec 21 '10 at 18:50

PaulHurleyuk

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So far, counting chunks worked for me. But I may consider using labels from now on. – Roman Luštrik Dec 22 '10 at 08:58
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I agree. Labels are the way to go. I label most code blocks. In addition to aiding debugging, you can reuse code blocks, and importantly, it helps with the general readability of your Sweave document. – Jeromy Anglim Jan 01 '11 at 13:18

score 2 · Answer 2 · answered Dec 22 '10 at 09:33

In noweb mode in emacs M-n i inserts the chunk and asks for the label. You can navigate between them with M-n g which is very handy with completion packages like ido or icicles. With ido you must use this hack to activate it for all completion-read based functions such as noweb-goto-chunk from above.

score 1 · Answer 3 · answered Feb 18 '11 at 17:28

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Another thing that might help is setting options(error=recover) in your R environment before sweaving. That will give you a chance to investigate the state of things just before an error is thrown.

answered Feb 18 '11 at 17:28

Neil Best

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Thanks. I finally implemented this and it is really helpful. – David LeBauer May 05 '11 at 14:21

How do I identify which Sweave code chunk gives an error?

3 Answers3