Some examples don't work

[sckott]

Hi @dwinter Trying to update the tutorial on our website for rentrez.

Some of the examples don't work though. E.g.

In this function R complains that rettype arg is missing with no default

entrez_fetch(db = "nuccore", WebEnv = cookie, query_key = qk, file_format = "fasta", retmax = 10)

And in entrez_search the readme has an example

summaries <- entrez_summary(db="popset", id=katipo_search$ids)
xpathSApply(summaries, "//Item[@Name='Title']", xmlValue)

But this doesn't work. Seems that an XML object used to be returned, but not anymore?

Here's the tutorial here that I'm working on: https://gist.github.com/sckott/9b4d0d5296ddc845c3c4

[dwinter]

Ahuh - yeah, I made a nicer front-end to the esummary requests, but failed to (a) include these example in the documentation tests and (b) update the all the docs to reflect the change.

I can do the README and the tests when I get a chance. For the tutorial, is it easiest if I fork the gist and make the updates?

[sckott]

Thanks. For the tutorial, yeah, fork and fix. I think most examples work.

[dwinter]

Commite reference above and a couple of others I've just pushed take care of the examples, and the code in the README. Leaving this open until I get check the tutorial.

[sckott]

what do you mean by "until I get check the tutorial". Do you want to see the draft html version for our site before I put it up?

[dwinter]

Sorry. I mean I haven't had time to confirm everything in the tutorial (the gist) runs as expected. I'll do that in the next day or two, and add tests for anything that isn't covered.

On Wed, May 14, 2014 at 12:49 PM, Scott Chamberlain < notifications@github.com> wrote:

what do you mean by "until I get check the tutorial". Do you want to see the draft html version for our site before I put it up?

— Reply to this email directly or view it on GitHubhttps://github.com/ropensci/rentrez/issues/10#issuecomment-43128669 .

David Winter Postdoctoral Research Associate Center for Evolutionary Medicine and Informatics The Biodesign Institute Arizona State University

ph: +1 480 519 5113 w: www.david-winter.info lab: http://cartwrig.ht/lab/ blog: sciblogs.co.nz/the-atavism

[sckott]

Ah, cool, thx

[dwinter]

OK @sckott, I think every looks good now. Here's a slightly edited version of the tutorial in Rmd, which compiles nicely for me. Note, this is for a the latest version of rentrez which went up on CRAN last night at deals with this bug that I uncovered while doing this (so thanks for reporting this!)

[sckott]

@dwinter Cool. I'll work on getting the vignette up as a tutorial on our website.

[sckott]

@dwinter Okay, check it out http://ropensci.org/tutorials/rentrez_tutorial.html Look good?

Also, we need some extra bits for the vignette: knitr should be in Suggests in the Desc file, and if you want vignettes to install for users to see you should have VignetteBuilder: knitr in the Desc file

[dwinter]

Thanks @sckott, looks great. I will make the changes for the vignette too

[sckott]

okay :+1:

[dwinter]

Still having some trouble with the vignette -- have a question on SO which covers the problems I'm having:

http://stackoverflow.com/questions/24436928/r-cmd-build-skips-knitr-rmd-vignettes-outputs-listed-in-build-vignette-rds