Vignettes not found during check on windows/linux for R 3.1

[sckott]

Seems to work fine on my local OSX machine, but for Winbuilder and Travis-CI (i.e., linux) the package installs fine, test run without fail, but then vignettes can't be found for some reason whether they are in vignettes/ dir, or in inst/doc/ dir.

Here's an example build on Travis https://travis-ci.org/ropensci/rgbif/builds/23174029#L1938 - where the check fails saying that the vignettes can not be found.

Anyone have any thoughts? @cboettig @gavinsimpson

[cboettig]

Passes check() on my Linux box (Ubuntu 13.10). No idea what's up with travis.

---

Carl Boettiger http://carlboettiger.info

sent from mobile device; my apologies for any terseness or typos On Apr 16, 2014 9:06 PM, "Scott Chamberlain" notifications@github.com wrote:

Seems to work fine on my local OSX machine, but for Winbuilder and Travis-CI (i.e., linux) the package installs fine, test run without fail, but then vignettes can't be found for some reason whether they are in vignettes/ dir, or in inst/doc/ dir.

Anyone have any thoughts? @cboettig https://github.com/cboettig @gavinsimpson https://github.com/gavinsimpson

— Reply to this email directly or view it on GitHubhttps://github.com/ropensci/rgbif/issues/78 .

[gavinsimpson]

Is there a reason you are using --no-build-vignettes on R CMD check in Travis? I can see a reason for not building them (though that is why you are getting the warnings about there not being a corresponding PDF for each vignette), but you should probably be building vignettes as part of check.

Another issue is that you should have knitr listed in the Suggests (Or Imports or Depends, but Suggests is probably the place for this as you only need it for the vignette building. See Non-Sweave Vignettes in the Writing R Extensions manual.

Vignettes supposed to be in vignettes so ignore inst/doc/ as part of this.

It's difficult to say more than this at the moment; the above things may have some role or they may not, but lets rule them out and go from there?

[sckott]

Hey @gavinsimpson , Thanks for the feedback. I didn't mean to do --no-build-vignettes. Not sure why that is happening. Perhaps something I can tweak in the travis file.

Aha! This is something I forgot before. I think it is the lack of knitr in Suggests. I'll try adding in knitr first.

[sckott]

Passes now with knitr in Suggests - thanks for catching that @gavinsimpson !

Still seeing the vignette error though. Found this https://github.com/csgillespie/travis-examples/tree/master/vignette

Seems that vignettes are not build by default with r-travis - been so for a while I think. That repo suggests adding

env:
   global:
     - R_BUILD_ARGS=" " 
     - R_CHECK_ARGS="--as-cran"
     - BOOTSTRAP_LATEX="1"

Trying it out

[sckott]

That change in the travis file seemed to fix the vignette issue https://travis-ci.org/ropensci/rgbif/builds/23217355