From kevinushey at gmail.com  Mon Aug 25 20:17:34 2014
From: kevinushey at gmail.com (Kevin Ushey)
Date: Mon, 25 Aug 2014 11:17:34 -0700
Subject: [Rd] vignette index going AWOL
In-Reply-To: <BDF32633-2F32-4757-8B8A-3DCDA8FB92D5@calvin.edu>
References: <BDF32633-2F32-4757-8B8A-3DCDA8FB92D5@calvin.edu>
Message-ID: <CAJXgQP1ZMVW+nqp+dAqFHL7sBTcTK4N9megYCTpbiS2vR_87jg@mail.gmail.com>

Hi Randall,

I notice that, in your .Rbuildignore, you have the entry:

    ^build$

and I suspect this is the culprit (having being bitten by a similar
problem before). Some part of the R build / install process creates /
uses that directory, but having it excluded in .Rbuildignore will
cause you grief.

In general, you probably have to consider `build` reserved for use by
R, when developing R packages.

Cheers,
Kevin

On Mon, Aug 25, 2014 at 11:10 AM, Randall Pruim <rpruim at calvin.edu> wrote:
> I?m preparing a package (fastR) for submission to CRAN, but the vignette index keeps going AWOL, or at least R CMD check ?as-cran thinks so. I?ve tried several things and gave myself the weekend to think of other things, but I can?t figure it out.  Perhaps someone on the list can lend a hand.
>
> Here?s one example situation, where I build the index.html file myself and put it in inst/doc/index.html
>
> $ cat fastR.Rcheck/00check.log | grep -v OK
> * using log directory ?/Users/rpruim/projects/github/fastR/fastR.Rcheck?
> * using R Under development (unstable) (2014-08-21 r66456)
> * using platform: x86_64-apple-darwin13.1.0 (64-bit)
> * using session charset: UTF-8
> * checking extension type ... Package
> * this is package ?fastR? version ?0.8-0?
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ?Randall Pruim <rpruim at calvin.edu>?
> Package has a VignetteBuilder field but no prebuilt vignette index.
> NOTE: There was 1 note.
>
> $ tar -tf fastR_0.8-0.tar.gz | grep inst/doc
> fastR/inst/doc/
> fastR/inst/doc/Errata.Rnw
> fastR/inst/doc/Errata.pdf
> fastR/inst/doc/Updates.R
> fastR/inst/doc/Updates.Rnw
> fastR/inst/doc/Updates.pdf
> fastR/inst/doc/index.html
>
> There is an index.html in the tar ball.  And If I install the package from the tar ball, the index appears as it should in the package.
>
> I would be happy with the auto-generated index, but that doesn?t seem to be working either.  If I remove index.html I get
>
> $ grep -v OK fastR.Rcheck/00check.log
> * using log directory ?/Users/rpruim/projects/github/fastR/fastR.Rcheck?
> * using R Under development (unstable) (2014-08-21 r66456)
> * using platform: x86_64-apple-darwin13.1.0 (64-bit)
> * using session charset: UTF-8
> * checking extension type ... Package
> * this is package ?fastR? version ?0.8-1?
> * checking CRAN incoming feasibility ... NOTE
> Maintainer: ?Randall Pruim <rpruim at calvin.edu>?
> Package has a VignetteBuilder field but no prebuilt vignette index.
> NOTE: There was 1 note.
>
> $ tar -tf fastR_0.8-1.tar.gz | grep inst/doc
> fastR/inst/doc/
> fastR/inst/doc/Errata.Rnw
> fastR/inst/doc/Errata.pdf
> fastR/inst/doc/Updates.R
> fastR/inst/doc/Updates.Rnw
> fastR/inst/doc/Updates.pdf
>
> Comparing with other successful packages created last week, it doesn?t appear that the tar ball contains the vignette index for those either ? or perhaps I don?t know what I?m looking for.
>
> $ tar -tf mosaic_0.9.1-3.tar.gz | grep -i index
> mosaic/demo/00Index
>
> (mosaic passes checks fine and are already on CRAN.)
>
> Both packages use knitr to convert Rnw to PDF.  mosaic also uses R.rsp to include static PDFs.
>
> $ grep -i vig  mosaic/DESCRIPTION
> VignetteBuilder: knitr, R.rsp
>
> [09:22][rpruim at Mac21521:~/projects/github]
> $ grep -i vig  fastR/DESCRIPTION
> VignetteBuilder: knitr
>
> $ grep  Vig mosaic/vignettes/*Rnw
> %\VignetteIndexEntry{mosaic resources}
> %\VignettePackage{mosaic}
> %\VignetteKeywords{mosaic, vignettes, resources, references}
> %\VignetteEngine{knitr::knitr}
>
> $ grep  Vig fastR/vignettes/*Rnw
> fastR/vignettes/Errata.Rnw:%\VignetteEngine{knitr::knitr}
> fastR/vignettes/Errata.Rnw:%\VignetteIndexEntry{Errata}
> fastR/vignettes/Errata.Rnw:%\VignettePackage{fastR}
> fastR/vignettes/Errata.Rnw:%\VignetteKeywords{fastR, vignettes}
> fastR/vignettes/Updates.Rnw:%\VignetteEngine{knitr::knitr}
> fastR/vignettes/Updates.Rnw:%\VignetteIndexEntry{Updates to R Programming in FASt}
> fastR/vignettes/Updates.Rnw:%\VignettePackage{fastR}
> fastR/vignettes/Updates.Rnw:%\VignetteKeywords{mosaic, fastR, vignettes, resources}
>
> There must be some subtle difference between my two packages that I just can?t spot.
>
> Thanks in advance for any pointers about where to look.
>
> ?rjp
>
> PS.  The package is on github and installs fine (vignette index included, even though there is no index.html in the repo) using install_github("fastR", "rpruim")
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[Rd] vignette index going AWOL
Kevin Ushey