From rpruim at calvin.edu  Mon Aug 25 20:10:48 2014
From: rpruim at calvin.edu (Randall Pruim)
Date: Mon, 25 Aug 2014 18:10:48 +0000
Subject: [Rd] vignette index going AWOL
Message-ID: <BDF32633-2F32-4757-8B8A-3DCDA8FB92D5@calvin.edu>

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")


[Rd] vignette index going AWOL
Randall Pruim