Problem in vignette packaging of Sweave in utils package

Tue, Jul 3, 2012 12:21 PM

The HTML help related pages are dynamically generated upon request, so there are no static pages that would exist otherwise. I can get to the index pages for each of the packages mentioned in Yihui's post.

That being said, I can replicate the vignette issue on:

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"

which was a clean install on OSX Lion using the OSX binary on CRAN.

No vignettes found by browseVignettes("utils")

No vignettes found by browseVignettes("grid")

No vignettes found by browseVignettes("parallel")

Warning message:
vignette ?Sweave? not found 


However, Matrix and survival did work.

Curiously, testInstalledPackages() did work for the vignettes without returning an error:

Running vignettes for package ?utils?
Running vignettes for package ?grid?
Running vignettes for package ?parallel?
Running vignettes for package ?Matrix?
Running vignettes for package ?survival?

[1] 0


I then installed:

R version 2.15.1 Patched (2012-07-02 r59715) -- "Roasted Marshmallows"

from Simon's site and:

all worked. 

So it would appear that there was something amiss with the 2.15.1 release packaging or something involving the vignettes at least for those packages. A review of the NEWS file did not reveal anything obvious to me that would be relevant.

Regards,

Marc Schwartz

On Jul 3, 2012, at 12:54 PM, Yihui Xie wrote:

Strange enough; I just noticed the HTML index pages of several base
packages were gone (e.g. base, stats, tools, utils) under Ubuntu. Not
sure if this is a problem of Debian packages or R itself.

sessionInfo()

R version 2.15.1 (2012-06-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C                 LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA


On Tue, Jul 3, 2012 at 1:34 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

On 03/07/2012 1:21 PM, Paul Johnson wrote:

In ?Sweave, it refers to Sweave User Manual. In the doc folder of
utils package, I see "Sweave.pdf".

However, I can't find it from within R

vignette("Sweave User Manual")

Warning message:
vignette ?Sweave User Manual? not found

browseVignettes("utils")

No vignettes found by browseVignettes("utils")

library(help=utils)

does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?


The vignette name is "Sweave", so you should see it when you say

vignette("Sweave")

but you should also have seen it in

browseVignettes("utils")

and

library(help=utils)

and the page for utils in the HTML help.  So it looks as though something is
wrong in your install.  I do see it in 2.15.1 patched on Windows.

Duncan Murdoch

Problem in vignette packaging of Sweave in utils package

Thread (9 messages)