From marc_schwartz at me.com  Tue Jul  3 21:21:06 2012
From: marc_schwartz at me.com (Marc Schwartz)
Date: Tue, 03 Jul 2012 14:21:06 -0500
Subject: [Rd] Problem in vignette packaging of Sweave in utils package
In-Reply-To: <CANROs4e6mpBwbcmqCwGUPdfUJb1iriDw2Xq=DYsDrZu8R2Z_xw@mail.gmail.com>
References: <CAErODj_9n7cjy5iPkjr-GOocL23hnJwX2QCYSd+4zJfgu0SUpA@mail.gmail.com>
	<4FF32D10.2070803@gmail.com>
	<CANROs4e6mpBwbcmqCwGUPdfUJb1iriDw2Xq=DYsDrZu8R2Z_xw@mail.gmail.com>
Message-ID: <10B60ABF-DF86-426F-8F02-61F056D0A12A@me.com>

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.


> browseVignettes("utils")
No vignettes found by browseVignettes("utils")

> browseVignettes("grid")
No vignettes found by browseVignettes("grid")

> browseVignettes("parallel")
No vignettes found by browseVignettes("parallel")

> vignette("Sweave")
Warning message:
vignette ?Sweave? not found 


However, Matrix and survival did work.

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

> Result <- testInstalledPackages(types = "vignettes")
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?
> Result
[1] 0


I then installed:

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

from Simon's site and:

> browseVignettes("utils")
> browseVignettes("grid")
> browseVignettes("parallel")
> vignette("Sweave")

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



[Rd] Problem in vignette packaging of Sweave in utils package
Marc Schwartz