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Paul Johnson | 3 Jul 2012 19:21

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Problem in vignette packaging of Sweave in utils package

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?

(Continue reading)

Duncan Murdoch | 3 Jul 2012 19:34

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Re: Problem in vignette packaging of Sweave in utils package

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}

(Continue reading)

Yihui Xie | 3 Jul 2012 19:54

Re: Problem in vignette packaging of Sweave in utils package

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:
>>

(Continue reading)

Marc Schwartz | 3 Jul 2012 21:21

Re: Problem in vignette packaging of Sweave in utils package

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’

(Continue reading)

Paul Johnson | 3 Jul 2012 21:23

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Re: Problem in vignette packaging of Sweave in utils package

On Tue, Jul 3, 2012 at 12:54 PM, Yihui Xie <xie <at> yihui.name> 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.
>

It is not only on Debian where I see:

> vignette("Sweave")
Warning message:
vignette ‘Sweave’ not found

This afflicts RPM based installs as well. It is not a new problem, AFAICT.

Here's output from R-2.15.0 on a Centos Linux cluster node.:

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

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C

(Continue reading)

Duncan Murdoch | 7 Jul 2012 14:25

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Re: Problem in vignette packaging of Sweave in utils package

On 12-07-03 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

Turns out there was a bug in the code to install from tarballs, so base 
package vignettes weren't fully installed.  I've fixed it; installs from 
R-patched or R-devel revisions after 59750 should be okay.

Duncan Murdoch

>
>
>> 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

(Continue reading)

Paul Johnson | 27 Jul 2012 07:23

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Re: Problem in vignette packaging of Sweave in utils package

New help request below

On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <murdoch.duncan <at> gmail.com> wrote:
> On 12-07-03 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
>
>
> Turns out there was a bug in the code to install from tarballs, so base
> package vignettes weren't fully installed.  I've fixed it; installs from
> R-patched or R-devel revisions after 59750 should be okay.
>
> Duncan Murdoch
>
>

Thanks, Duncan

Can I ask you to check this one again?

I just built RPMS for R-2.15.1-patched 2012-07-25 on a Rocks Cluster

(Continue reading)

Duncan Murdoch | 27 Jul 2012 16:54

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Re: Problem in vignette packaging of Sweave in utils package

On 12-07-27 1:23 AM, Paul Johnson wrote:
> New help request below
>
> On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <murdoch.duncan <at> gmail.com> wrote:
>> On 12-07-03 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
>>
>>
>> Turns out there was a bug in the code to install from tarballs, so base
>> package vignettes weren't fully installed.  I've fixed it; installs from
>> R-patched or R-devel revisions after 59750 should be okay.
>>
>> Duncan Murdoch
>>
>>
>
> Thanks, Duncan
>
> Can I ask you to check this one again?

(Continue reading)

Paul Johnson | 27 Jul 2012 22:55

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Re: Problem in vignette packaging of Sweave in utils package

On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch
<murdoch.duncan <at> gmail.com> wrote:
> On 12-07-27 1:23 AM, Paul Johnson wrote:
>>
>> New help request below
>>
>> On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <murdoch.duncan <at> gmail.com>
>> wrote:
>>>
>>> On 12-07-03 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
>>>
>>>
>>>
>>> Turns out there was a bug in the code to install from tarballs, so base
>>> package vignettes weren't fully installed.  I've fixed it; installs from
>>> R-patched or R-devel revisions after 59750 should be okay.
>>>

(Continue reading)

Prof Brian Ripley | 4 Aug 2012 22:07

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Re: Problem in vignette packaging of Sweave in utils package

I believe the issue is actually quite simple: you need to run

make vignettes

when building from a tarball if you want the tangled vignettes and the 
indices.

I'll make that automatic after more testing.

On 27/07/2012 21:55, Paul Johnson wrote:
> On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch
> <murdoch.duncan <at> gmail.com> wrote:
>> On 12-07-27 1:23 AM, Paul Johnson wrote:
>>>
>>> New help request below
>>>
>>> On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <murdoch.duncan <at> gmail.com>
>>> wrote:
>>>>
>>>> On 12-07-03 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")
>>>>>

(Continue reading)

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