R-devel CMD build fails when vignette present

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R-devel CMD build fails when vignette present

Martin Morgan
If I try to build a package with a vignette

  R CMD build Biobase

I see

* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... OK
* cleaning src
Error in setwd(pkgname) : cannot change working directory
Execution halted

This is because prepare_pkg invoked at tools/R/build.R:605 changes the
directory (e.g., from /tmp/RtmprGGHhU/Rbuild257d6d93 to
/tmp/RtmprGGHhU/Rbuild257d6d93/Biobase), in turn because the on.exit at
build.R:223 is usurped by on.exit at build.R:256/259.

Martin
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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Re: R-devel CMD build fails when vignette present

Prof Brian Ripley
Biobase is not self-contained so I cannot easily test it, but as far
as I know this is now resolved.

On Sun, 24 Oct 2010, Martin Morgan wrote:

> If I try to build a package with a vignette
>
>  R CMD build Biobase
>
> I see
>
> * checking for file 'Biobase/DESCRIPTION' ... OK
> * preparing 'Biobase':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to re-build vignettes
> * creating vignettes ... OK
> * cleaning src
> Error in setwd(pkgname) : cannot change working directory
> Execution halted
>
> This is because prepare_pkg invoked at tools/R/build.R:605 changes the
> directory (e.g., from /tmp/RtmprGGHhU/Rbuild257d6d93 to
> /tmp/RtmprGGHhU/Rbuild257d6d93/Biobase), in turn because the on.exit at
> build.R:223 is usurped by on.exit at build.R:256/259.
>
> Martin
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: R-devel CMD build fails when vignette present

Martin Morgan
On 10/25/2010 03:21 AM, Prof Brian Ripley wrote:
> Biobase is not self-contained so I cannot easily test it, but as far as
> I know this is now resolved.

Thank you it is. Martin

>
> On Sun, 24 Oct 2010, Martin Morgan wrote:
>
>> If I try to build a package with a vignette
>>
>>  R CMD build Biobase
>>
>> I see
>>
>> * checking for file 'Biobase/DESCRIPTION' ... OK
>> * preparing 'Biobase':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to re-build vignettes
>> * creating vignettes ... OK
>> * cleaning src
>> Error in setwd(pkgname) : cannot change working directory
>> Execution halted
>>
>> This is because prepare_pkg invoked at tools/R/build.R:605 changes the
>> directory (e.g., from /tmp/RtmprGGHhU/Rbuild257d6d93 to
>> /tmp/RtmprGGHhU/Rbuild257d6d93/Biobase), in turn because the on.exit at
>> build.R:223 is usurped by on.exit at build.R:256/259.
>>
>> Martin
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
>


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

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