[Bioc-devel] package building & checking

[Martin Morgan]

On 09/15/2011 11:56 PM, Andreas Heider wrote:
> You are right Vincent,
> I get the very same error!
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>    unable to run 'pdflatex' on 'XYZ'
> Calls:<Anonymous>  ->  texi2pdf ->  texi2dvi
> Execution halted
>
> But I am quite confused about how to solve this problem. It sounds kind of
> strange to me.
> Why does the call fail? The pdf is generated fine!

Having Stangle'd the Rnw file, you can also run texi2dvi --pdf on the 
command line

   R CMD texi2dvi --pdf XYZ.tex

maybe that gives an easier way of trouble-shooting.

Reading Vince's commentary, I would have conceded defeat to LaTeX and 
removed the dependency on pstricks from my vignette.

Martin

> Will my problems be solved just by installing Tex Live?
>
> 2011/9/15 Vincent Carey<stvjc at channing.harvard.edu>
>
>> As I have had various issues with latex lately I will comment a little.
>> For developers, I think it is fair to say that R-latex interaction has
>> become more important of late, owing to documentation capabiliites and
>> requirements.  Recently Herve added a comment to various vignettes
>>
>> % With MikTeX 2.9, using pstricks also requires using auto-pst-pdf or
>> running
>> % pdflatex will fail. Note that using auto-pst-pdf requires to set
>> environment
>> % variable MIKTEX_ENABLEWRITE18=t on Windows, and to set shell_escape = t
>> in
>> % texmf.cnf for Tex Live on Unix/Linux/Mac.
>>
>> which says a lot.  This mentions a few things I have not been directly
>> concerned with: write18 (?), pstricks, auto-pst-pdf and so on.
>>
>> Witnessing build error messages like
>>
>> Output written on parody.pdf (8 pages, 107975 bytes).
>> Transcript written on parody.log.
>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>>
>>    unable to run 'pdflatex' on 'parody.tex'
>> Calls:<Anonymous>  ->  texi2pdf ->  texi2dvi
>> Execution halted
>>
>> is somewhat confusing and might need to go to R-devel, as "unable to run"
>> seems not quite right.  It ran, and pdf was generated, but untoward events
>> did occur, and demise of the build is probably rightly called for.
>>
>> I bit the bullet and asked for installation of TexLive 2011.  I then had to
>> get rid of various .sty files in my TEXINPUTS that were no longer up to
>> date.  I followed the shell_escape setting noted by Herve, in a personal
>> texmf.cnf that can be identified through the TEXMFCNF environment variable
>> -- be sure to have : as a suffix to the value.
>>
>> No more "Execution halted".  I am free to deal with my other problems now.
>>
>>
>>
>> On Thu, Sep 15, 2011 at 10:12 AM, James W. MacDonald<
>> jmacdon at med.umich.edu>  wrote:
>>
>>> Hi Andreas,
>>>
>>>
>>> On 9/15/2011 9:03 AM, Andreas Heider wrote:
>>>
>>>> Dear mailing list,
>>>> I've setup everything in my local package derectory including Sweave
>>>> vignette and a PDF version of it.
>>>> The "Sweave" command runs fine, so does checking the package directly
>>>> from
>>>> the source directory.
>>>> However, when I try to BUILD from the source directory (via R CMD BUILD
>>>> directory) it throws me an error that texi2dvi stopped with error.
>>>>
>>>> What is wrong? How can I find out?
>>>>
>>>
>>> Without some output, nobody can tell what is wrong. And this is really an
>>> R-help and possibly an R-devel question.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>
>>>
>>>> Thanks in advacne, Andreas
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Douglas Lab
>>> University of Michigan
>>> Department of Human Genetics
>>> 5912 Buhl
>>> 1241 E. Catherine St.
>>> Ann Arbor MI 48109-5618
>>> 734-615-7826
>>>
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>>
>>
>
> 	[[alternative HTML version deleted]]
>
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