From cstrato at aon.at  Fri Aug 30 21:50:24 2013
From: cstrato at aon.at (cstrato)
Date: Fri, 30 Aug 2013 21:50:24 +0200
Subject: [Rd] Problem with texi2pdf(..,clean=TRUE)
In-Reply-To: <CAFDcVCSRbFwDAee0sUtkQHwEK-488b=5uhq142n_eKgwCjV1RA@mail.gmail.com>
References: <5220EBBE.8080504@aon.at>
	<D9E36BC9-3F08-4735-A61C-C183486D59C3@me.com>
	<5220EF23.5040400@gmail.com> <5220F0B7.2000107@aon.at>
	<CAFDcVCSRbFwDAee0sUtkQHwEK-488b=5uhq142n_eKgwCjV1RA@mail.gmail.com>
Message-ID: <5220F780.8080507@aon.at>

Dear Henrik,

Thank you for your explanation.

Yes, this behavior is reproducible many times.

When I copy both lines together into R, i.e.
    Sweave("QAReport.Rnw")
    tools::texi2pdf("QAReport.tex", clean = TRUE)

then the auxiliary files are deleted. However, when I keep the *.tex 
file only and run:
    tools::texi2pdf("QAReport.tex", clean = TRUE)

then these files are not deleted. I can delete them manually many times 
and run texi2pdf() again, they will never be deleted.

I really hope that your patch will be applied, so that it works as 
expected with the next Bioconductor release on October.

Best regards,
Christian


On 8/30/13 9:36 PM, Henrik Bengtsson wrote:
> On Fri, Aug 30, 2013 at 12:21 PM, cstrato <cstrato at aon.at> wrote:
>> Dear Duncan, dear Marc,
>>
>> Thank you for your fast reply.
>>
>> Can you please tell me:
>> If texi2pdf() won't delete files how are the files deleted when the
>> directory structure is Test/inst/doc/?
>
> Check if what you're observing is reproducible when you run it *many*
> times.  If not, see my previous reply.
>
> /Henrik
>
>> Is this done by Sweave()?
>>
>> Best regards,
>> Christian
>>
>>
>>
>> On 8/30/13 9:14 PM, Duncan Murdoch wrote:
>>>
>>> On 30/08/2013 3:09 PM, Marc Schwartz wrote:
>>>>
>>>> On Aug 30, 2013, at 2:00 PM, cstrato <cstrato at aon.at> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> To create a *.pdf file from a *.Rnw file I do:
>>>>>
>>>>>       olddir <- getwd();
>>>>>       setwd(outdir);
>>>>>
>>>>>       tryCatch({Sweave("QAReport.Rnw");
>>>>>                 tools::texi2pdf("QAReport.tex", clean=TRUE)
>>>>>                },
>>>>>                finally = setwd(olddir)
>>>>>               );
>>>>>
>>>>> This works fine, however 'clean=TRUE' does only work when:
>>>>>      outdir <- "Test/inst/doc/"
>>>>> but does not remove the files *.aux, *.log, *.toc when:
>>>>>      outdir <- "Test/"
>>>>>
>>>>> Why does function texi2pdf() require the directory structure for
>>>> vignettes for the deletion of interim files?
>>>>>
>>>>> (The help file?texi2pdf does not mention that this structure is
>>>> necessary.)
>>>>>
>>>>> Best regards
>>>>> Christian
>>>>
>>>>
>>>> In the Details section of ?texi2pdf, there is:
>>>>
>>>> "Despite the name, this is used in R to compile LaTeX files,
>>>> specifically those generated from vignettes."
>>>>
>>>>
>>>> Since it is intended specifically for package vignettes, the path
>>>> requirement should not be a surprise. :-)
>>>>
>>>
>>> There is no path requirement.  Christian was incorrect in his diagnosis.
>>>
>>> texi2pdf won't delete files that existed before it was run, whether or
>>> not they were changed during the run.  That's likely what Christian was
>>> seeing.
>>>
>>> Duncan Murdoch
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Problem with texi2pdf(..,clean=TRUE)
cstrato