From hb at biostat.ucsf.edu  Fri Aug 30 22:23:49 2013
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Fri, 30 Aug 2013 13:23:49 -0700
Subject: [Rd] Problem with texi2pdf(..,clean=TRUE)
In-Reply-To: <5220FAF7.5080603@aon.at>
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	<5220F780.8080507@aon.at> <5220FAF7.5080603@aon.at>
Message-ID: <CAFDcVCQVQA6R2M5URVZONpQZWk7eW64z0utU0tvsqmHKTAK2XQ@mail.gmail.com>

Just checked the SVN logs and the comparison towards file timestamps
have been dropped in R devel and R 3.0.1 SVN r63690 (Aug 25, 2013) and
newer.  It is now simply comparing the set of files before and after.
Try with one of those and I'll bet you that clean=TRUE does what it
supposed to.

/Henrik


On Fri, Aug 30, 2013 at 1:05 PM, cstrato <cstrato at aon.at> wrote:
> Dear Henrik,
>
> I am trying to attach the 'QAReport.Rnw' file which I am using on my Mac to
> reproduce your problem.
>
> Best regards,
> Christian
>
>
>
> On 8/30/13 9:50 PM, cstrato wrote:
>>
>> 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)
Henrik Bengtsson