From cstrato at aon.at  Sat Aug 31 00:12:23 2013
From: cstrato at aon.at (cstrato)
Date: Sat, 31 Aug 2013 00:12:23 +0200
Subject: [Rd] Problem with texi2pdf(..,clean=TRUE)
In-Reply-To: <CAFDcVCQVQA6R2M5URVZONpQZWk7eW64z0utU0tvsqmHKTAK2XQ@mail.gmail.com>
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	<5220EF23.5040400@gmail.com> <5220F0B7.2000107@aon.at>
	<CAFDcVCSRbFwDAee0sUtkQHwEK-488b=5uhq142n_eKgwCjV1RA@mail.gmail.com>
	<5220F780.8080507@aon.at> <5220FAF7.5080603@aon.at>
	<CAFDcVCQVQA6R2M5URVZONpQZWk7eW64z0utU0tvsqmHKTAK2XQ@mail.gmail.com>
Message-ID: <522118C7.4070305@aon.at>

Dear Henrik,

Thank you for this information, I will try to install the patched version.

Best regards,
Christian


On 8/30/13 10:23 PM, Henrik Bengtsson wrote:
> 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)
cstrato