On Fri, Apr 12, 2013 at 3:53 PM, Kasper Daniel Hansen
<kasperdanielhan...@gmail.com> wrote:
> Dan,
>
> This error looks _very_ similar to what I reported regarding the use of
> 'foreach' inside a windows vignette, on the bioc-devel email list. As you
> say, it looks funny that it lists the tex file, yet fails to find it.
It's not looking for the TeX file, but the PDF file - that is what the
error message is referring to by "Failed to locate the 'texi2pdf'
output file". [ Note that in this error message I use the term
"vignette" in a conceptual sense, not necessarily the vignette
*source* file (here *.Rnw) - maybe that is what is confusing. ]
Immediately after calling tools::texi2pdf("OrganismDbi.tex"), the code
tries to locate the texi2pdf output file, that is, 'OrganismDbi.pdf',
which it cannot find. This indicates that tools::texi2pdf() gave an
error (an error message which is currently not reported/available),
which in turn indicates that the 'OrganismDbi.tex' file is
corrupt/incomplete.
>
> The issue had to do with closing relevant connections (for foreach, this
> was a Windows issue because the default foreach backend on Windows uses
> connections). For my particular case, solving it was a bit difficult
> because I could not just close all connections since a vignette is being
> run inside sink().
>
> The package name makes me suspect a database connection. As a starting
> point I suggest closing all existing connections in the vignette.
I think it's worth looking into what Kasper says - that's hopefully the reason.
/Henrik
PS. I do find it odd that these issues starting to occur now, because
most of the vignette framework is performing the same steps as in R (<
3.0.0). The main difference is see is that it now validates/asserts
that the expected output file is there *immediately* after trying to
generate them (using weave, tangle, and texi2pdf). If for some reason
texi2pdf generates the PDF in a background process which is not
completed in full when returning the control to R, then the PDF is not
there and you would get this error. I don't know if this can happen.
The reason why I came to think of this is because I recall that I've
seen this behavior when using bitmap() and Ghostscript to create PNGs.
Just a shot from the hip, though.
>
> Kasper
>
>
>
> On Fri, Apr 12, 2013 at 5:34 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
>
>> Hi,
>> Every day a few Bioconductor packages (different ones each day) fail
>> to build, on Windows only, with an error like this:
>>
>> D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD
>> build --keep-empty-dirs --no-resave-data OrganismDbi
>> [...]
>> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
>> Failed to locate the 'texi2pdf' output file (by engine
>> 'utils::Sweave') for vignette with name 'OrganismDbi'. The following
>> files exists in directory '.': 'OrganismDbi.Rnw', 'OrganismDbi.tex',
>> 'databaseTypes.pdf'
>> Calls: <Anonymous> -> find_vignette_product
>> Execution halted
>>
>> This is puzzling to me because I would have thought that
>> 'OrganismDbi.tex' was the file it was looking for, yet it says that
>> file exists.
>>
>> These build errors are transient...if I re-run the build, the error
>> does not recur. So I was hesitant to report the problem because can't
>> be reproduced consistently. Nevertheless it is a problem.
>>
>> > sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: i386-w64-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> Thanks,
>> Dan
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
