R devel - Apr 2013 - "Failed to locate the 'texi2pdf' output file"

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

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.

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.

Kasper



On Fri, Apr 12, 2013 at 5:34 PM, Dan Tenenbaum <dtenenba@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]]

On Fri, Apr 12, 2013 at 4:23 PM, Henrik Bengtsson <hb at biostat.ucsf.edu>
wrote:
> On Fri, Apr 12, 2013 at 3:53 PM, Kasper Daniel Hansen
> <kasperdanielhansen at 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.
>

Just to follow up on this a bit--today we got this error with a data
package that has no dependencies of any kind, and no R code. All the
vignette does is load three datasets which are all data frames.

So this suggests that the problem, in this case anyway, has nothing to
do with database connections or parallelism. Duncan's suggestion about
a virus scanner is a good one, but there is no such software running
on the machine in question.

So it sounds maybe more like what Henrik describes above. Wondering if
there are more insights to be had...

Thanks,
Dan

>>
>> Kasper
>>
>>
>>
>> On Fri, Apr 12, 2013 at 5:34 PM, Dan Tenenbaum <dtenenba at
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 at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel