R devel - Mar 2013 - Failed to locate 'weave' output file / vignette product does not have a known filename extension

Hello,

I'm seeing three different vignette-related errors with recent
versions of R-3.0.0 alpha.

First, with the package BitSeq
(http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get
the following when trying to build the package:

Error: processing vignette ?BitSeq.Rnw' failed with diagnostics:
Failed to locate the ?weave? output file (by engine ?utils::Sweave?)
for vignette with name ?BitSeq?. The following files exists in
directory ?.?: ?data-C0.est?, ?data-C1.est?, ?data-c0b0.prob?,
?data-c0b0.rpkm?, ?data-c0b0.sam?, ?data-c0b0.thetaMeans?,
?data-c0b1.rpkm?, ?data-c1b0.rpkm?, ?data-c1b1.rpkm?, ?data.estVar?,
?data.means?, ?data.par?, ?data.pplr?, ?data.tr?, ?ensSelect1.fasta?,
?ensSelect1.tr?, ?parameters1.txt?
Execution halted

My guess is it's looking for BitSeq.tex, but it's not clear where
it's
looking; the package is pretty straightforward, inst/doc contains
BitSeq.Rnw and nothing else (no Makefile).

Next, the package ppiData whose source is here:
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData
(login: readonly password: readonly)

As you can see, there is no .tex file in the source of the package,
but after running R CMD build on it, the resulting .tar.gz file
contains
ppiData/inst/doc/ppiData.tex
Then the package fails check (excerpt of ppiData.Rcheck/00install.out):

Error in vignette_type(Outfile) :
  Vignette product ?ppiData.tex? does not have a known filename extension (?NA?)
ERROR: installing vignettes failed
* removing
?/home/biocbuild/bbs-2.12-data-experiment/meat/ppiData.Rcheck/ppiData?

This package does not have a vignette Makefile either, so I'm not sure
why the tex file is included in the .tar.gz.

These two errors are with:
> sessionInfo()
R version 3.0.0 alpha (2013-03-09 r62188)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


I also get another error on windows only ( it builds successfully on
Mac and Linux) when trying to build bumphunter
http://bioconductor.org/packages/2.12/bioc/html/bumphunter.html

Warning: running command
'"C:\PROGRA?2\MIKTEX?1.9\miktex\bin\texi2dvi.exe" --quiet --pdf
"bumphunter.tex"  -I
"E:/biocbld/bbs-2.12-bioc/R/share/texmf/tex/latex" -I
"E:/biocbld/bbs-2.12-bioc/R/share/texmf/bibtex/bst"' had status 1
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 'bumphunter'. The
following
files exists in directory '.': 'bumphunter-clusterplot.pdf',
'bumphunter-plotSegments.pdf', 'bumphunter.Rnw',
'bumphunter.bib',
'bumphunter.tex'
Calls: <Anonymous> -> find_vignette_product
Execution halted

I guess it's looking for bumphunter.pdf.

This is with:
> sessionInfo()
R version 3.0.0 alpha (2013-03-09 r62188)
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

Hi,

I contributed code to R r62130 which may be responsible for that (not
sure).  I'll investigate as soon as got the time.

/Henrik

On Wed, Mar 13, 2013 at 10:17 AM, Dan Tenenbaum <dtenenba at fhcrc.org>
wrote:
> Hello,
>
> I'm seeing three different vignette-related errors with recent
> versions of R-3.0.0 alpha.
>
> First, with the package BitSeq
> (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get
> the following when trying to build the package:
>
> Error: processing vignette ?BitSeq.Rnw' failed with diagnostics:
> Failed to locate the ?weave? output file (by engine ?utils::Sweave?)
> for vignette with name ?BitSeq?. The following files exists in
> directory ?.?: ?data-C0.est?, ?data-C1.est?, ?data-c0b0.prob?,
> ?data-c0b0.rpkm?, ?data-c0b0.sam?, ?data-c0b0.thetaMeans?,
> ?data-c0b1.rpkm?, ?data-c1b0.rpkm?, ?data-c1b1.rpkm?, ?data.estVar?,
> ?data.means?, ?data.par?, ?data.pplr?, ?data.tr?, ?ensSelect1.fasta?,
> ?ensSelect1.tr?, ?parameters1.txt?
> Execution halted
>
> My guess is it's looking for BitSeq.tex, but it's not clear where
it's
> looking; the package is pretty straightforward, inst/doc contains
> BitSeq.Rnw and nothing else (no Makefile).
>
> Next, the package ppiData whose source is here:
> https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ppiData
> (login: readonly password: readonly)
>
> As you can see, there is no .tex file in the source of the package,
> but after running R CMD build on it, the resulting .tar.gz file
> contains
> ppiData/inst/doc/ppiData.tex
> Then the package fails check (excerpt of ppiData.Rcheck/00install.out):
>
> Error in vignette_type(Outfile) :
>   Vignette product ?ppiData.tex? does not have a known filename extension
(?NA?)
> ERROR: installing vignettes failed
> * removing
?/home/biocbuild/bbs-2.12-data-experiment/meat/ppiData.Rcheck/ppiData?
>
> This package does not have a vignette Makefile either, so I'm not sure
> why the tex file is included in the .tar.gz.
>
> These two errors are with:
>
>> sessionInfo()
> R version 3.0.0 alpha (2013-03-09 r62188)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> I also get another error on windows only ( it builds successfully on
> Mac and Linux) when trying to build bumphunter
> http://bioconductor.org/packages/2.12/bioc/html/bumphunter.html
>
> Warning: running command
> '"C:\PROGRA?2\MIKTEX?1.9\miktex\bin\texi2dvi.exe" --quiet
--pdf
> "bumphunter.tex"  -I
> "E:/biocbld/bbs-2.12-bioc/R/share/texmf/tex/latex" -I
> "E:/biocbld/bbs-2.12-bioc/R/share/texmf/bibtex/bst"' had
status 1
> 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 'bumphunter'. The
following
> files exists in directory '.':
'bumphunter-clusterplot.pdf',
> 'bumphunter-plotSegments.pdf', 'bumphunter.Rnw',
'bumphunter.bib',
> 'bumphunter.tex'
> Calls: <Anonymous> -> find_vignette_product
> Execution halted
>
> I guess it's looking for bumphunter.pdf.
>
> This is with:
>
>> sessionInfo()
> R version 3.0.0 alpha (2013-03-09 r62188)
> 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
>
> ______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-devel