From dtenenba at fhcrc.org  Wed Mar 13 18:17:04 2013
From: dtenenba at fhcrc.org (Dan Tenenbaum)
Date: Wed, 13 Mar 2013 10:17:04 -0700
Subject: [Rd] Failed to locate 'weave' output file / vignette product does
 not have a known filename extension
Message-ID: <CAF42j20rv=oXrCQ7=C=bp8cPQKOUnXjzg8yuE_MQaMzoN04g8g@mail.gmail.com>

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



[Rd] Failed to locate 'weave' output file / vignette product does not have a known filename extension
Dan Tenenbaum