From hpages at fhcrc.org  Thu Sep 16 01:55:29 2010
From: hpages at fhcrc.org (=?ISO-8859-1?Q?Herv=E9_Pag=E8s?=)
Date: Wed, 15 Sep 2010 16:55:29 -0700
Subject: [Rd] running 'make' failed during vignette creation ('R CMD build')
 on Windows
Message-ID: <4C915CF1.9020304@fhcrc.org>

Hi,

This is a follow-up to the problem reported here:

   https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html

After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system,
some of the packages that have a Makefile in <pkg>/inst/doc still
don't build on Windows. For example, 'R\bin\R.exe CMD build adSplit'
gives:

* checking for file 'adSplit/DESCRIPTION' ... OK
* preparing 'adSplit':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: hu6800.db
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
   determining 1000 random DLD-scores with 20 probe sets each (wait for 
10 dots)
   ..........
epstopdf splitSet.eps
pdflatex tr_2005_02
This is pdfTeX, Version 3.1415926-1.40.9 (MiKTeX 2.7)
entering extended mode
(tr_2005_02.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, dumylang, 
nohyphenation, ge
rman, ngerman, french, loaded.
("C:\Program Files\MiKTeX 2.7\tex\latex\base\report.cls"
Document Class: report 2007/10/19 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.7\tex\latex\base\size11.clo")) (compdiag.sty
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifpdf.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\graphicx.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\keyval.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\graphics.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\trig.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\graphics.cfg")
("C:\Program Files\MiKTeX 2.7\tex\latex\pdftex-def\pdftex.def")))
("C:\Program Files\MiKTeX 2.7\tex\latex\graphics\color.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\color.cfg"))
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hyperref.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ltxcmds.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\kvsetkeys.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\infwarerr.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\etexcmds.sty"))
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdfescape.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\pdftexcmds.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifluatex.sty")))
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\ifvtex.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\ifxetex\ifxetex.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\hycolor.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\xcolor-patch.sty"))
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\letltxmacro.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\pd1enc.def")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\intcalc.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\00miktex\hyperref.cfg")
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\kvoptions.sty")
Implicit mode ON; LaTeX internals redefined
("C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\url.sty")
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bitset.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\bigintcalc.sty"))
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\atbegshi.sty"))
* hyperref using driver hpdftex *
("C:\Program Files\MiKTeX 2.7\tex\latex\hyperref\hpdftex.def"
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\atveryend.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\oberdiek\rerunfilecheck.sty"
("C:\Program Files\MiKTeX 2.7\tex\generic\oberdiek\uniquecounter.sty")))
("C:\Program Files\MiKTeX 2.7\tex\latex\ntgclass\a4.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\geometry\geometry.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\geometry\geometry.cfg"))
("C:\Program Files\MiKTeX 2.7\tex\latex\tools\theorem.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\tools\thp.sty"))
("C:\Program Files\MiKTeX 2.7\tex\latex\tools\thb.sty"))
("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsmath.sty"
For additional information on amsmath, use the `?' option.
("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amstext.sty"
("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsgen.sty"))
("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsbsy.sty")
("C:\Program Files\MiKTeX 2.7\tex\latex\ams\math\amsopn.sty"))

! LaTeX Error: File `Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name:
! Emergency stop.
<read *>

l.39 \begin
            {document}
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on tr_2005_02.log.
make: *** [pdf] Error 1
Error in tools::buildVignettes(dir = ".") : running 'make' failed
Execution halted

What's different though with this updated R, it that now I get an
error instead of a timeout. Maybe the code that fires the R subprocess
in charge of running tools::buildVignettes() now does better error
checking/handling, I don't know (it seems to have changed between
the 2 versions of R).

A new mystery is why the tilingArray package now does build on
Windows (it was timing out with the previous version of R).
I already sent the content of adSplit/inst/doc/Makefile
in the previous thread and tilingArray does nothing different:

all: findsegments costMatrix assessNorm segmentation plotAlongChrom clean

findsegments: findsegments.tex
         pdflatex findsegments
         pdflatex findsegments

costMatrix: costMatrix.tex
         pdflatex costMatrix
         pdflatex costMatrix

assessNorm: assessNorm.tex
         cp -p ../scripts/assessNorm.pdf .

segmentation: segmentation.tex
         cp -p ../scripts/segmentation.pdf .

plotAlongChrom: plotAlongChrom.tex
         pdflatex plotAlongChrom
         pdflatex plotAlongChrom
clean:
         rm -f *.out *.bbl *.log *.aux *.blg *.brf *.toc *.tex
         rm -f *.dvi *.ps findsegments-* costMatrix-* plotAlongChrom-* 
Rplots.pdf

Another thing that is really puzzling is that if I cd to
adSplit/inst/doc and run 'R CMD make' then it works.

Any help/comment on this will be highly appreciated.

Thanks,
H.


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] running 'make' failed during vignette creation ('R CMD build') on Windows
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