From rossini at blindglobe.net  Wed Sep 10 16:34:20 2003
From: rossini at blindglobe.net (A.J. Rossini)
Date: Thu Sep 11 00:37:01 2003
Subject: [Rd] potentially nasty interaction between R 1.8.0 and tetex
Message-ID: <854qzkjms3.fsf@blindglobe.net>


I've been having problems building vignettes in bioconductor packages
with R-devel.  Turns out that Rdevel/share/texmf/hyperref.cfg wants
Blue and Red predefined, when only blue and red are defined (as of
rsync Rdevel, Sept 10th).  This is on a Debian unstable system (Sept
9th version).  Might not apply to all other tetex systems.  Seems to
have bitten the bioconductor build system, though.

Symptom:  


512$ R CMD build --force Biobase
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking whether 'INDEX' is up-to-date ... OK
* creating vignettes ... ERROR
/usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/lib/R/bin/texi2dvi: see Bioconductor.log for errors.
Error in buildVignettes(dir = ".") : running texi2dvi on
Bioconductor.tex failed
Execution halted



Change produces: 

517$ R CMD build --force Biobase
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking whether 'INDEX' is up-to-date ... OK
* creating vignettes ... OK
* removing junk files
* building 'Biobase_1.3.31.tar.gz'


YMMV.

best,
-tony

-- 
A.J. Rossini     			
rossini@u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW   :              FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email

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[Rd] potentially nasty interaction between R 1.8.0 and tetex
A.J. Rossini