R devel - Sep 2003 - potentially nasty interaction between R 1.8.0 and tetex

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
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rossini@blindglobe.net (A.J. Rossini) writes:
> 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'
Change being Blue --> blue, Red --> red in hyperref.cfg I presume? Odd
thing is that it doesn't happen with RedHat 8.0 tetex and ordinary
"make pdf". Shouldn't the hyperlinks in the manuals have the same
problem?

BTW, this uncovered another problem in that "make pdf" didn't work
when srcdir != builddir because of

$(texinputs_BASE): FORCE $(top_srcdir)/share/perl/build-help.pl

but configure makes $(top_builddir)/share/perl/build-help.pl from a
.in file

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907