From simon.urbanek at r-project.org  Tue Jan 13 02:50:35 2015
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Mon, 12 Jan 2015 20:50:35 -0500
Subject: [Rd] R CMD build looking for texi2dvi in the wrong place
	(R-devel)
In-Reply-To: <758779124.2843994.1421110227452.JavaMail.root@fredhutch.org>
References: <758779124.2843994.1421110227452.JavaMail.root@fredhutch.org>
Message-ID: <9553C20C-9002-4960-99CE-0030655C948E@r-project.org>

Dan,

On Jan 12, 2015, at 7:50 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:

> R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin.
> 

No, you're looking at the wrong package - texi2dvi comes from texinfo which is now mandatory in version 5.2+ located in /usr/local since OS X comes with an old version. You should install it from

http://r.research.att.com/libs/texinfo-5.2-darwin10.tar.gz

Cheers,
Simon



> $ R CMD build IRanges
> * checking for file 'IRanges/DESCRIPTION' ... OK
> * preparing 'IRanges':
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> [...]
> Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) :
>  argument 'replacement' has length > 1 and only the first element will be used
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
>  Running 'texi2dvi' on 'IRangesOverview.tex' failed.
> Messages:
> sh: /usr/local/bin/texi2dvi: No such file or directory
> Calls: <Anonymous> -> texi2pdf -> texi2dvi
> Execution halted
> 
> That's with:
> 
> R Under development (unstable) (2015-01-11 r67421)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.9.5 (Mavericks)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base 
> 
> The same command works without error on:
> 
> R Under development (unstable) (2014-11-11 r66970)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> Setting 
> options(texi2dvi='/usr/bin/texi2dvi')
> 
> in my ~/.Rprofile did not help, I suspect because R CMD build runs buildVignettes() in a subprocess started with --vanilla. Creating a symlink from /usr/bin/texi2dvi to /usr/local/bin/texi2dvi gave me a "too many levels of symbolic links" error. Making it a hard link works, but seems like a real hack (what if the executable was not relocatable?). 
> 
> Thanks in advance,
> Dan
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 



[Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)
Simon Urbanek