R devel - Jan 2015 - R CMD build looking for texi2dvi in the wrong place (R-devel)

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.

$ 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

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
>

----- Original Message -----
> From: "Simon Urbanek" <simon.urbanek at r-project.org>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "R-devel" <r-devel at r-project.org>
> Sent: Monday, January 12, 2015 5:50:35 PM
> Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place
(R-devel)
> 
> 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
> 
Thanks, was there an announcement that I missed about this and if so, where was
it?

Dan


> 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
> > 
> 
>