Dan Tenenbaum
2015-Jan-13 00:50 UTC
[Rd] 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
Simon Urbanek
2015-Jan-13 01:50 UTC
[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 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 >
Dan Tenenbaum
2015-Jan-13 02:26 UTC
[Rd] R CMD build looking for texi2dvi in the wrong place (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 > > > >