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
R CMD build looking for texi2dvi in the wrong place (R-devel)
5 messages · Simon Urbanek, Duncan Murdoch, Dan Tenenbaum
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
On 12/01/2015 6:26 PM, Dan Tenenbaum wrote:
----- 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?
It has been in the NEWS file since Jan 6. You can see it there, and would have seen it announced here: http://developer.r-project.org/blosxom.cgi/R-devel/2015/01/06#n2015-01-06 Duncan Murdoch
----- Original Message -----
From: "Duncan Murdoch" <murdoch.duncan at gmail.com> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Simon Urbanek" <simon.urbanek at r-project.org> Cc: "R-devel" <r-devel at r-project.org> Sent: Monday, January 12, 2015 8:40:07 PM Subject: Re: [Rd] R CMD build looking for texi2dvi in the wrong place (R-devel) On 12/01/2015 6:26 PM, Dan Tenenbaum wrote:
----- 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?
It has been in the NEWS file since Jan 6. You can see it there, and would have seen it announced here: http://developer.r-project.org/blosxom.cgi/R-devel/2015/01/06#n2015-01-06
Thanks, I'll subscribe to these feeds. Dan
Duncan Murdoch