[R-SIG-Mac] problem checking packages with R 2.13.0
John Fox
jfox at mcmaster.ca
Sun Apr 17 22:21:25 CEST 2011
Dear Brian and others,
Yes, I installed the CRAN build of R, and yes, something is changing the
path in R.app, and in eclipse, but not apparently when R is run in a
terminal window.
>From a terminal window:
------------- snip --------------
John-Foxs-MacBook-Pro:Rmpi jfox$ R
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing ISBN
3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
. . .
> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin"
------------- snip --------------
In R.app (and in R64.app):
------------- snip --------------
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing ISBN
3-900051-07-0
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
. . .
[R.app GUI 1.40 (5751) i386-apple-darwin9.8.0]
[History restored from /Users/jfox/.Rapp.history]
> Sys.getenv("PATH")
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
------------- snip --------------
And in eclipse:
------------- snip --------------
R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing ISBN
3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
. . .
> Sys.getenv("PATH")
[1]
"/Library/Frameworks/R.framework/Versions/2.13/Resources/bin:/usr/bin:/bin:/
usr/sbin:/sbin"
------------- snip --------------
I've had no luck, however, figuring out what's changing the path: As far as
I can tell, I have no Rprofile.site file, no .Rprofile file, and the
R_PROFILE and R_PROFILE_USER environment variables are unset. In fact the
only R initialization files that I could find anywhere on my system are the
Rprofile files in the base and Rmpi packages; as far as I can see, the
former can't shorten the path and I'm not using the latter.
Finally, looking more closely at the errors I'm getting when I try to check
a package, the errors in a terminal window and from eclipse look different:
>From a terminal window, I think that pdflatex is actually found; to repeat
the error message:
------------- snip --------------
* checking PDF version of manual ... WARNING LaTeX errors when
creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex (file 8r.enc): cannot open encoding file for
reading ==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without hyperrefs or index ... ERROR
------------- snip --------------
>From eclipse, pdflatex clearly isn't found:
------------- snip --------------
* checking PDF version of manual ... WARNING LaTeX errors when
creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
You may want to clean up by 'rm -rf
/var/folders/ay/ayD+f6yQFomFC5SGQV6vP++++TI/-Tmp-
//RtmpopONVs/Rd2pdf16f793c'
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
pdflatex is not available
Error in running tools::texi2dvi
------------- snip --------------
So there are possibly two independent problems here.
I'm not sure where to look next, so again any help would be appreciated.
Best,
John
> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk]
> Sent: April-17-11 1:37 AM
> To: John Fox
> Cc: r-sig-mac at r-project.org
> Subject: Re: [R-SIG-Mac] problem checking packages with R 2.13.0
>
> On Sat, 16 Apr 2011, John Fox wrote:
>
> > Dear list members,
> >
> > I'm experiencing a problem checking packages with R 2.13.0 on a new
> > Mac OS X 10.6.7 system. As far as I can tell, R isn't finding my LaTeX
> > installation. Packages seem to build fine. Some details
> > follow:
>
> Assuming this is the CRAN build of R, it is looking on the path. So all I
> can think is that you have the path set incorrectly somewhere in your R
> statrtup files.
>
>
> >
> > Here's what happens when I try to check a package:
> >
> > ----- snip ------
> >
> > John-Foxs-MacBook-Pro:workspace jfox$ R CMD check car
> > * using log directory ?/Users/jfox/Documents/workspace/car.Rcheck?
> > * using R version 2.13.0 (2011-04-13)
> > * using platform: x86_64-apple-darwin9.8.0 (64-bit)
> > * using session charset: UTF-8
> > * checking for file ?car/DESCRIPTION? ... OK
> > * this is package ?car? version ?2.0-10?
> > . . .
> > * checking examples ... OK
> > * checking PDF version of manual ... WARNING LaTeX errors when
> > creating PDF version.
> > This typically indicates Rd problems.
> > LaTeX errors found:
> > !pdfTeX error: pdflatex (file 8r.enc): cannot open encoding file for
> > reading ==> Fatal error occurred, no output PDF file produced!
> > * checking PDF version of manual without hyperrefs or index ... ERROR
> >
> > ----- snip ------
> >
> > I get the following error when I try to check the package under
> eclipse/StatET (deleting the lines before the error):
> >
> >
> > ----- snip ------
> >
> > * checking PDF version of manual ... WARNING LaTeX errors when
> > creating PDF version.
> > This typically indicates Rd problems.
> > * checking PDF version of manual without hyperrefs or index ... ERROR
> > Re-running with no redirection of stdout/stderr.
> > Hmm ... looks like a package
> > You may want to clean up by 'rm -rf
> /var/folders/ay/ayD+f6yQFomFC5SGQV6vP++++TI/-Tmp-
> //RtmpopONVs/Rd2pdf16f793c'
> > Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
> > pdflatex is not available
> > Error in running tools::texi2dvi
> >
> >
> > ----- snip ------
> >
> > But I have no problem running pdflatex from a terminal window:
> >
> >
> > ----- snip ------
> >
> > John-Foxs-MacBook-Pro:~ jfox$ pdflatex --help
> > Usage: pdftex [OPTION]... [TEXNAME[.tex]] [COMMANDS]
> > or: pdftex [OPTION]... \FIRST-LINE
> >
> > ----- snip -----------
> >
> > Nor does Sys.which() seem to find pdflatex:
> >
> > ----- snip ------
> >
> > R version 2.13.0 (2011-04-13)
> > Copyright (C) 2011 The R Foundation for Statistical Computing ISBN
> > 3-900051-07-0
> > Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >
> > . . .
> >
> > [R.app GUI 1.40 (5751) i386-apple-darwin9.8.0]
> >
> > [History restored from /Users/jfox/.Rapp.history]
> >
> >> Sys.which("pdflatex")
> > pdflatex
> > ""
> >
> > ----- snip ------
> >
> > Some more information about my system:
> >
> > ----- snip ------
> >
> >> Sys.info()
> >
> sysname
> >
> "Darwin"
> >
> release
> >
> "10.7.3"
> >
> > version "Darwin Kernel Version 10.7.3: Sun Mar 6 13:37:56 PST 2011;
> root:xnu-1504.14.2~1/RELEASE_X86_64"
> >
> nodename
> >
> "John-Foxs-MacBook-Pro.local"
> >
> machine
> >
> "x86_64"
> >
> login
> >
> "jfox"
> >
> user
> >
> "jfox"
> >
> >> sessionInfo()
> > R version 2.13.0 (2011-04-13)
> > Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >
> > locale:
> > [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > ----- snip ------
> >
> > Any suggestions would be appreciated.
> >
> > Thanks,
> > John
> >
> > ------------------------------------------------
> > John Fox
> > Sen. William McMaster Prof. of Social Statistics Department of
> > Sociology McMaster University Hamilton, Ontario, Canada
> > http://socserv.mcmaster.ca/jfox/
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
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