[R-SIG-Mac] problem checking packages with R 2.13.0
John Fox
jfox at mcmaster.ca
Mon Apr 18 01:16:04 CEST 2011
Dear Kaspar,
> -----Original Message-----
> From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com]
> Sent: April-17-11 5:59 PM
> To: John Fox
> Cc: Prof Brian Ripley; r-sig-mac at r-project.org
> Subject: Re: [R-SIG-Mac] problem checking packages with R 2.13.0
>
> John,
>
> I don't know about Eclipse, but on a Mac it is completely standard that a
> GUI does not inherit anything from .bashrc/.profile. So it is pretty
> standard that you may have problems with environment variables.
> You can do two things
> (1) use environment.plist (google it)
> (2) use Sys.setenv() inside your .Rprofile
That helps a bit. That is, I didn't previously have a .Rprofile file, so I
put one in my home directory, setting the PATH to
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin. Now
both R CMD check in a terminal window and checking inside eclipse fail with
the same error, "!pdfTeX error: pdflatex (file 8r.enc): cannot open encoding
file (etc.)", rather than with different errors. So, at this point, I don't
think that finding pdflatex is the issue.
>
> Now, regarding latex, the standard on Mac would be to run MacTex. I am
> unaware of how R.app deals with MacTex but I would be ready to guess that
> the PATH might be semi-build in (I am sure some of the R.app people will
> correct me on this). So you might want to add info about what tex
> distribution you are using.
Good point. I used the MacTeX-2010 distribution, which I got to from item
2.1 in the R for Mac OS X FAQ.
Thanks for trying to help.
John
>
> Kasper
>
>
>
> On Sun, Apr 17, 2011 at 4:21 PM, John Fox <jfox at mcmaster.ca> wrote:
> > 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
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
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