[R-SIG-Mac] problem checking packages with R 2.13.0

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Sun Apr 17 23:58:34 CEST 2011 

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

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.

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
>
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