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

John Fox jfox at mcmaster.ca
Tue Apr 19 03:49:49 CEST 2011 

Dear Brian,

On Mon, 18 Apr 2011 14:34:31 +0100 (BST)
 Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> John,
> 
> Having resolved the path issues, I think you do have a problem with your latex installation.  Try (in the terminal)
> 
> tystie% kpsewhich 8r.enc
> /usr/local/texlive/2010/texmf-dist/fonts/enc/dvips/base/8r.enc
> 

That is indeed empty.

> If that comes back empty, try (possibly with sudo) tystie% texhash to rebuild the indices.  If that doesn't work, you need to work out how you have an incomplete installation, something I've never seen with Mactex.
> 

(I'm just lucky, I guess.) I tried this and it didn't fix the problem. 

I then reinstalled MacTeX-2010, taking all of the defaults in the installer, as I did before, and that fixed the problem. Obviously, my original TeX installation was broken.

I don't think that I should have to set the PATH explicitly in my .Rprofile when I use eclipse (I've never had to before, on any platform), but that works too. I'll investigate further and maybe send a message to the StatET list.

Thank you for all of your help -- I really appreciate it. 

John

> (FWIW 8r.enc is what tells latex how to encode output for Type 1 fonts: it is nothing to do with the encoding of the latex inputs.)
> 
> Brian
> 
> On Sun, 17 Apr 2011, John Fox wrote:
> 
> > Dear Kasper,
> >
> >> -----Original Message-----
> >> From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com]
> >> Sent: April-17-11 7:27 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
> >>
> >> On Sun, Apr 17, 2011 at 7:16 PM, John Fox <jfox at mcmaster.ca> wrote:
> >>> 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
> >>>>
> >
> > . . .
> >
> >>
> >> Since this is a new Mac, what file system are you using?  I have no idea
> >> on how to troubleshoot your error, but I guess that info about the file
> >> system might help more knowledgeable people.
> >
> > I'm afraid I don't know how to answer: I didn't make any changes to the file
> > system that came with the machine. Don't Macs use the HFS+ file system?
> 
> By defualt .....
> 
> >
> >>
> >> Or could this be e problem with the encoding of (one of) the help files in
> >> the package?
> >
> > I don't think so: The car package checks on my Windows 7 system, on an older
> > Mac, and on R-Forge.
> >
> > Thanks again 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
> >>>>>
> >>>
> >>>
> >
> >
> 
> -- 
> 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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