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

John Fox jfox at mcmaster.ca
Tue Apr 19 04:50:53 CEST 2011 

Dear Kasper,

On Mon, 18 Apr 2011 22:32:35 -0400
 Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:
> On Mon, Apr 18, 2011 at 9:49 PM, John Fox <jfox at mcmaster.ca> wrote:
> > 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.
> 
> I don't set my PATH either, but it is useful for various purposes.  If
> you use the CRAN binary of R, my guess would be that most programs
> "know" where to look.  But that does depend on the program you use.

Remember that the problem was that eclipse wasn't finding pdflatex when I checked R packages; eclipse had no problem finding R since defining an R environment in eclipse involves pointing to R_HOME. Anyway, as I mentioned in my previous email, Brian's suggestions led me to a solution.

Best,
 John

> 
> Kasper
> 
> >
> > 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
> >
> >

------------------------------------------------
John Fox
Sen. William McMaster Prof. of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/

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