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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Tue Apr 19 04:32:35 CEST 2011 

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.

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
>
>

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