Dear Brian, Thank you very much for this. I'm in my office today without my MacBook but will give this a try tonight.
Best, John On Mon, 18 Apr 2011 14:34:31 +0100 (BST) Prof Brian Ripley <[email protected]> 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 > > 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. > > (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:[email protected]] > >> Sent: April-17-11 7:27 PM > >> To: John Fox > >> Cc: Prof Brian Ripley; [email protected] > >> Subject: Re: [R-SIG-Mac] problem checking packages with R 2.13.0 > >> > >> On Sun, Apr 17, 2011 at 7:16 PM, John Fox <[email protected]> wrote: > >>> Dear Kaspar, > >>> > >>>> -----Original Message----- > >>>> From: Kasper Daniel Hansen [mailto:[email protected]] > >>>> Sent: April-17-11 5:59 PM > >>>> To: John Fox > >>>> Cc: Prof Brian Ripley; [email protected] > >>>> 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 <[email protected]> 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:[email protected]] > >>>>>> Sent: April-17-11 1:37 AM > >>>>>> To: John Fox > >>>>>> Cc: [email protected] > >>>>>> 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 > >>>>>>> [email protected] > >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>>>>> > >>>>>> > >>>>>> -- > >>>>>> Brian D. Ripley, [email protected] 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 > >>>>> [email protected] > >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >>>>> > >>> > >>> > > > > > > -- > Brian D. Ripley, [email protected] > 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/ _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
