Dear Kasper, On Mon, 18 Apr 2011 22:32:35 -0400 Kasper Daniel Hansen <[email protected]> wrote: > On Mon, Apr 18, 2011 at 9:49 PM, John Fox <[email protected]> wrote: > > Dear Brian, > > > > 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 > >> > > > > 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:[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
