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? > > 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 > >> > > > > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
