[R-SIG-Mac] problem checking packages with R 2.13.0
John Fox
jfox at mcmaster.ca
Mon Apr 18 02:08:24 CEST 2011
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?
>
> 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
> >> >
> >
> >
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