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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Apr 18 01:27:28 CEST 2011 

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
>>
>> John,
>>
>> I don't know about Eclipse, but on a Mac it is completely standard that a
>> GUI does not inherit anything from .bashrc/.profile.  So it is pretty
>> standard that you may have problems with environment variables.
>>  You can do two things
>>   (1) use environment.plist (google it)
>>   (2) use Sys.setenv() inside your .Rprofile
>
> That helps a bit. That is, I didn't previously have a .Rprofile file, so I
> put one in my home directory, setting the PATH to
> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin. Now
> both R CMD check in a terminal window and checking inside eclipse fail with
> the same error, "!pdfTeX error: pdflatex (file 8r.enc): cannot open encoding
> file (etc.)", rather than with different errors. So, at this point, I don't
> think that finding pdflatex is the issue.
>
>>
>> Now, regarding latex, the standard on Mac would be to run MacTex.  I am
>> unaware of how R.app deals with MacTex but I would be ready to guess that
>> the PATH might be semi-build in (I am sure some of the R.app people will
>> correct me on this).  So you might want to add info about what tex
>> distribution you are using.
>
> Good point. I used the MacTeX-2010 distribution, which I got to from item
> 2.1 in the R for Mac OS X FAQ.
>
> Thanks for trying to

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.

Or could this be e problem with the encoding of (one of) the help
files in the package?

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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