problem checking packages with R 2.13.0
Dear Brian, On Mon, 18 Apr 2011 14:34:31 +0100 (BST)
Prof Brian Ripley <ripley at stats.ox.ac.uk> 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. 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: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?
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 <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/
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-- 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