problem checking packages with R 2.13.0

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/

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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

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problem checking packages with R 2.13.0

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