problem checking packages with R 2.13.0

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

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/

--
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