Experiences with El Capitan

CLT = command line tools.  Otherwise you only have the compilers from the Xcode interface.

in order to have tex2dvi, you need a tex distribution installed.  I do remember if Simon has one on his R mac site, nut you can do an install from say  (as the RStudio help says):

To build manuals and vignettes you'll also need to install the MacTeX LaTeX distribution (or another version of LaTeX for the Mac). You can download MacTeX from here:http://www.tug.org/mactex/downloading.html.

HTH,

Roy

On Oct 12, 2015, at 7:58 PM, Spencer Graves<spencer.graves at prodsyse.com>  wrote:



On 10/12/2015 8:51 PM, Kevin Ushey wrote:

The simplest way to fix your issue is to symlink R to /usr/local/bin, e.g.

     ln -s /Library/Frameworks/R.framework/Resources/bin/R /usr/local/bin/R

This worked.  Thanks.  Spencer


... but not completely:  "R CMD build" worked.  "R CMD check" ended with:


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
  pdflatex is not available


	

Or, as Professor Ripley said in his initial post, R installers from
3.2.2 on El Capitan will now install a symlink at /usr/local/bin/R, so
you might want to just re-install or update R.

Updating the CLT is normally just a matter of downloading the latest

What's CLT?  Central Limit Theorem?  Charlotte Douglas International Airport?

version of Xcode from the App Store, if I understand correctly. (You

	  I requested "Xcode" at the App Store.  It asked for my Apple password then went away.  I rebooted and still got "pdflatex is not available".

may need to read + confirm a license agreement on your next run of the
clang compiler -- try running 'clang' after installing Xcode to see if
you're prompted)

$ clang
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun


	  Thanks again for your prompt reply.  Other suggestions?  (All this worked before I upgraded to OS X 10.11.)  Spencer

Kevin

On Mon, Oct 12, 2015 at 6:33 PM, Spencer Graves
<spencer.graves at prodsyse.com>  wrote:

On 10/5/2015 2:46 PM, Simon Urbanek wrote:

On Oct 5, 2015, at 3:34 AM, Rainer M Krug<Rainer at krugs.de>  wrote:

peter dalgaard<pdalgd at gmail.com>  writes:

<Round of applause, please!>

Agreed.

I just would like to dd that in the case of using homebrew, which
installs everything under /usr/local/... which did not cause any
problems at all. I moved the contents of /usr/local to an other location
before upgrade because the upgrade to Yosemite took because of a large
/usr/local several hours instead of about half an hour, moved it back
afterwards and everything worked fins without problems.

One question concerning mixed usage of homebrew and the Official R
installers:

do the Official R installers fail if an R binary already exist, or do
they raise a warning?

To make this easier, would it be possible, to install the binaries under
/usr/local/bin/R.X.Y.Z and then just create links in /usr/local/bin ?
Tghis would make the whole process more transparent and easier to switch
between different versions and means of installation.

R installer never installs any R binaries outside of the framework/app.
The only thing we provide on 10.10 is a softlink for R and Rscript in
/usr/local/bin into the framework (removing anything else in that name if it
exists). In earlier OS X versions this applies to /usr/bin instead.

Cheers,
Simon

Thanks for the clarifications,

Rainer

-pd

On 04 Oct 2015, at 18:53 , Prof Brian Ripley<ripley at stats.ox.ac.uk>
wrote:

The machine which provides the 'r-devel-osx-x86_64-clang' checks on
the CRAN check farm has been upgraded from Yosemite to El Capitan
and a complete round of checks has been run.


1) There is a lot of misinformation around about 'System Integrity
Protection' aka 'rootless'.

Upgrading to El Capitan moves files which are not allowed under /usr
to /Library/SystemMigration/usr, so you will be able to see what was
lost. This includes /usr/bin/R, /usr/bin/Rscript (but the installer
installs these under /usr/local/bin on El Capitan as from R 3.2.2),
/usr/X11R6, /usr/texbin .  Contrary to reports from betas, the link
/usr/X11 is preserved.

If an installer tries to create a disallowed file such as
/usr/bin/R, this is silently ignored (at least in the cases we
tested).  So you can install e.g. R 3.1.3 but the executables will
not appear in the default Terminal path (more details in the current
manual).


2) After updating you need to re-install the Command Line Tools and
R (to get the links in /usr/local).  I did not need to re-install
Java nor XQuartz.

       How do you suggest I "re-install the Command Line Tools and R"?


       I upgraded to 10.11 days ago but only now tried "R CMD build" and got,
"-bash: R: command not found". How can I get past this?


       Thanks,
       Spencer


p.s.  Thanks very much for all your work, including the comments on this
thread.

3) All the 'Mavericks' binary packages tested worked.  The source
packages of rJava and rgl (only) cannot be installed and the
maintainers have patched versions available.


There is updated information in the latest 'R Installation and
Administration' manual in R-patched and R-devel (in the sources, or
the online versions athttps://cran.r-project.org/manuals.html  will
update in a day or two).

--
Brian D. Ripley,ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK

--
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail:Roy.Mendelssohn at noaa.gov  www:http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.