From kevin.r.coombes at gmail.com  Fri Apr 19 23:37:07 2013
From: kevin.r.coombes at gmail.com (Kevin Coombes)
Date: Fri, 19 Apr 2013 16:37:07 -0500
Subject: [Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
Message-ID: <5171B903.50401@gmail.com>

Having finally found some free time, I was going to use it to update a 
bunch of R packages from 2.15 to 3.0.

I am running Windows 7, 64-bit professional.  This is on a brand-new 
laptop using vanilla settings when installing the operating system.

Problem 1: I installed R3.0 to the default location (C:\Program 
FIles\R\R-3.0.0).  The first thing I tried to do was install 
BioConductor.  This failed (permission denied). Thinking that this might 
be a BioConductor problem, I then tried to install a (semirandom) 
package from CRAN.  This also failed.

In both cases, when using the GUI, the error message is almost 
incomprehensible.  You get a pop-up window that *only* says "Do you want 
to use a private library instead?"  Since this wasn't what I wanted to 
do I said "no".  Only after the pop-up closes does the command window 
print the error message telling me that permission was denied for R to 
write to its own library location.

Dumb Fix to Problem 1: So, I uninstalled R and then reinstalled to a 
nonstandard location (C:\R\R-3.0.0).  Now I can successfully install 
packages from CRAN and BioConductor (hooray!). But I run directly into:

Problem 2: Emacs Speaks Statistics (ESS) can no longer find the R 
binary. When R was installed in the default location, ESS worked. When R 
2.15 (or earlier) was installed in the same nonstandard location, I 
could get ESS to find the R binaries by including (setq 
ess-directory-containing-r "C:") in my .emacs file, but that no longer 
works.

Dumb Fix to Problem 2:  Hack into ess-site.el and put the complete, 
explicit path to the correct binary into
(setq-default inferior-R-program-name 'FULLPATHHERE")
which will break as soon as I upgrade R (assuming I am foolish enough to 
ever do that again).


Now I am ready to rebuild my R packages.  I have this nice perl script 
that goes through the following procedure:

1. Set the path to include the correct Rtools directory.  (For reasons 
that Gabor Grothendieck has pointed out previously, this is not a 
permanent part of the path since doing so would override some built-in 
Windows commands.)
2. Build a source tarball via
     R CMD build $package
3. Build a Windows binary version (as a zip file) via
     R CMD INSTALL --build $tarball
4. Check the package via
     R CMD check --as-cran $tarball
5. Install the package via
     R CMD INSTALL $tarball

Problem 3: Step 3 fails, withe the error message "Running 'zip' failed".

Dumb Fix to Problem 3: Install the GnbuWin32 version of zip, and make 
sure that its location is earlier in ter path than the version that 
comes with Rtools.

Problem 4: Step 4 fails when running the test scripts that accompany the 
package.  The error message is the semicryptic
     "cannot open file 'c:\Users\krc\AppData\Local\Temp\Rtmp....' 
Permission denied"

Dumb Fix to Problem 4: Write this email message and hope someone with 
even more patience than I have has already found a better way to get all 
this stuff to work.

Tired of spinning my wheels,
     Kevin



[Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
Kevin Coombes