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
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