I have a 64 bit machine running 64 bit windows 7 pro, 64 bit MySQL, and 64
bit R 2.11.1.

I have also installed RTools for 64 bit windows for this version of R
(archive name is oldWin64toolchain.zip; the install path for its contents
is C:\RTools, if that matters).  I can open up a commandline window and
invoke any of the programs in both bin directories (both added to the system
path).
There are several packages for which I could not find 64 bit binaries
RMySQL, RPostgreSQL, RQRMlib, &c.  While I don't have time at present to
develop ne packages for R, these packages are things I routinely use on my
32 bit machine (where, thankfully, all seems to be working fine).
Therefore, my only interest is in getting or making the 64 bit binaries for
these packages so I can duplicate on the new 64 bit machine what I had been
doing on the old 32 bit machine.

Note, I routinely develop new software using MS VS (originally v 6, and then
VS 2005, and now vs 2010), and if I need to work up code to run on some
flavour of unix, I use the cygwin environment.  Therefore, I have no qualms
about compiling programs I use from source.  I just prefer not to if there
is already a binary distribution for whatever platform I happen to be using.

I began by trying to follow the instructions provided on
http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL, and found a couple
issues.



First, there was no Renviron.site in C:/Program Files/R/R-2.11.1-x64/etc so
I made one and placed in it the following:

MYSQL_HOME=C:\PROGRA~1\MySQL\MYSQLS~1.1

The full path to the installation of MySQL is: C:\Program Files\MySQL\MySQL
Server 5.1

Unlike what is said on the biostat.mc.vanderbilt.edu pages, MYSQL_HOME is
still empty:


> Sys.getenv('MYSQL_HOME')
MYSQL_HOME
        ""
This is when I start R AFTER having made the Renviron.site file.

Something I notice, though, that may have a bearing on this is that although
Emacs finds my new Renviron.site file when I navigate to that directory, it
does not appear in Windows Explorer.  I am wondering if Windows 7 is somehow
blocking access to it.  If that guess is correct, the question becomes, how
do I fix that?  If it isn't correct, what should I check?  This is not an
insurmountable problem, though as I can always set that environment variable
at the beginning of a session.  I do that already on other systems that are
32 bit clients that have to talk to 64 bit servers.  It is just mildly
disturbing that R does not seem to know about the Renviron.site file I made
for it.

Second, I read in the instructions the following:


> 3. *Re-start R and execute install.packages('RMySQL',type='source')* at
> the R prompt.
>
> As long as you followed the above steps correctly, RMySQL<https://mail.google.com/wiki/Main/RMySQL>will install cleanly and you will be able to immediately load it and use it.
>
However, when I follow this instruction I get:
> install.packages('RMySQL',type='source')
Warning in install.packages("RMySQL", type = "source") :
  argument 'lib' is missing: using
'C:\Users\Ted\Documents/R/win64-library/2.11'
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://probability.ca/cran/src/contrib/RMySQL_0.7-5.tar.gz'
Content type 'application/x-gzip' length 160769 bytes (157 Kb)
opened URL
downloaded 157 Kb
* installing *source* package 'RMySQL' ...
Warning in system("sh ./configure.win") : sh not found
ERROR: configuration failed for package 'RMySQL'
* removing 'C:/Users/Ted/Documents/R/win64-library/2.11/RMySQL'
The downloaded packages are in
        ‘C:\Users\Ted\AppData\Local\Temp\Rtmp7xg8yb\downloaded_packages’
Warning message:
In install.packages("RMySQL", type = "source") :
  installation of package 'RMySQL' had non-zero exit status
>

It is clearly failing before it could choke on the MYSQL_HOME value.  On
reading it, it is no surprise to me that it failed to find sh as I recognize
that as one of several unix shells.  What I don't know is how I should alter
the instructions provided on the vanderbilt site so that the install works
on Windows 7.  I know I have access to sh in cygwin, but I really don't want
to confound my cygwin environment with what I use for R.

While I have not used RTools before, I would assume that whatever issues I
am presently facing would impact any package for which I need to build 64
bit binaries for Windows 7.  So what do I need to know in order to
effectively use RTools on compiling an arbitrary package, perhaps using
RMySQL as an example (since that is the first one I need to compile).

Thanks

Ted

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