R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony
Because it can conflict with other Windows software unless you add a layer over it. What other popular software that runs on Windows has these problems? I can't think of any. The closest I can come up with was that for a short time after git was ported to Windows it would change the font of the Windows console but there was an immediate hue and cry about it having no business messing with the rest of Windows and it was quickly rectified.
I don't understand: unless you modify settings in the default install, Rtools *does not* affect other windows software in any way.
If its the case that it now works from the cmd line without setting the Rtools path before issuing R CMD ... that would be great. If so it must have occurred silently at some point since I have spent hours in past years trying to track down why another program I was using did not work only to discover that it was Rtools. Surely this was also your own understanding since devtools, maintains an Rtools path database which ought to be unnecessary if R is able to find Rtools itself.
I think we are having a failure of communication: Rtools does not set the path, so that you must do so, every time you use it. There is no other way to prevent it from interfering from some other windows software, except by tightly confining the scope in which it enters the path. When I first starting working with Rtools, I thought this was a terribly frustrating decision - why didn't the default installer always put rtools on the path? But now I see it's the only way - it avoids conflicts with other software, and without that default there'd be no way to have multiple versions of rtools installed. That said, I think the logic that Rstudio and devtools uses to find rtools would have been helpful to include in base R, but that's not so important now that it's available in a package. (And if any big change was made, I'd probably argue it'd be better just to always bundle rtools with R on windows - I think it's a key part of the philosophy of R that users can easily become developers. But there are obviously other considerations.) To clarify, the rtools database in devtools does not contain a list of locations of rtools, but the directories inside of an rtools installation that need to be available on the path. This list has changed over time as the tools needed by R have changed. I don't see any way of avoiding that (except perhaps by storing those in the registry, but regardless there's no way to go back in time and fix old decisions). Devtools (following the logic of rstudio) looks in a number of places to find rtools, first looking in the path and then in the registry, and takes considerable care to ensure that the versions of R and rtools match (another reason why the database is necessary). Hadley -- Chief Scientist, RStudio http://had.co.nz/