I got the same error message and the symlink was recreated. I also presume that removing a package from the system library will make it unavailable to all non-packrat projects.
I tried deleting the packrat/lib-R directory and that was recreated along with all the symlinks in it, and I still get the error message. Finally, I notice that the update packages dialog is still showing the updated packages as needing update.
A couple of weeks ago, I decided that I'd do a standard upgrade to Mac OS X Snow Leopard. I could safe boot in to the system with my account (holding down shift button when starting) but a standard log in would not work. Apparently there is, and this is where I found the details about clearing a font cache in Mac OS X.
User Event Agent-Login Window): Exited: Terminated Report Crash: Formulating crash report for process lsregisterReport Crash: Saved crashreport to /Library/Logs/Crash Reporter/lsregister_timestamp.crash using uid: 0 gid: 0, euid: 0 egid: 0kernel: Set Crypto Key R: len 32, idx 1Report Crash: Formulating crash report for process Report CrashReport Crash: Saved crashreport to /Users/userid/Library/Logs/Crash Reporter/Report Crash_timestamp.crash using uid: uid gid: gid, euid: uid egid: gidcom.apple.launchd (com.apple.
Once I tried to change the default startup disk on my Mac running Snow Leopard and the following error appeared: “you can’t change the startup disk to the selected disk.
Clearly something is hosed, and fortunately I was able to fix it.
I tried the suggested solutions — booting in safe mode and logging in (still had the same problem); running a file system check in single user mode (no errors reported); deleting the login window plists; and changing the password — but they had no effect.
I've done a good deal of tweaking in the Terminal to get things set up for the sake of web development. Until last night, I was quite pleased with the progress.
However, having faith, I went ahead and did it any way. Right away when booting in to my account the system would hang. Happy with the installation and configuration of the system, I started transferring files. I copied the contents of the ~/Library/Fonts directory from the leopard disk to my clean snow leopard disk. I copied the contents of the ~/Library/Font Collections directory in the same way. I'd get the spinning beach ball, and the magnifying glass for Spotlight appearing in the top right corner. Honestly, I didn't even know if there was such a thing.packrat options: Automatically snapshot local changes: TRUE Use global cache for installed packages: FALSE The error is not specific to boot, MASS, and spatial - they are just the packages for which there were updates available. However, I now see that I have the package in both libraries.I tried updating cluster and got the same error message. I tried deleting the symlink to boot and updating boot. I presume that this is safe and that code run in the packrat project will search the packrat library before the system library.Thanks -- I definitely agree that packrat should do what it can to move symlinks out of the way on package install, and this is something I hope we'll get to for the next packrat release. I've noticed the packages affected are packages that are updated when R is updated. When I use the update packages button for a package in the System Library the generated code tries to install it in the Packrat Library install.packages("boot", lib="/home/ross/CA/projects/active/project_name/subproject_name/packrat/lib-R") trying URL ' https://cran.revolutionanalytics.com/src/contrib/boot_1.3-18gz' downloaded 226 KB ERROR: ‘boot’ is not a legal package name Warning in install.packages : installation of package ‘boot’ had non-zero exit status install.packages("some_system_library_package") updates the package OK without needing to remove it first.