This is part of the underlying UNIX nature of Mac OSX, and was the only place I found that gave clues to what was going on.
Here is a portion of the log file that occurs right after hitting return at the login screen:loginwindow: USER_PROCESS: 23 consolecom.apple.launchd (com.apple.
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.
All the symlinks in lib-R are owned by root and have restrictive permissions. That is, it appears to be looking at all packages in the packrat and system libraries and flagging if any of them need updating.
UTF-8 LC_NAME=C LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_AU. UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics gr Devices utils datasets methods base other attached packages:  RMy SQL_0.10.8 DBI_0.3.1 loaded via a namespace (and not attached):  Rcpp_0.12.4 packrat_0.4.7-1 digest_0.6.9 dplyr_0.4.3 assertthat_0.1  R6_2.1.2 format R_1.3 magrittr_1.5 stringi_1.0-1 rmarkdown_0.9.5  tools_3.2.4 stringr_1.0.0 yaml_2.1.13 parallel_3.2.4 htmltools_0.3.5  knitr_1.12.3 Get the same error. I also noted the following points: The RStudio packages pane divides packages into two separate sections: Packrat Library, System Library The packages that cause an error message when I attempt to update via the update button are all in the System Library.
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.
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.
Turn off your device and then hold down the [Home] [Volume Up] [Power] keys until a screen that reads, "Recovery booting" appears: This document, titled "How To Wipe the Android System Cache ," is available under the Creative Commons license.
Any copy, reuse, or modification of the content should be sufficiently credited to CCM (ccm.net).
Wiping the system cache will drastically improve the responsiveness of your device.
Furthermore, it is recommended that you purge the system cache after major system updates as it may contain obsolete app data.