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    Shouldn't the behaviour in a packrat project be that if a package exists in the packrat and system libraries then the update dialog should only look at the package in the packrat library?

    Ross On 19 July 2016 at , Phil Mike Jones [email protected]: Thanks @kevinushey https://github.com/kevinushey that seems to have done the trick — You are receiving this because you were mentioned.

    Furthermore, it is recommended that you purge the system cache after major system updates as it may contain obsolete app data.

    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 [10] LC_TELEPHONE=C LC_MEASUREMENT=en_AU. UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics gr Devices utils datasets methods base other attached packages: [1] RMy SQL_0.10.8 DBI_0.3.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.4 packrat_0.4.7-1 digest_0.6.9 dplyr_0.4.3 assertthat_0.1 [6] R6_2.1.2 format R_1.3 magrittr_1.5 stringi_1.0-1 rmarkdown_0.9.5 [11] tools_3.2.4 stringr_1.0.0 yaml_2.1.13 parallel_3.2.4 htmltools_0.3.5 [16] 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 could log into the temporary admin account I give to Apple when the machine is sent in for service, so I knew it was something specific to my day-to-day account.

    I was able to get into single user mode (hold down Command-S right after the startup twang) and examine the /var/log/file.

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