installed directory not writable, cannot update packages 'boot', 'class', 'KernSmooth', 'mgcv', 'nnet', 'rpart', 'spatial'

Question

I installed the Bioconductor packages on R version 3.1.2 on Ubuntu 14.04 and received the message below:

The downloaded source packages are in ‘/t

Answer 1

I faced the same problem today when installing three Bioconductor packages under Windows. Two (dependencies of the package I really wanted) were already on my system in newer forms (as described in @Martin-Morgan solution) and so no action was necessary. However, one was not installed. For this, third package, I had success in doing an installation from the local file that was downloaded during the failed install without having to escalate privileges (which was my next step as outlined by @Ninadmw).

In R, go to the menu Packages/Install Package(s) from local files and navigate to the local download directory listed, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages, and select the package you want to install.

In RStudio (which you should use), go to the menu Tools\Install Packages, change the install from field to Package Archive File (.zip; .tar.gz), use Browse... to navigate to the listed download directory, which in your case was /tmp/RtmpZYw0Qp/downloaded_packages and select the package you want to install. Then click on the Install button.