A number of students and I have found that when following the directions for installing RMark on a Mac, as described at http://www.phidot.org/software/mark/rmark/linux/, it has not worked with recent releases of OS X, such as Yosemite and El Capitan. However, it worked when I followed the steps about a year ago, and has continued to work as I’ve updated OS X (but I’ve been wary to update my RMark package). A particularly savvy student, Spencer Hudson, found that the problem was associated with the gfortran install. To help others, I’m outlining the full set of steps that seems to work for first-time installs on a Mac with a recent release of OS X (such as Yosemite or El Capitan).
1. Install Xcode from the App Store if not already installed on your computer
2. Instead of installing gfortran from https://gcc.gnu.org/wiki/GFortranBinaries#MacOS, which did not work for us, we had success installing GCC builds and gfortran from http://hpc.sourceforge.net/
3. From the sourceforge site, download the appropriate pair of tar.gz binary files. For OS X El Capitan these would be gcc-6.0-bin.tar.gz & gfortran-6.0-bin.tar.gz. These binaries will download into your ‘Downloads’ folder (note that this may take some time).
4. From here, there are several options for unzipping and loading. One way is to run the following lines of code in Terminal (Terminal is a command line interface that is akin to the Command Prompt in Microsoft Windows; it can be found in the Utilities folder located within your Applications folder). Be sure to pay attention to spaces, and you may be asked for your app installation password.
cd ~/Downloads
gunzip gfortran-6.0-bin.tar.gz
gunzip gcc-6.0-bin.tar.gz
sudo tar -xvf gfortran-6.0-bin.tar -C /
sudo tar -xvf gcc-6.0-bin.tar -C /
5. Now you are ready to download the zipped file containing the build of the MARK numerical routines executable from the first bulleted suggestion at http://www.phidot.org/software/mark/rmark/linux/. Extract the file mark.64.osx from mark.osx.zip (by clicking on the zip file).
6. Next, rename the file “mark” by deleting the .64.osx extension of the file name.
7. As pointed out by Arpat Ozgul in an earlier post on this Forum, copy the renamed mark file to the hidden folder /usr/local/bin. This folder can be accessed by opening your Terminal and typing:
open -a Finder /usr/local/bin
8. In Terminal, simply type “mark” (without the quotes) to make sure the file is executable. If you get the message “No input file was specified, so MARK job is done”, then everything worked!
9. Now you can finally install the RMark package from CRAN into R (https://cran.r-project.org/). Use the .tar.gz install instead of the binaries. You may need to install other packages that RMark depends upon.