This section unfortunately has not been maintained due to a lack of time. My general comment is for MacOS, do things the Apple way and you will have no problems. Apple’s been quite clever in how they control permissions, but it’s hard to find the details.
Notes on turning my Mac into a serious developer’s machine. This odyssey started with OS X 10.10.4 and continues today covering OS X 10.11.6.
My system is different in ways that will turn out to be significant:
pick up revisions here… The rest is a work in progress.
My best practice is to keep config files under source control and have an easy process to keep each Mac up-to-date with any config file changes. I do this by creating symlinks from R’s file names to the actual files in my git working directory.
First, if you have not installed Apple’s XCode tools, or have done a major OS X upgrade:
xcode-select --installIf your R environment isn’t what you thought it should be, use R.home to verify the path to the various pieces of R.
I like to jump into a new technology and with R, I was hooked on ggplot2. At some point you need to step back understand some of the console error or warning messages that scrolled by. I’ve written up some of my lessons learned in this section
I’m in the process of documenting how I created the rest of my R setup. It’s a work in progress which gets updated a few times a week.
My first R setup was done by downloading XQuartz, R, and RStudio as Mac binaries and installing them in the order listed. I call this the seminar setup. As an aside, there is an online environment (at the time is was www.compileonline.com), http://www.tutorialspoint.com/r_terminal_online.php, if you don’t want to install anything.
My second R setup, to take advantage of the RStudio-git integration, was done mainly by following these instructions - http://burnedpixel.com/blog/beginners-setup-guide-for-ruby-node-git-github-on-your-mac/ and stopping before installing Ruby.
MacTeX was installed for PDF file generation. And that’s when I found that homebrew, really ruby, stopped working because of a character encoding setting.
Since my Rproject.site wasn’t being found either, it was time to figure things with a more structured approach.
No one I know uses the github desktop software which is why it’s not included in the above list. Another IDE is eclipse, but I wanted something lightweight and easy for less software developer types to learn. Some developers like the Sublime Text editor, but I have no experience with it.
The majority of solutions to R problems seem to be developed on Linux distributions. Sometimes they do not work on OS X. My goal is to figure out how to take advantage of this wealth of knowledge while using my Mac. What follows is a comprehensive model to make your environment more like Linux without giving up all the wonderfulness of a Mac. The areas I cover are:
Need some motivation? Here’s an example of something simple that turns out to be more complicated. My Mac has 2 disk drives, with the 2nd drive storing my R programs. I want to cd among my different directories using tab completion. The CDPATH environment does just that, but not with tab completion. The bash-completion code needs to be installed. If you want the performance fix for bash-completion, bash 4.x needs to be installed. But OS X 10.10 ships with Bash 3.x.
My bash configuration files are in my home-profiles project.
The Mac is an interesting platform because the GUI side and the command line side are mostly separate. GUI software is installed by running an installer or dragging the application to the Applications folder.
/usr/bin/ is owned by Apple and they update it for major releases and provide occasional patches. If you modify it, you run the risk of breaking something from Apple./usr/local/bin is available and can be owned by you. More on that to come./Applications is for GUI applications.When the Mac became a multiuser system, I created two accounts. An admin account and a regular user account. In the early days, I used this structure to found out which apps were well behaved. As security risks increased over the years, I adopted the use the least privileges philosophy so I work from a Standard account (in the Users & Groups System Preference). Below is a table comparing the Standard and Admin accounts.
====== Insert table =========
If you review the output from ls -alFeG /Applications, you see that developers are not fully checking user and group setting and occasionally set group file protection to include write. ‘Repair Permissions’ in Disk Utility compares the files and their initial permissions in the BOM (bill of materials) in the receipt to the ones installed and changes the permissions to match the BOMTC1.
==== script to check and fix this will updated later on ====
My practice for GUI apps is to install them from my Standard user account. For Linux apps I do the following from the Terminal:
su - MyAdmin
# Execute the instructionsThe - is critical to establish the shell with only the MyAdmin environment and nothing from your account.
My Mac has multiple users and by default, all folders and files you create outside of the folders in your home directory that have icons (like Documents, Downloads, Pictures, Movies ) are readable and executable by anyone else on your Mac. I preference is keep my files private and to grant others access on a specific basis. That pattern can be implemented by setting the default file and folder permissions for
sudo launchctl config user umask 066 from an admin account. Then reboot for it to take effect.umask 066. This should be added to one of your bash start up files.Note that these settings will only be applied to new files created. Existing files need to be changed manually. I also use Access Control Lists for even finer grained control. Additional information can be found with these search terms.
Note: 11-Aug-2015 I found that RStudio v0.99.467 w/R v3.2.1 generates a permission denied error when creating a new project in an empty directory. Creating the folder in Finder works and then RStudio does not generate an error. BBEdit works correctly so I’ll look into this, but it’s low priority for now.
OS X does not have package manager like yum, rpm, homebrew, etc. There are two comamnds, installer and pkgutil. Apple seems to actively discourge developers from using installer. pkgutil just reads the receipt database which is helpful. Note that apps installed by dragging to the Applications folder don’t seem to appear in the receipt database. If you want to know what’s installed, I much prefer using the terminal to get a listing for comparison or refinement.
I selected homebrew because my colleagues are quite satisfied using and I want to leverage their development methods.
su - MyAdmin
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
# Binaries installed in /usr/local/bin"My initial plan of using homebrew and cask to install R, RStudio, and the text editors came to an abrupt halt on 12-Aug-2015 with the announcement of Changes to homebrew-cask installation behaviour. The summary is cask is transitioning from linking to /Applications to moving files. I’ll wait for this change to become stable and revaluate what do in the future.
There are people using homebrew to install R. Here’s one link - http://apple.stackexchange.com/questions/121401/how-do-i-install-r-on-os-x.
My Macs have either multiple disks or multiple partitions and they had descriptive names that had spaces in them. There is nothing more confusing than networking mounting a disk on a remote machine and seeing two Macintosh HDs. My Mac tenure started with System 7 and spaces in path names was not an issue. Along came OS X, which is based on BSD, and now spaces in the file path become a real hassle. Some OS X apps figure out where the files are when you rename the partition and others need to be reconnected. When I renamed my partitions, these apps needed some help to find their files:
You want your PATH environment variable to start with /usr/local/bin/ so the software you install is executed instead of Apple’s versions. Check the /etc/paths file and update as needed.
Your GUI apps, roughly those in /Applications, don’t use the same path as your terminal sessions. Those apps use the path defined in ~/.MacOSX/environment.plist. So far, I have not encountered any issues, but mention it as one of those facts to keep in the recesses of your mind.
XQuartz needs to be reinstalled any time OS X is upgraded. This includes point releases such as 10.10.5.
R installer asks if you want to install them. Select the ‘Yes’ option.
Github is a huge asset and widely used so I wanted to use it for some of my work. However, the free github account only allows public projects. Gitlab allows for some free private projects so I use both remote repositories. Recommend using the same email address for both accounts so that these git global settings are the same:
git config --global user.email "you@example.com"
git config --global user.name "Your Name"While many git tutorials tell you to set these values, at least for git 2.4.x and 2.5.x, there’s no need. The first time you do a git commit -m, you are prompted for the info. You may not have the luxury if you have multiple repository accounts in which case just issue the same command without --global in the working directory for that project.
The first time I installed git from https://git\-scm.com/download/mac. When I setup my ssh URL, and tried to clone a repository, this error happened
ssh_askpass: exec(/usr/libexec/ssh-askpass): No such file or directoryIf you are only using git, and install the git OS X Keychain Helper, the script is not needed. Instead a dialog box will appear asking for your SSH password the first time you do git clone command line and then you are all set.
Prior to the 14-June-2015 release of MacTex, the installation location was /usr/??. As a result of an El Captain security change, the new location is /Library. This change ⌘-L will show the log during a running installation.
Apple ships an older version of ruby with Yosemite OS X 10.10.4. After installing MacTex, you’ll encounter this error when you use brew.
Error: invalid byte sequence in US-ASCIIDefine these 4 environments variables for your session so this older version of ruby will be happy again:
export LANGUAGE="en_US:en"
export LC_MESSAGES="en_US.UTF-8"
export LC_CTYPE="en_US.UTF-8"
export LC_COLLATE="en_US.UTF-8"You made it this far - great! I’ve been using Hadley’s style guide for my code. It’s a simple guide well worth the time investment. Experienced programmers may like http://www.johndcook.com/blog/r_language_for_programmers/ which summarizes some differences between R and other languages.
Footnotes & Links to info on the page:
External Cites:
Select R package repository: https://stat.ethz.ch/R-manual/R-devel/library/utils/html/setRepositories.html