PSA on R

The Solution

If you trying to install a package in R and get hit with “Error: package ‘foo’ was built before 3.0.0: please re-install it“, or in installation fails because of uninstalled dependencies, then run the following in R or RScript:

    update.packages(checkBuilt = TRUE, ask = FALSE)

If this fails because of permissions problems with updating the R library directory, then try again as root.

Thanks to anonymous user3003714 on StackOverflow for that blessed cure.

How I Got There

I am taking a data science course from Coursera.  Our homework assignments this week are in R, and learning R has been left as an exercise for the student.

The biggest problem I have had has been getting R to work at all.  Package caret was recommended for our assignment, and it would not install because of dependency issues, or because a 2.x rather than 3.x version was installed.  When I tried to install the prerequisite packages, I found that they, too, had dependencies.

(N.b., installing the various packages also required fiddling with /etc/apt/source.list, coping with expired package keys, and increasing the memory configured for the VM on which I was working.)

Google did not immediately turn up a general solution, so I kept inching my way up the dependency tree, one package at a time.  For awhile it seemed that I was finding three new dependencies for every one that I resolved. I have not experienced this sort of dependency Hell since the days before wrapping C header files with #ifndef HEADER_NAME .. #endif became standard practice. It was certainly a match for any DLL Hell problem I’ve faced.

After hours of work, the caret library would load. All the while, I kept wondering how could so many people use R when it’s this hard to set up?

So finally I could actually start on the homework.  Well into it,  a problem description recommended the use of package rpart, and I hit a similar 2.x problem that I’d run into with caret, but worse than before because a simple re-install did not fix it.

It was back to Google, but this time (thank God!), the  search struck gold, in the form of the first section of this post.



Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s