blabr

An R library for working in the BLAB

Installing

In R console:

remotes::install_github("BergelsonLab/blabr")

This command will also update your version of blabr if it's already installed.

You might need to install remotes first if you haven't already.

Subprocess Issue:

If you are getting an issue with the subprocess package (which is now archived, and hence is not available from the main CRAN archive), run this command:

install.packages("https://cran.r-project.org/src/contrib/Archive/subprocess/subprocess_0.8.3.tar.gz", repos = NULL)

This command simply installs the latest available version of the package before it was archived.

Usage

• all_basiclevel

• BLAB_DATA sync/load

Troubleshooting

I updated blabr but nothing has changed!

Try restarting the R session.

OK, it helped but what was happening?

Only the first library/require call actually loads the library. All the consequent calls don't do anything. The reason for that is that a lot of code will try to load the same library many times. So, loading it again and again would (a) take a lot of time, (b) lead to unpredictable results if the installed version changed between the calls.

My script doesn't work anymore!

There have been a few changes to blabr that might make your scripts not work anymore. Below are the solutions for the two most common ones.

Note: it is recommended to use renv for managing an independent r library for each individual project. See Virtual environments for more details.

• Error in xxx() : could not find function "xxx".

  Most likely xxx is a function from one of the tidyverse packages. Solution: google "tidyverse xxx", see what package it came from, load that package with the corresponding library(yyy) call.

• Error: 'xxx' is not an exported object from 'namespace:blabr'

  'xxx' is a blabr function/variable that is not accessible after attaching blabr (library(blabr)) or using the double-colon (blabr::xxx). Solution: use triple colon operator - blabr:::xxx AND tell Zhenya to start exporting xxx in future versions.