Solving Issues to Submit Your R Package to CRAN

Last updated on 5 min read

R Package Submission to CRAN

I just submitted an R package, prewas, that I wrote with my colleagues Zena and Stephanie. The whole process took many more hours than I had anticipated. This post details the snags I ran into and their fixes. Hopefully, this will help other package submission newbies!

General resources:

There are many resources that spell most of what you need to know to submit a package. My two favorites were R Packages by Hadley Wickham and a more compact version by Karl Broman.

What follows are the issues that I ran into that these two resources didn’t address.

Issue 1: Working on R devel

R devel is the version of R currently under development. In January 2020, the release version of R was 3.6.2 and the development version of R was 4.0. The development version of R is relevant to package development and submission because the package must pass the CHECK on R devel without ERRORs or WARNINGs. Naive R programmer that I was, I assumed my code was robust and would therefore work on 3.5 (where it was developed), 3.6.2 (what I’m currently working with), and on 4.0. Boy, was I wrong!

1A) How to know if you code passes CHECK on R devel

I used devtools::check_win_devel() to test if my package passed the CHECK on R devel. This function tests the package on a windows server and emails you the results in ~15-30 minutes. I got my results back and learned that I had something like ~30 failed unit tests on 4.0 despite a perfect record on 3.6.2. Finding this out left me with the big question: “What do I do now?” I decided to download 4.0 and troubleshoot on my local computer because I coudln’t make sense of the CHECK results.

Skip to 2) if your code passed CHECK on R devel

1B) Getting R devel on my mac

I installed R devel on my mac (and reinstalled R release for good measure so I’d know they both go to the same location):

> cd /  
> tar -xvzf /path/to/R-release-name.tar.gz  
> tar -xvzf /path/to/R-devel-name.tar.gz

1C) Switching between R devel and R release

To access both R versions in RStudio and switch between them with ease I used the AMAZING program RSwitch.

1D) Getting packages installed on R devel

Install your package’s dependencies. While most CRAN packages should install with no trouble on R devel, but I ran into several problems:

  • Using the wrong install.packages() type
  • Packages that depended on fortran/C/C++ (ex: ape)
  • Packages that didn’t pass CHECK on R devel

Using the wrong install.packages() type:
The most robust way to install R packages on R devel is

install.packages("package_name", type = "both")

because it looks for either source or binary installations (some packages only have one).

Packages that depended on fortran/C/C++:

When I tried to install the package ape I got a long error message the end of which is below

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'  
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'  
ld: library not found for -lgfortran  
clang: error: linker command failed with exit code 1 (use -v to see invocation)  
make: *** [ape.so] Error 1  
ERROR: compilation failed for package ‘ape’ 
removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ape’  
Warning in install.packages :  
  installation of package ‘ape’ had non-zero exit status .

This error message meant that I needed to install fortran and Xcode on my mac .

Packages that don’t pass CHECK on R devel:
For prewas() dependencies that didn’t pass CHECK on R devel I simply rewrote my package’s code so as to no longer depend on the bum packages. Luckily for me, the changes were minor and I was done in less than ten minutes.

1E) Resolving my test failures in R devel

The errors in my package were caused by a change to 4.0 that broke several functions and unit tests.

In 4.0 you cannot use

if (class(r_object) == "class_name")  {}

Instead you should use

if (methods::is(r_object, "class_name")  {}

This wonderful post brought this issue to my attention and explains the why behind the change. You can also check the R news to learn about changes occuring in R devel.

Once I updated my class checking code I had just a couple minor unit test tweaks to make to get my code to pass CHECK on both R release and R devel.

Issue 2: Git

At that point I tried to submit to CRAN with

devtools::release()

but was foiled again, this time by git issues. I got the following error message

ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol

To solve this problem I updated my authentication method.

2A) Getting a personal access token (PAT)

There are three ways to authenticate with git:

  1. ssh
  2. https + username + password
  3. https + PAT

I’ve loved using ssh, but devtools::release() wasn’t playing nicely with ssh so I switched to https + PAT. To generate a PAT I used

usethis::browse_github_token()

which took me to github where I generated the token. I immediately saved the token in two locations: my password manager and my .Renviron. To edit the .Renviron:

usethis::edit_r_environ()

which opens the .Renviron file and I copied in

GITHUB_PAT=my_really_long_numerical_token

Notice that there is a empty new line in the file- I’m told this is necessary. Then I restarted R and checked that the PAT saved

Sys.getenv("GITHUB_PAT") .

2B) Switching from ssh to https + PAT

I also changed from ssh to https on the terminal. This is what it looks like when you’re set up with ssh:

$ git remote -v  
> origin  git@github.com:user/repo.git (fetch)  
> origin  git@github.com:user/repo.git (push)

To change to https:

$ git remote set-url origin https://github.com/user/repo.git

Then check that it worked:

$ git remote -v  
> origin  https://github.com/user/repo.git (fetch)  
> origin  https://github.com/user/repo.git (push)

After I made those two changes I could pass the github section of devtools::release().

Good luck on your package submission!