Incompatible R package binaries (packrat)

Installed R packages are not always compatible with other packages installed into the same library.

This repository contains an example of what may happen when installing from source packages in one environment and installing from binary packages in another.

The packrat package is used to create the environment.

An renv example is also available.

This example uses an RStudio Package Manager repository time-stamp. https://packagemanager.rstudio.com/all/2021-09-01+Y3JhbjoyMDIxLTA4LTMxLDI6NDUyNjIxNTs3Rjc5MTcxQw" This corresponds to a date after the Rcpp-1.0.7 release, but just prior to the httpuv-1.6.3 release. The httpuv-1.6.3 started requiring Rcpp-1.0.7 to help folks avoid the binary package incompatibility seen here.

RSPM does not currently support binary packages on macOS, but it does support binaries for Ubuntu 18.04 (Bionic Beaver). We take advantage of this difference in order to create a situation where a development (macOS) environment has a working configuration, yet the same environment will fail to run in the "production" (Ubuntu Linux) environment. This difference in behavior is caused by installing R packages binary packages on Linux.

R -s -f bootstrap.R
R -s -f install.R

The run.R script adjusts the repos option to reference either the regular repository URL or one that can supply binary Linux packages. The packrat.lock is rewritten to reference this target repository.

The renv variation of this example does not adjust its lockfile because renv automatically detects and pulls binaries from RSPM.

# Successfully run an httpuv server. Control-C to stop.
R -s -f run.R

# Fail to run in Linux; packrat is instructed to use binary packages.
docker run -it --rm \
    -v $(pwd):/content \
    -w /content \
    rstudio/r-base:3.6.3-bionic \
    R -s -f run.R

The resulting error is:

Error in loadNamespace(name) : there is no package called ‘httpuv’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart

To clean-up and retry this experiment, run the following within this repository:

rm -rf .Rprofile packrat manifest.json

This example uses packrat to demonstrate the problem, but its use is not required.

Should you want a Shiny application to deploy:

tar zcf bundle.tar.gz app.R manifest.json

aronatkins/incompatible-r-package-binaries-packrat

Incompatible R package binaries (packrat)