17 Dependency Management

How do I make sure that all my software and configurations needed for a projects are portable?

  • renv captures package versions and sources as well as R version. renv also records python versions and virtual environments for projects that used both languages.

    • The capsule package can be useful when you want version control/depedency management but not the full weight of renv. Sometimes, renv can be an impediment for smaller and highly collaborative projects, that is where capsule can be useful. Ultimately, capsule will allow to setup renv for a project when it gets to a stable state.

  • Docker allows you to create virtual machines, meaning you can capture all system dependencies in addition to the dependencies captured in renv. It works for essentially any programming language and is extremely flexible.

  • Makefiles can automate a complex, multipart project. Here’s a lesson on them from Software Carpentry

  • R packages can be a useful project output. We have some in-house R packages to provide access to internal data and generate reports, and may be developing more for external audiences. Hadley Wickham’s R Packages Book provides guidance for these, and we expect our packages to be up to rOpenSci standards.

17.1 GCC and mac silicon

  • R package installation can be especially tricky on Mac computers with Apple Silicon. Below are some steps to get package install set ups.

  1. Install the R compilation tool chain https://mac.thecoatlessprofessor.com/macrtools/. If any issues with FORTRAN, follow instructions for downloading FORTRAN compiler here for Apple silicon Macs: https://mac.r-project.org/tools/

  2. Install gcc brew install gcc. This requires having brew set up.

  3. Make sure homebrew is in terminal path. Add it by export PATH=$PATH:/opt/homebrew/bin.

  4. Create ~/.R/Makevars and insert the following. This will need to be updated depending on gcc version.

CXX14FLAGS += -O3 -arch arm64 -ftemplate-depth-256
FC = /opt/homebrew/Cellar/gcc/13.2.0/bin/gfortran
F77 = /opt/homebrew/Cellar/gcc/13.2.0/bin/gfortran
FLIBS = -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13

  1. RStudio may have a bug in accessing the correct terminal path. The workaround is to copy your terminal path (echo $PATH) into .Renviron per instructions here: https://community.rstudio.com/t/how-to-get-rstudio-ide-to-use-the-correct-terminal-path-in-mac-os-x/131528/6

  2. Some packages may need additional help for R to find the correct paths. For units: remotes::install_version(package = "units", version = "0.8-5", configure.args = "--with-udunits2-lib=/opt/homebrew/Cellar/udunits/2.2.28/lib --with-udunits2-include=/opt/homebrew/Cellar/udunits/2.2.28/include")

17.2

Historically some projects used Packrat or checkpoint to fix R package versions. These systems have been superceded by renv.