BUILD.md

In kingaa/ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Instructions for building, checking, and installing

Makefile usage

A Makefile is provided. Most of the rules are defined in the rules.mk file. The following key variables are defined in the Makefile.

• REPODIR: the name of the directory in which a local copy of the Git repo used for publishing source and documentation is located.
• INCLUDES: names of header files that will be copied to inst/includes
• HEADERS: names of header files that must be rebuilt whenever source code changes.

The key targets are:

• roxy: runs devtools::document() to build the help pages (in man/), the package NAMESPACE, and the collation order in DESCRIPTION.
• dist: builds the package source tarball.
• install: installs the package locally for testing.
• tests: runs make in the tests/ directory, causing tests to be updated as needed.
• clean: cleans the directory of files created during builds and tests.

• fresh: resets the directory for a fresh rebuild.

• htmlhelp: builds the package manual in HTML and PDF formats. This command also causes doxygen to be run, which produces HTML documentation of the C/C++ source code. These documentation files are installed into the REPODIR/manuals directory.

• www: installs the package and runs make in the www directory. This causes vignettes to be updated, among other things.
• NEWS: builds the plain-text package NEWS file.

• instdocs: runs make in the inst/docs directory.

• check: runs devtools::check().

• qcheck: like check, but tests in tests/ are not run.
• qqcheck: like qcheck, but checks for code-documentation mismatch and examples are not run.
• xcheck: runs devtools::check(cran=TRUE), i.e., the additional checks for CRAN suitability are also run.
• ycheck: runs xcheck but tests and examples that are ordinarily not run (because expensive) are run.
• vcheck: runs check and then tests for memory leaks using valgrind. One must examine the output (printed to the console and also stored in a file, the name of which ends in -Ex.Rout.
• revdeps: causes checks of reverse-dependent packages to run. The outputs are stored under the revdep directory.

• rchk: runs Kalibera's rchk utility. This uses docker to download and run a Docker container. The stdout for this is stored in rchk.out.

• session: installs the package locally and then runs an R session for interactive testing. This session is controlled by the RSESSION environment variable. By default, this runs an emacs -f R session.

• rsession: like session, but a naked R session is started: RSESSION=R.

• debug: like rsession, but the R session is started under a debugger. By default, the gdb debugger is used: RSESSION=R -d gdb.

• publish: causes source and binary tarballs to be installed in the REPODIR respository.

• covr: runs covr::package_coverage() to evaluate unit-test coverage. Results are stored in covr.rds.
• vcovr: like covr, but results are displayed in a browser.

Github Actions

Several Github Actions are defined in .github/workflows:

• r-cmd-check: runs checks on various platforms.
• test-coverage: runs covr::codecov to upload unit-test coverage information to codecov.io.
• binary-build: causes binary tarballs to be built for OS X and Windows platforms.

These must be updated manually from time to time as the Actions on which they depend change.

kingaa/ouch documentation built on June 14, 2025, 9:11 a.m.