load_allalias now has
helpers = FALSEset by default, to speed up package loads significantly.
install: Added new
autoconfoption, which will automatically set internal configuration overrides automatically for some problematic packages (e.g. rgl on macOS).
load_all, which is very useful for debugging package load time and dependency chain.
installnow ensures data.table gets built from source automatically. Currently on macOS, the prebuilt CRAN binaries don’t enable parallel threading by default due to improper OpenMP configuration, which is annoying. Since we install the fxcoudert GCC compiler by default, let’s use this instead to enable OpenMP and parallel processing support. May want to consider a similar approach in the future for Rcpp, etc.
autoconfhandling for data.table, geos, rgl, and sf packages. Refer to internal
.autoconfcode for details.
autoconfhandling for data.table, now using
~/.R/Makevarsdynamically to define gfortran GCC compiler options used to enable OpenMP support for parallel threads on macOS.
install: Bug fix for
installRecommendedPackages: Made this function more modular, allowing for the user to specify which types of extra packages should be installed. Applies primarily to Bioconductor (i.e. next-generation sequencing) analysis packages, which can often be quite large and inappropriate for a compact virtual machine instance.
clearWarningsfrom exports, which doesn’t seem to be compatible with R 4.1 due to inability to assign
last.warningto base environment.
memfree: Now using
sprintfcall, due to hardened change in R 4.1.
check: Made lintr, urlchecker, and BiocCheck checks optional if these packages are not installed. This can be the case inside Docker images.
installRecommendedPackages: Added GRmetrics and dr4pl, for IC50 calculations.
coveragearguments. Now checking package coverage for at least 80% coverage by default.
check: Now always runs
rcmdcheckin some cases doesn’t run unit tests in R 4.1.