diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-13 05:19:08 +0100 |
| commit | 8d1a84ac2190538ed3bac53a303064e281595868 (patch) | |
| tree | acb894d85ab7ec87c4911c355a5264a77e08e34b /GNUmakefile | |
| parent | 51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff) | |
| parent | 4200e566ad2600f56bc3987669aeab88582139eb (diff) | |
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'GNUmakefile')
| -rw-r--r-- | GNUmakefile | 19 |
1 files changed, 11 insertions, 8 deletions
diff --git a/GNUmakefile b/GNUmakefile index 6e75d666..9f268335 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -24,7 +24,9 @@ pkgfiles = \ DESCRIPTION \ inst/WORDLIST \ inst/dataset_generation/* \ - inst/testdata/fit_old_FOCUS_D.rda \ + inst/rmarkdown/templates/hierarchical_kinetics/template.yaml \ + inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd \ + inst/testdata/* \ man/* \ NAMESPACE \ NEWS.md \ @@ -35,10 +37,6 @@ pkgfiles = \ all: build $(TGZ): $(pkgfiles) vignettes - $(RM) -r vignettes/*_cache - $(RM) -r vignettes/*_files - $(RM) -r vignettes/*.R - $(RM) -r vignettes/web_only/*.R $(RM) Rplots.pdf "$(RBIN)/R" CMD build . 2>&1 | tee log/build.log @@ -80,12 +78,16 @@ clean: $(RM) -r vignettes/web_only/*.R $(RM) Rplots.pdf +# We set PROCESSX_NOTIFY_OLD_SIGCHILD in order to avoid the message +# "Error while shutting down parallel: unable to terminate some child processes", +# which is said to be harmless, see https://processx.r-lib.org/#mixing-processx-and-the-parallel-base-r-package +# and https://github.com/r-lib/processx/issues/236 test: install - "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test.log + PROCESSX_NOTIFY_OLD_SIGCHLD=true "$(RBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test.log sed -i -e "s/.*\r.*\r//" log/test.log devtest: devinstall - "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test_dev.log + PROCESSX_NOTIFY_OLD_SIGCHLD=true "$(RDEVBIN)/Rscript" -e 'options(cli.dynamic = TRUE); devtools::test()' 2>&1 | tee log/test_dev.log sed -i -e "s/\r.*\r//" log/test_dev.log slowtests: install @@ -105,7 +107,8 @@ vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vig vignettes/web_only/%.html: vignettes/references.bib vignettes/web_only/%.rmd "$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/web_only/$*.rmd', dir = 'vignettes/web_only', keep=c('mkin_benchmarks.rda', 'saem_benchmarks.rda'))" -articles: vignettes/web_only/FOCUS_Z.html vignettes/web_only/compiled_models.html vignettes/web_only/benchmarks.html vignettes/web_only/dimethenamid_2018.html vignettes/web_only/multistart.html +vignettes/prebuilt/%.pdf: vignettes/prebuilt/references.bib vignettes/prebuilt/%.rmd + "$(RBIN)/Rscript" -e "rmarkdown::render('vignettes/prebuilt/$*.rmd')" pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" |