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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-13 05:19:08 +0100
commit8d1a84ac2190538ed3bac53a303064e281595868 (patch)
treeacb894d85ab7ec87c4911c355a5264a77e08e34b /GNUmakefile
parent51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent4200e566ad2600f56bc3987669aeab88582139eb (diff)
Merge branch 'main' into custom_lsoda_call
Diffstat (limited to 'GNUmakefile')
-rw-r--r--GNUmakefile19
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)"

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