From 240568bf65f2257f1185927ac811dde18aeabe1d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 2 Dec 2022 13:25:56 +0100 Subject: Avoid error message at testthat termination https://github.com/r-lib/processx/issues/236 --- GNUmakefile | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) (limited to 'GNUmakefile') diff --git a/GNUmakefile b/GNUmakefile index 6e75d666..e5f83c1f 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -80,12 +80,16 @@ 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 -- cgit v1.2.1 From 0023df3c31fac29b5f9337ecd732a5dfd4d51a2d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 06:37:32 +0100 Subject: Template and spreadsheet for hierarchical kinetics The template only shows parent data evaluation without covariate models for now. The spreadsheet will also be useful for unit testing of the read_spreadsheet function. --- GNUmakefile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'GNUmakefile') diff --git a/GNUmakefile b/GNUmakefile index e5f83c1f..4680514c 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/hier/template.yaml \ + inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd \ + inst/testdata/* \ man/* \ NAMESPACE \ NEWS.md \ -- cgit v1.2.1 From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 12:31:56 +0100 Subject: Rename template folder, create format Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of. --- GNUmakefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'GNUmakefile') diff --git a/GNUmakefile b/GNUmakefile index 4680514c..4a33c538 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -24,8 +24,8 @@ pkgfiles = \ DESCRIPTION \ inst/WORDLIST \ inst/dataset_generation/* \ - inst/rmarkdown/templates/hier/template.yaml \ - inst/rmarkdown/templates/hier/skeleton/skeleton.Rmd \ + inst/rmarkdown/templates/hierarchical_kinetics/template.yaml \ + inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd \ inst/testdata/* \ man/* \ NAMESPACE \ -- cgit v1.2.1 From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- GNUmakefile | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) (limited to 'GNUmakefile') diff --git a/GNUmakefile b/GNUmakefile index 4a33c538..9f268335 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -37,10 +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 @@ -111,7 +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)" -- cgit v1.2.1