rchk works

kingaa · Apr 16, 2024 · 8f59a9d · 8f59a9d
1 parent 871ded7
commit 8f59a9d
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Showing 7 changed files with 421 additions and 1,856 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -21,6 +21,7 @@ README\.(.?)$
 CRAN\.md$
 TODO\.md$
 BUILD\.md$
+^rchk\.out$
 ^\.gitignore$
 \.github
 ^\.travis\.yml$

diff --git a/.gitignore b/.gitignore
@@ -20,9 +20,10 @@
 *.pdf
 *.sif
 /scripts
+check
 lib
 library
-check
+rchk
 repo
 wiki
 tmp

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,13 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.3.1
-Date: 2024-04-01
+Version: 0.10.4.0
+Date: 2024-04-16
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )
 Description: Tools for phylodynamic analysis.
+biocViews:
 Depends: R(>= 4.2)
 Imports: grid, ggtree, yaml, ggplot2, scales, ape, dplyr, tibble, foreach, tidyr, pomp(>= 5.2.4.3), cowplot
 LinkingTo: pomp

diff --git a/rchk.out b/rchk.out
diff --git a/rchk/Makefile b/rchk/Makefile
diff --git a/rchk/rchk.out b/rchk/rchk.out
diff --git a/rules.mk b/rules.mk
@@ -133,8 +133,9 @@ session debug rsession: .session
 rchk: .rchk
 
 .rchk: .dist
+	mkdir -p rchk
 	$(CP) $(TARBALL) rchk
-	make -C rchk
+	docker run -v $(PWD)/rchk:/rchk/packages kalibera/rchk:latest /rchk/packages/$(TARBALL) | tee rchk.out
 
 revdeps: .dist
 	mkdir -p revdep
@@ -218,14 +219,13 @@ inst/include/%.h: src/%.h
 clean:
 	$(RM) -r check
 	$(RM) src/*.o src/*.so src/symbols.rds
-	$(RM) -r lib
+	$(RM) -r lib rchk
 	$(RM) -r *-Ex.Rout *-Ex.timings *-Ex.pdf Rplots.*
 	$(RM) *.tar.gz $(PKGVERS).zip $(PKGVERS).tgz $(PKG).pdf
 	$(MAKE) -C www clean
 	$(MAKE) -C inst/doc clean
 	$(MAKE) -C tests clean
 	$(MAKE) -C revdep clean
-	$(MAKE) -C rchk clean
 	$(RM) .dist
 
 fresh: clean
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,9 +20,10 @@ @@
     *.pdf
     *.sif
     /scripts
+    check
     lib
     library
-    check
+    rchk
     repo
     wiki
     tmp
@@ Expand Down @@