cleaning up r-build

.github/workflows/cmake.yml

@@ -122,21 +122,13 @@ jobs:
         shell: Rscript {0}
 
       - name: versioning
-        run: ./jenkins-R-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
+        run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
 
-      # - name: versioning
+      - name: build
-      #   run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
+        run: cd R && make build
 
-      # - name: R
+      - name: check
-      #   run: |
+        run: cd R && make check
-      #     cd R
-      #     mkdir -p phreeqc/man
-      #     mkdir -p phreeqc/src/phreeqcpp
-      #     mkdir -p phreeqc/R
-      #     mkdir -p phreeqc/data
-      #     echo "# Generated by roxygen2: do not edit by hand" > phreeqc/NAMESPACE
-      #     DATE=$(date -d ${{ needs.init.outputs.DATE }} "+%Y-%m-%d")
-      #     make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=$DATE build
 
       - uses: actions/upload-artifact@v2
         with:

R/Makefile

@@ -1,19 +1,36 @@
+# phreeqc                   TOPDIR
+# ├── data                  DATADIR
+# ├── inst                  INST
+# ├── man                   MAN
+# ├── R
+# └── src                   IDEST
+#     └── phreeqcpp         DEST
+#
+
 CP=cp -f
-TOPDIR=phreeqc
+TOPDIR ?= phreeqc
-IDEST=phreeqc/src
+IDEST=$(TOPDIR)/src
-DEST=phreeqc/src/phreeqcpp
+DEST=$(TOPDIR)/src/phreeqcpp
 ISRC=../src
 SRC=../src/phreeqcpp
-INST=phreeqc/inst
+INST=$(TOPDIR)/inst
 DBDIR=../database
-DATADIR=phreeqc/data
+DATADIR=$(TOPDIR)/data
 EXDIR=../phreeqc3-examples
-MAN=phreeqc/man
+MAN=$(TOPDIR)/man
+R=$(TOPDIR)/R
 
-SVN_URL := http://internalbrr.cr.usgs.gov/svn_GW
+_TOPDIR := $(shell mkdir -p $(TOPDIR))
-RELEASE ?= $(shell svn info $(SVN_URL) | egrep "Revision:" | cut -b 10- | ( read one two ; echo $$one ) )
+_IDEST := $(shell mkdir -p $(IDEST))
+_DEST := $(shell mkdir -p $(DEST))
+_INST := $(shell mkdir -p $(INST))
+_DATADIR := $(shell mkdir -p $(DATADIR))
+_MAN := $(shell mkdir -p $(MAN))
+_R := $(shell mkdir -p $(R))
+
+RELEASE ?= $(shell curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3 -)
 RELEASE_DATE ?= $(shell date "+%Y-%m-%d")
-VERSION ?= 1.0
+VERSION ?= $(shell curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | /bin/sh)
 
 DBS = \
 	Amm.ascii \
@@ -281,11 +298,12 @@ $(DATADIR)/examples.rda : $(EXS) build-examples.R
 	R --no-save --no-restore CMD BATCH build-examples.R
 	rm -f .RData
 
-roxygenize $(MAN)/phreeqc-package.Rd : phreeqc/R/phreeqc.R
+# roxygenize $(MAN)/phreeqc-package.Rd : $(R)/phreeqc.R
-	rm -f $(RDFILES)
+# 	rm -f $(RDFILES)
-	rm -f .RData
+# 	rm -f .RData
-	R --no-save --no-restore CMD BATCH roxygenize.R
+# #	R --no-save --no-restore CMD BATCH roxygenize.R
-	touch $(MAN)/phreeqc-package.Rd
+# #	touch $(MAN)/phreeqc-package.Rd
+# 	Rscript -e 'devtools::document(pkg = "phreeqc")'
 
 
 ##$(PSRC): $(DEST)
@@ -809,8 +827,18 @@ $(INST)/ex2 : ../phreeqc3-examples/ex2
 
 ########################################
 
+roxygenize $(MAN)/phreeqc-package.Rd : $(R)/phreeqc.R
+	rm -f $(RDFILES)
+	rm -f .RData
+#	R --no-save --no-restore CMD BATCH roxygenize.R
+#	touch $(MAN)/phreeqc-package.Rd
+	Rscript -e 'devtools::document(pkg = "phreeqc")'
+
 check : all
-	Rscript -e "devtools::check('phreeqc')"
+	Rscript -e "devtools::check(pkg = 'phreeqc')"
+
+# check_built :
+# 	Rscript -e "devtools::check_built()"
 
 valgrind : install
 	R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
@@ -818,12 +846,14 @@ valgrind : install
 install : all
 	R CMD INSTALL --build phreeqc
 
+$(TOPDIR)/R/phreeqc.R : phreeqc.R.in export_sed
 
-phreeqc/R/phreeqc.R : export_sed
+$(TOPDIR)/DESCRIPTION : DESCRIPTION.in export_sed
 
-phreeqc/DESCRIPTION : export_sed
+$(TOPDIR)/inst/CITATION : CITATION.in export_sed
 
-export_sed :
+.PHONY: export_sed
+export_sed : check-vars
 	sed \
 	 -e 's/@VERSION@/$(VERSION)/g' \
 	< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
@@ -831,6 +861,9 @@ export_sed :
 	 -e 's/@VERSION@/$(VERSION)/g' \
 	 -e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
 	< phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
+	echo "# Generated by roxygen2: do not edit by hand" > $(TOPDIR)/NAMESPACE
+	$(CP) CITATION $(TOPDIR)/inst/CITATION
+	$(CP) LICENSE.note $(TOPDIR)/LICENSE.note
 
 build : all
 	R CMD build --resave-data phreeqc
@@ -847,10 +880,19 @@ $(IDEST)/R.cpp : R.cpp
 	< $< > $@
 
 $(IDEST):
-	mkdir $(IDEST)
+	mkdir -p $(IDEST)
 
 $(DEST):
-	mkdir $(DEST)
+	mkdir -p $(DEST)
 
 clean :
 	rm -f $(PSRC) $(XSRC) $(DEST)/*.o $(IDEST)/*.o $(DEST)/*.so
+
+.PHONY: check-vars
+check-vars:
+ifndef VERSION
+	$(error VERSION is undefined)
+endif
+ifndef RELEASE_DATE
+	$(error RELEASE_DATE is undefined)
+endif

jenkins-R-dist.sh

@@ -4,28 +4,28 @@
 # set DATE
 #
 if [ -z "$DATE" ]; then
- DATE=$(date "+%x")
+  DATE=$(date "+%x")
 fi
-DATE=$(date -d $DATE "+%Y-%m-%d")
+DATE=$(date -d $DATE --rfc-3339=date)
 
 #
 # set VER
 #
 if [ -z "$VER" ]; then
- ###wget https://cran.r-project.org/package=phreeqc -O index.xhtml 2> /dev/null
+  ###wget https://cran.r-project.org/package=phreeqc -O index.xhtml 2> /dev/null
- ###VER=`xmlstarlet sel -t -m "/_:html/_:body/_:table[1]/_:tr[1]/_:td[2]" -v . -n index.xhtml 2> /dev/null`
+  ###VER=`xmlstarlet sel -t -m "/_:html/_:body/_:table[1]/_:tr[1]/_:td[2]" -v . -n index.xhtml 2> /dev/null`
- VER=$(curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/phreeqc-version.txt)
+  VER=$(curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/phreeqc-version.txt)
- ver_major=$(echo "$VER" | cut -d '.' -f 1)
+  ver_major=$(echo "$VER" | cut -d '.' -f 1)
- ver_minor=$(echo "$VER" | cut -d '.' -f 2)
+  ver_minor=$(echo "$VER" | cut -d '.' -f 2)
- ver_patch=$(echo "$VER" | cut -d '.' -f 3)
+  ver_patch=$(echo "$VER" | cut -d '.' -f 3)
- ver_patch=$((ver_patch+1))
+  ver_patch=$((ver_patch+1))
 else
- ver_major=$(echo "$VER" | cut -d '.' -f 1)
+  ver_major=$(echo "$VER" | cut -d '.' -f 1)
- ver_minor=$(echo "$VER" | cut -d '.' -f 2)
+  ver_minor=$(echo "$VER" | cut -d '.' -f 2)
- ver_patch=$(echo "$VER" | cut -d '.' -f 3)
+  ver_patch=$(echo "$VER" | cut -d '.' -f 3)
 fi
 if [ -z "$ver_major" ] || [ -z "$ver_minor" ] || [ -z "$ver_patch" ]; then
- exit 1
+  exit 1
 fi
 VER="${ver_major}.${ver_minor}.${ver_patch}"
 export VER
@@ -36,16 +36,11 @@ export VER
 curl https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/ver.py -o ver.py
 HEAD=$(python3 ver.py)
 if [ -z "$REL" ]; then
- REL="$HEAD"
+  REL="$HEAD"
 fi
 
 # sed files
 /bin/sh jenkins-dist.sh -v ${VER} -r ${REL} -d ${DATE} -pr ${TAG}
 cd R
-mkdir -p phreeqc/man
+make VERSION=${VER} RELEASE_DATE=${DATE} build
-mkdir -p phreeqc/src/phreeqcpp
-mkdir -p phreeqc/R
-mkdir -p phreeqc/data
-echo "# Generated by roxygen2: do not edit by hand" > phreeqc/NAMESPACE
-# make VERSION=${VER} RELEASE_DATE=${DATE} build
 make VERSION=${VER} RELEASE_DATE=${DATE} check