working on R dist

.gitignore

@@ -21,23 +21,24 @@
 /libx64
 /x64
 
+# dist files
+**/*.dist
+doc/NOTICE
+doc/README
+doc/RELEASE
+
+# TIMESTAMP files
+**/*.TIMESTAMP
+
 # /R/
-/R/Amm.ascii
+/R/*.tar.gz
-/R/iso.ascii
+/R/*.ascii
-/R/llnl.ascii
-/R/minteq.ascii
-/R/minteq.v4.ascii
-/R/phreeqc.ascii
-/R/pitzer.ascii
-/R/sit.ascii
-/R/wateq4f.ascii
-/R/phreeqc.Rcheck
-/R/build-databases.Rout
-/R/build-examples.Rout
 /R/.RData
+/R/*.Rout
+/R/phreeqc.Rcheck
 
 # /R/phreeqc/
-/R/phreeqc/NAMESPACE
+/R/phreeqc
 
 # /R/phreeqc/data/
 /R/phreeqc/data/csv.RData

R/DESCRIPTION.in

@@ -1,18 +1,18 @@
 Package: phreeqc
-Version: @VERSION@
 Title: R Interface to Geochemical Modeling Software
+Version: @VERSION@
 License: GPL-3
 NeedsCompilation: yes
-Depends:
+Depends: R (>= 3.5.0)
-    R (>= 3.0)
+Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
-Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions  
+    from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
-    from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,  
+    R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUNDIALS
-    R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
 URL: https://www.usgs.gov/software/phreeqc-version-3
 Description: A geochemical modeling program developed by the US Geological
     Survey that is designed to perform a wide variety of aqueous geochemical
     calculations, including speciation, batch-reaction, one-dimensional 
     reactive-transport, and inverse geochemical calculations.
 Maintainer: S.R. Charlton <charlton@usgs.gov>
+BugReports: https://github.com/usgs-coupled/iphreeqc/issues
 LazyData: yes
 Encoding: UTF-8

R/Makefile

@@ -269,7 +269,7 @@ DATA = \
 	$(DATADIR)/databases.rda \
 	$(DATADIR)/examples.rda
 
-all: export_sed $(PSRC) $(XSRC) $(DATA) $(MAN)/phreeqc-package.Rd
+all: $(PSRC) $(XSRC) $(DATA) $(MAN)/phreeqc-package.Rd
 
 $(DATADIR)/databases.rda : $(DBS) build-databases.R
 	rm -f .RData
@@ -290,12 +290,16 @@ $(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
+document : $(MAN)/phreeqc-package.Rd
-	rm -f $(RDFILES)
-	rm -f .RData
-	R --no-save --no-restore CMD BATCH roxygenize.R
-	touch $(MAN)/phreeqc-package.Rd
 
+$(MAN)/phreeqc-package.Rd : $(TOPDIR)/R/phreeqc.R $(TOPDIR)/DESCRIPTION $(TOPDIR)/NAMESPACE
+	rm -f $(RDFILES)
+	Rscript -e 'devtools::document("phreeqc")'
+
+build : phreeqc_$(VERSION).tar.gz
+
+phreeqc_$(VERSION).tar.gz : $(MAN)/phreeqc-package.Rd
+	Rscript -e 'devtools::build("phreeqc")'
 
 ##$(PSRC): $(DEST)
 
@@ -821,28 +825,52 @@ $(INST)/ex2 : ../phreeqc3-examples/ex2
 check : all
 	R CMD check --as-cran phreeqc
 
+#check_built : phreeqc_$(VERSION).tar.gz
+
+check_built : phreeqc_$(VERSION).tar.gz
+	Rscript -e "devtools::check_built(path=\"phreeqc_$(VERSION).tar.gz\")"
+
 valgrind : install
-	R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
+	echo R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
 
 install : all
-	R CMD INSTALL --build phreeqc
+	echo R CMD INSTALL --build phreeqc
 
+$(TOPDIR)/NAMESPACE : NAMESPACE
+	$(CP) $< $@
 
-phreeqc/R/phreeqc.R : export_sed
+$(TOPDIR)/R/phreeqc.R : phreeqc.R.in phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
-
+	rm phreeqc.R-*.TIMESTAMP
-phreeqc/DESCRIPTION : export_sed
-
-export_sed :
-	sed \
-	 -e 's/@VERSION@/$(VERSION)/g' \
-	< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
 	sed \
 	 -e 's/@VERSION@/$(VERSION)/g' \
 	 -e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
 	< phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
+	touch phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
 
-build : all
+phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP :
-	R CMD build --resave-data phreeqc
+	touch phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
+
+$(TOPDIR)/DESCRIPTION : DESCRIPTION.in DESCRIPTION-$(VERSION).TIMESTAMP
+	rm DESCRIPTION-*.TIMESTAMP
+	sed \
+	 -e 's/@VERSION@/$(VERSION)/g' \
+	< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
+	touch DESCRIPTION-$(VERSION).TIMESTAMP
+
+DESCRIPTION-$(VERSION).TIMESTAMP :
+	touch DESCRIPTION-$(VERSION).TIMESTAMP
+
+# export_sed :
+# 	sed \
+# 	 -e 's/@VERSION@/$(VERSION)/g' \
+# 	< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
+# 	sed \
+# 	 -e 's/@VERSION@/$(VERSION)/g' \
+# 	 -e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
+# 	< phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
+
+# build : all
+# 	R CMD build --resave-data phreeqc
 
 uninstall :
 	R CMD REMOVE phreeqc

R/NAMESPACE

@@ -0,0 +1,45 @@
+# Generated by roxygen2: do not edit by hand
+
+export(phrAccumulateLine)
+export(phrClearAccumulatedLines)
+export(phrGetAccumulatedLines)
+export(phrGetComponentList)
+export(phrGetDumpFileName)
+export(phrGetDumpFileOn)
+export(phrGetDumpStrings)
+export(phrGetDumpStringsOn)
+export(phrGetErrorFileName)
+export(phrGetErrorFileOn)
+export(phrGetErrorStrings)
+export(phrGetErrorStringsOn)
+export(phrGetLogFileName)
+export(phrGetLogFileOn)
+export(phrGetLogStrings)
+export(phrGetLogStringsOn)
+export(phrGetOutputFileName)
+export(phrGetOutputFileOn)
+export(phrGetOutputStrings)
+export(phrGetOutputStringsOn)
+export(phrGetSelectedOutput)
+export(phrGetSelectedOutputFileName)
+export(phrGetWarningStrings)
+export(phrLoadDatabase)
+export(phrLoadDatabaseString)
+export(phrRunAccumulated)
+export(phrRunFile)
+export(phrRunString)
+export(phrSetDumpFileName)
+export(phrSetDumpFileOn)
+export(phrSetDumpStringsOn)
+export(phrSetErrorFileName)
+export(phrSetErrorFileOn)
+export(phrSetErrorStringsOn)
+export(phrSetLogFileName)
+export(phrSetLogFileOn)
+export(phrSetLogStringsOn)
+export(phrSetOutputFileName)
+export(phrSetOutputFileOn)
+export(phrSetOutputStringsOn)
+export(phrSetSelectedOutputFileName)
+export(phrSetSelectedOutputFileOn)
+useDynLib(phreeqc, .registration = TRUE)

jenkins-R-dist.sh

@@ -9,6 +9,13 @@ fi
 DATE=$(date -d $DATE --rfc-3339=date)
 export DATE
 
+#
+# create directories
+#
+mkdir -p R/phreeqc/R
+mkdir -p R/phreeqc/src/phreeqcpp
+mkdir -p R/phreeqc/data
+
 #
 # set VER
 #
@@ -44,5 +51,4 @@ export REL
 # sed files
 /bin/sh jenkins-dist.sh -v ${VER} -r ${REL} -d ${DATE} -pr ${TAG}
 cd R
-make VERSION=${VER} RELEASE_DATE=${DATE} check
+make VERSION=${VER} RELEASE_DATE=${DATE} check_built
-make VERSION=${VER} RELEASE_DATE=${DATE} build