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working on R dist
This commit is contained in:
Charlton, Scott R
parent
6d34a2a8cb
commit
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27
.gitignore
vendored
27
.gitignore
vendored
@ -21,23 +21,24 @@
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/libx64
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/x64
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# dist files
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**/*.dist
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doc/NOTICE
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doc/README
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doc/RELEASE
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# TIMESTAMP files
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**/*.TIMESTAMP
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# /R/
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/R/Amm.ascii
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/R/iso.ascii
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/R/llnl.ascii
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/R/minteq.ascii
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/R/minteq.v4.ascii
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/R/phreeqc.ascii
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/R/pitzer.ascii
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/R/sit.ascii
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/R/wateq4f.ascii
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/R/phreeqc.Rcheck
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/R/build-databases.Rout
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/R/build-examples.Rout
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/R/*.tar.gz
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/R/*.ascii
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/R/.RData
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/R/*.Rout
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/R/phreeqc.Rcheck
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# /R/phreeqc/
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/R/phreeqc/NAMESPACE
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/R/phreeqc
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# /R/phreeqc/data/
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/R/phreeqc/data/csv.RData
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@ -1,18 +1,18 @@
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Package: phreeqc
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Version: @VERSION@
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Title: R Interface to Geochemical Modeling Software
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Version: @VERSION@
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License: GPL-3
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NeedsCompilation: yes
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Depends:
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R (>= 3.0)
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Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
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from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
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R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
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Depends: R (>= 3.5.0)
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Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
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from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
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R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUNDIALS
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URL: https://www.usgs.gov/software/phreeqc-version-3
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Description: A geochemical modeling program developed by the US Geological
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Survey that is designed to perform a wide variety of aqueous geochemical
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calculations, including speciation, batch-reaction, one-dimensional
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reactive-transport, and inverse geochemical calculations.
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Maintainer: S.R. Charlton <charlton@usgs.gov>
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BugReports: https://github.com/usgs-coupled/iphreeqc/issues
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LazyData: yes
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Encoding: UTF-8
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64
R/Makefile
64
R/Makefile
@ -269,7 +269,7 @@ DATA = \
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$(DATADIR)/databases.rda \
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$(DATADIR)/examples.rda
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all: export_sed $(PSRC) $(XSRC) $(DATA) $(MAN)/phreeqc-package.Rd
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all: $(PSRC) $(XSRC) $(DATA) $(MAN)/phreeqc-package.Rd
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$(DATADIR)/databases.rda : $(DBS) build-databases.R
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rm -f .RData
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@ -290,12 +290,16 @@ $(DATADIR)/examples.rda : $(EXS) build-examples.R
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R --no-save --no-restore CMD BATCH build-examples.R
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rm -f .RData
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roxygenize $(MAN)/phreeqc-package.Rd : phreeqc/R/phreeqc.R
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rm -f $(RDFILES)
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rm -f .RData
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R --no-save --no-restore CMD BATCH roxygenize.R
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touch $(MAN)/phreeqc-package.Rd
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document : $(MAN)/phreeqc-package.Rd
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$(MAN)/phreeqc-package.Rd : $(TOPDIR)/R/phreeqc.R $(TOPDIR)/DESCRIPTION $(TOPDIR)/NAMESPACE
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rm -f $(RDFILES)
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Rscript -e 'devtools::document("phreeqc")'
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build : phreeqc_$(VERSION).tar.gz
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phreeqc_$(VERSION).tar.gz : $(MAN)/phreeqc-package.Rd
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Rscript -e 'devtools::build("phreeqc")'
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##$(PSRC): $(DEST)
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@ -821,28 +825,52 @@ $(INST)/ex2 : ../phreeqc3-examples/ex2
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check : all
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R CMD check --as-cran phreeqc
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#check_built : phreeqc_$(VERSION).tar.gz
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check_built : phreeqc_$(VERSION).tar.gz
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Rscript -e "devtools::check_built(path=\"phreeqc_$(VERSION).tar.gz\")"
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valgrind : install
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R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
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echo R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < valgrind.R 2>&1 | tee valgrind.full.out
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install : all
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R CMD INSTALL --build phreeqc
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echo R CMD INSTALL --build phreeqc
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$(TOPDIR)/NAMESPACE : NAMESPACE
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$(CP) $< $@
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phreeqc/R/phreeqc.R : export_sed
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phreeqc/DESCRIPTION : export_sed
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export_sed :
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sed \
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-e 's/@VERSION@/$(VERSION)/g' \
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< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
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$(TOPDIR)/R/phreeqc.R : phreeqc.R.in phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
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rm phreeqc.R-*.TIMESTAMP
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sed \
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-e 's/@VERSION@/$(VERSION)/g' \
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-e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
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< phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
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touch phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
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build : all
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R CMD build --resave-data phreeqc
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phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP :
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touch phreeqc.R-$(VERSION)_$(RELEASE_DATE).TIMESTAMP
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$(TOPDIR)/DESCRIPTION : DESCRIPTION.in DESCRIPTION-$(VERSION).TIMESTAMP
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rm DESCRIPTION-*.TIMESTAMP
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sed \
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-e 's/@VERSION@/$(VERSION)/g' \
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< DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
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touch DESCRIPTION-$(VERSION).TIMESTAMP
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DESCRIPTION-$(VERSION).TIMESTAMP :
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touch DESCRIPTION-$(VERSION).TIMESTAMP
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# export_sed :
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# sed \
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# -e 's/@VERSION@/$(VERSION)/g' \
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# < DESCRIPTION.in > $(TOPDIR)/DESCRIPTION
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# sed \
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# -e 's/@VERSION@/$(VERSION)/g' \
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# -e 's/@RELEASE_DATE@/$(RELEASE_DATE)/g' \
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# < phreeqc.R.in > $(TOPDIR)/R/phreeqc.R
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# build : all
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# R CMD build --resave-data phreeqc
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uninstall :
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R CMD REMOVE phreeqc
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45
R/NAMESPACE
Normal file
45
R/NAMESPACE
Normal file
@ -0,0 +1,45 @@
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# Generated by roxygen2: do not edit by hand
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export(phrAccumulateLine)
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export(phrClearAccumulatedLines)
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export(phrGetAccumulatedLines)
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export(phrGetComponentList)
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export(phrGetDumpFileName)
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export(phrGetDumpFileOn)
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export(phrGetDumpStrings)
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export(phrGetDumpStringsOn)
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export(phrGetErrorFileName)
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export(phrGetErrorFileOn)
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export(phrGetErrorStrings)
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export(phrGetErrorStringsOn)
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export(phrGetLogFileName)
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export(phrGetLogFileOn)
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export(phrGetLogStrings)
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export(phrGetLogStringsOn)
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export(phrGetOutputFileName)
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export(phrGetOutputFileOn)
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export(phrGetOutputStrings)
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export(phrGetOutputStringsOn)
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export(phrGetSelectedOutput)
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export(phrGetSelectedOutputFileName)
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export(phrGetWarningStrings)
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export(phrLoadDatabase)
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export(phrLoadDatabaseString)
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export(phrRunAccumulated)
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export(phrRunFile)
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export(phrRunString)
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export(phrSetDumpFileName)
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export(phrSetDumpFileOn)
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export(phrSetDumpStringsOn)
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export(phrSetErrorFileName)
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export(phrSetErrorFileOn)
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export(phrSetErrorStringsOn)
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export(phrSetLogFileName)
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export(phrSetLogFileOn)
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export(phrSetLogStringsOn)
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export(phrSetOutputFileName)
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export(phrSetOutputFileOn)
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export(phrSetOutputStringsOn)
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export(phrSetSelectedOutputFileName)
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export(phrSetSelectedOutputFileOn)
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useDynLib(phreeqc, .registration = TRUE)
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@ -9,6 +9,13 @@ fi
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DATE=$(date -d $DATE --rfc-3339=date)
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export DATE
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#
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# create directories
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#
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mkdir -p R/phreeqc/R
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mkdir -p R/phreeqc/src/phreeqcpp
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mkdir -p R/phreeqc/data
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#
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# set VER
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#
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@ -44,5 +51,4 @@ export REL
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# sed files
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/bin/sh jenkins-dist.sh -v ${VER} -r ${REL} -d ${DATE} -pr ${TAG}
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cd R
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make VERSION=${VER} RELEASE_DATE=${DATE} check
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make VERSION=${VER} RELEASE_DATE=${DATE} build
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make VERSION=${VER} RELEASE_DATE=${DATE} check_built
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