Automatically build against hdf5 from rwinlib (fixes #128) (#129)

* Automatically build against hdf5 from rwinlib

* Cleanup appveyor config

* Stick with hdf5 1.8.16

* Cleanup to remove code that generates Makevars.win

* Fixes for WinBuilder

Author: jeroen

.Rbuildignore

@@ -28,3 +28,5 @@ wercker.yml
 ^docs$
 ^_pkgdown\.yml$
 ^cran-comments\.md$
+windows
+

Makefile

@@ -20,16 +20,6 @@ CHECKPATH := $(PKG_NAME).Rcheck
 CHECKLOG := `cat $(CHECKPATH)/00check.log`
 CURRENT_DIR := $(shell pwd)
 
-# Makevars used for CRAN release
-HDF5_VERSION_USE=1_8_14
-WINC=$${LIB_HDF5}/include
-WLIB=$${LIB_HDF5}/lib$${R_ARCH}
-HDF5R_CPPFLAGS=
-DEFINE_H5FREE_MEMORY=0
-HDF5R_LIBS=-L${WLIB} -lhdf5 -lhdf5_hl -lz -lm
-HDF5R_CFLAGS=-I${WINC}/hdf5 -I${WINC}/hdf5_hl -I${WINC}/cmakeconf -I${HDF5_VERSION_USE} -I.
-# Makevars end
-
 .PHONY: all build check manual install clean compileAttributes roxygen\
 	build-cran check-cran doc 
 
@@ -45,18 +35,6 @@ $(PKG_NAME)_$(PKG_VERSION).tar.gz: $(PKG_FILES)
 build-cran:
 	@make clean
 	@make roxygen
-	# Generate src/Makevars.win
-	sed -e 's#@HDF5_VERSION_USE@#${HDF5_VERSION_USE}#g' -e 's#@HDF5R_CFLAGS@#${HDF5R_CFLAGS}#g'  \
--e  's#@HDF5R_CPPFLAGS@#${HDF5R_CPPFLAGS}#g' -e  's#@HDF5R_LIBS@#${HDF5R_LIBS}#g' \
--e  's#@DEFINE_H5FREE_MEMORY@#${DEFINE_H5FREE_MEMORY}#g' \
-src/Makevars.in > src/Makevars.win
-	# Swap configure.win
-	@cp configure.win configure.win.temp; cat /dev/null >| configure.win
-	R CMD build --resave-data .
-	# Unswap configure.win
-	@cp configure.win.temp configure.win; rm configure.win.temp
-	# Remove src/Makevars.win
-	rm src/Makevars.win
 
 roxygen: $(R_FILES)
 	$(R) 'devtools::load_all(".", reset=TRUE, recompile = FALSE, export_all=FALSE)';

appveyor.yml

@@ -13,7 +13,6 @@ install:
 # Adapt as necessary starting from here
 
 build_script:
-  - Rscript -e "source('https://bioconductor.org/biocLite.R')"
   - travis-tool.sh install_deps
   - echo %CD%
   - ls
@@ -28,7 +27,6 @@ environment:
   WARNINGS_ARE_ERRORS: 1
   _R_CHECK_FORCE_SUGGESTS_: FALSE
   R_ARCH: x64
-  HDF5_VERSION_USE: 1_8_14
 
 artifacts:
   - path: '*.Rcheck\**\*.log'

src/Makevars.win

@@ -0,0 +1,23 @@
+WRAP = 1_8_16
+VERSION = 1.8.16
+RWINLIB = ../windows/hdf5-$(VERSION)
+PKG_LIBS = -L${RWINLIB}/lib-4.9.3${R_ARCH} -lhdf5 -lhdf5_hl -lz -lm 
+PKG_CPPFLAGS = -I${RWINLIB}/include -I$(WRAP) -I. -D__USE_MINGW_ANSI_STDIO
+
+all: winlibs
+
+OBJECTS = $(WRAP)/const_export.o $(WRAP)/datatype_export.o $(WRAP)/Wrapper_auto_H5A.o \
+	$(WRAP)/Wrapper_auto_H5.o $(WRAP)/Wrapper_auto_H5D.o $(WRAP)/Wrapper_auto_H5DS.o $(WRAP)/Wrapper_auto_H5E.o \
+	$(WRAP)/Wrapper_auto_H5F.o $(WRAP)/Wrapper_auto_H5G.o $(WRAP)/Wrapper_auto_H5I.o $(WRAP)/Wrapper_auto_H5IM.o \
+	$(WRAP)/Wrapper_auto_H5L.o $(WRAP)/Wrapper_auto_H5LT.o $(WRAP)/Wrapper_auto_H5O.o $(WRAP)/Wrapper_auto_H5P.o \
+	$(WRAP)/Wrapper_auto_H5R.o $(WRAP)/Wrapper_auto_H5S.o $(WRAP)/Wrapper_auto_H5TB.o $(WRAP)/Wrapper_auto_H5T.o \
+	$(WRAP)/Wrapper_auto_H5Z.o $(WRAP)/Wrapper_auto_H5FDcore.o $(WRAP)/Wrapper_auto_H5FDfamily.o \
+	$(WRAP)/Wrapper_auto_H5FDlog.o $(WRAP)/Wrapper_auto_H5FDsec2.o $(WRAP)/Wrapper_auto_H5FDstdio.o \
+	convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o
+
+winlibs:
+	@echo "Linking to HDF5 $(RWINLIB)"
+	"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "../tools/winlibs.R" $(VERSION)
+
+.PHONY: all winlibs
+

tools/winlibs.R

@@ -0,0 +1,9 @@
+# Build against rwinlib build of hdf5
+VERSION <- commandArgs(TRUE)
+if(!file.exists(sprintf("../windows/hdf5-%s/include/hdf5.h", VERSION))){
+  download.file(sprintf("https://github.com/rwinlib/hdf5/archive/v%s.zip", VERSION),
+                "lib.zip", quiet = TRUE)
+  dir.create("../windows", showWarnings = FALSE)
+  unzip("lib.zip", exdir = "../windows")
+  unlink("lib.zip")
+}