Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 25 Apr 2019 07:33:49 +0200
Description: use Debian packaged libhdf5

--- r-bioc-rhdf5lib.orig/configure.ac
+++ r-bioc-rhdf5lib/configure.ac
@@ -192,7 +192,7 @@
   #############################################
 
 #untar the lib
-BASEPBNAME="hdf5"
+BASEPBNAME="/usr/include/hdf5"
 
 dnl if we've already extracted the HDF5 source assume it's also configured and built
 if test -d src/${BASEPBNAME}; then 
@@ -214,6 +214,21 @@
 AC_SUBST(WITH_S3_VFD)
 AC_SUBST(SHAREDLIB_RPATH)
 
-AC_CONFIG_FILES([src/Makevars])
+HDF5_INCLUDE="/usr/include/hdf5/serial"
+HDF5_CXX_INCLUDE="/usr/include/hdf5/serial"
+HDF5_HL_INCLUDE="/usr/include/hdf5/serial"
+HDF5_HL_CXX_INCLUDE="/usr/include/hdf5/serial"
+AC_SUBST(HDF5_INCLUDE)
+AC_SUBST(HDF5_CXX_INCLUDE)
+AC_SUBST(HDF5_HL_INCLUDE)
+AC_SUBST(HDF5_HL_CXX_INCLUDE)
+
+# AC_CONFIG_FILES([src/Makevars])
+#     ... so try things manually
+sed -e "s+@HDF5_INCLUDE@+${HDF5_INCLUDE}+g" \
+    -e "s+@HDF5_LIB@+${HDF5_LIB}+g" \
+    -e "s+@ZLIB_LIB@+${ZLIB_LIB}+g" \
+    -e "s+@ZLIB_INCLUDE@+${ZLIB_INCLUDE}+g" \
+    src/Makevars.in > src/Makevars
 
 AC_OUTPUT
--- r-bioc-rhdf5lib.orig/src/Makevars.in
+++ r-bioc-rhdf5lib/src/Makevars.in
@@ -1,13 +1,14 @@
 BASEPBNAME=hdf5
-HDF5_INCLUDE="${BASEPBNAME}/src"
-HDF5_CXX_INCLUDE="${BASEPBNAME}/c++/src"
-HDF5_HL_INCLUDE="${BASEPBNAME}/hl/src"
-HDF5_HL_CXX_INCLUDE="${BASEPBNAME}/hl/c++/src"
-
-HDF5_LIB="${BASEPBNAME}/src/.libs/libhdf5.a"
-HDF5_CXX_LIB="${BASEPBNAME}/c++/src/.libs/libhdf5_cpp.a"
-HDF5_HL_LIB="${BASEPBNAME}/hl/src/.libs/libhdf5_hl.a"
-HDF5_HL_CXX_LIB="${BASEPBNAME}/hl/c++/src/.libs/libhdf5_hl_cpp.a"
+HDF5_INCLUDE="/usr/include/hdf5/serial"
+HDF5_CXX_INCLUDE="/usr/include/hdf5/serial"
+HDF5_HL_INCLUDE="/usr/include/hdf5/serial"
+HDF5_HL_CXX_INCLUDE="/usr/include/hdf5/serial"
+
+MULTIARCH=$(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+HDF5_LIB="/usr/lib/${MULTIARCH}/hdf5/serial/"
+HDF5_CXX_LIB="/usr/lib/${MULTIARCH}/hdf5/serial/libhdf5_cpp.a"
+HDF5_HL_LIB="/usr/lib/${MULTIARCH}/hdf5/serial/libhdf5_hl.a"
+HDF5_HL_CXX_LIB="/usr/lib/${MULTIARCH}/hdf5/serial/libhdf5_hl_cpp.a"
 
 ZLIB_LIB=@ZLIB_LIB_PATH@
 ZLIB_INCLUDE=@ZLIB_INCLUDE_PATH@
@@ -16,10 +17,8 @@
 USER_INCLUDE_DIR = ${R_PACKAGE_DIR}/include
 USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
 
-PKG_CPPFLAGS = -I"${USER_INCLUDE_DIR}" ${ZLIB_INCLUDE}
+PKG_CPPFLAGS = -I${HDF5_INCLUDE} ${ZLIB_INCLUDE}
 PKG_CFLAGS = ${ZLIB_LIB}
-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
-
 
 
 all: $(SHLIB)