debian/changelog

+hdf5 (1.10.5+repack-1~exp5) experimental; urgency=medium
+
+  * Fix debian rules to run dh_install for -java and -jni packages
+  * New patch fix-HDFFV-10745.patch: fix type error in java method
+    H5.H5Pget_sym_k (closes: #926098)
+
+ -- Gilles Filippini <pini@debian.org>  Mon, 29 Apr 2019 13:55:52 +0200
+
 hdf5 (1.10.5+repack-1~exp4) experimental; urgency=medium
 
   * Add missing dependencies to libhdf5-{mpich,openmpi}-dev (closes:

debian/patches/fix-HDFFV-10745.patch

+Index: hdf5/java/src/jni/h5pFCPLImp.c
+===================================================================
+--- hdf5.orig/java/src/jni/h5pFCPLImp.c
++++ hdf5/java/src/jni/h5pFCPLImp.c
+@@ -240,7 +240,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1sym_1k
+ 
+ done:
+     if (theArray)
+-        UNPIN_LONG_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0);
++        UNPIN_INT_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0);
+ 
+     return (jint)status;
+ } /* end Java_hdf_hdf5lib_H5_H5Pget_1sym_1k */

debian/patches/series

@@ -4,3 +4,4 @@ ullong_force.diff
 relax-version-check.patch
 fix-unaligned-accesses.patch
 reproducibility.patch
+fix-HDFFV-10745.patch

debian/rules

@@ -38,10 +38,6 @@ sercpppack = $(package)-cpp-$(SONAME_CXX)
 openmpipack = $(package)-openmpi-$(SONAME)
 mpichpack = $(package)-mpich-$(SONAME)
 
-PACKAGES_serial := $(serpack) $(package)-fortran-$(SONAME_F) $(package)-hl-$(SONAME_HL) $(package)-hl-fortran-$(SONAME_HL_F) $(package)-dev hdf5-helpers hdf5-tools $(sercpppack) $(package)-hl-cpp-$(SONAME_HL_CXX) $(PACKAGES_java)
-PACKAGES_openmpi := $(openmpipack) $(package)-openmpi-fortran-$(SONAME_F) $(package)-openmpi-hl-$(SONAME_HL) $(package)-openmpi-hl-fortran-$(SONAME_HL_F) $(package)-openmpi-cpp-$(SONAME_CXX) $(package)-openmpi-hl-cpp-$(SONAME_HL_CXX) $(package)-openmpi-dev
-PACKAGES_mpich := $(mpichpack) $(package)-mpich-fortran-$(SONAME_F) $(package)-mpich-hl-$(SONAME_HL) $(package)-mpich-hl-fortran-$(SONAME_HL_F) $(package)-mpich-cpp-$(SONAME_CXX) $(package)-mpich-hl-cpp-$(SONAME_HL_CXX) $(package)-mpich-dev
-
 # Crossbuild and multiarch variables
 DEB_HOST_GNU_TYPE   ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
 DEB_BUILD_GNU_TYPE  ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
@@ -133,6 +129,10 @@ SERIAL_ENV += JAVACFLAGS="-source 1.8 -target 1.8"
 
 # END - Configure flags and environment variables
 
+PACKAGES_serial := $(serpack) $(package)-fortran-$(SONAME_F) $(package)-hl-$(SONAME_HL) $(package)-hl-fortran-$(SONAME_HL_F) $(package)-dev hdf5-helpers hdf5-tools $(sercpppack) $(package)-hl-cpp-$(SONAME_HL_CXX) $(PACKAGES_java)
+PACKAGES_openmpi := $(openmpipack) $(package)-openmpi-fortran-$(SONAME_F) $(package)-openmpi-hl-$(SONAME_HL) $(package)-openmpi-hl-fortran-$(SONAME_HL_F) $(package)-openmpi-cpp-$(SONAME_CXX) $(package)-openmpi-hl-cpp-$(SONAME_HL_CXX) $(package)-openmpi-dev
+PACKAGES_mpich := $(mpichpack) $(package)-mpich-fortran-$(SONAME_F) $(package)-mpich-hl-$(SONAME_HL) $(package)-mpich-hl-fortran-$(SONAME_HL_F) $(package)-mpich-cpp-$(SONAME_CXX) $(package)-mpich-hl-cpp-$(SONAME_HL_CXX) $(package)-mpich-dev
+
 # Compose the packages' name flavor part from $(flavor)
 flavorpkg = $(subst -serial,,-$(flavor))
 
@@ -167,6 +167,7 @@ sonames:
 # Informative target
 info: VARIABLES := package pkgversion upstreamversion libversion $(foreach interface,$(INTERFACES),SONAME$(istr))
 info: VARIABLES += FLAVORS DH_OPTIONS DEBIAN_OUT
+info: VARIABLES += $(foreach flavor,serial openmpi mpich,PACKAGES_$(flavor))
 info:
 	@$(foreach var,$(VARIABLES), echo "$(shell printf "%30s" "$(var)") = $($(var))" &&) true