Bug#1090898: fast5: autopkgtest regressions with HDF5 1.14

[pini]

Control: tags -1 + patch

Le 2024-12-20 18:35, Gilles Filippini a écrit :

Since the upload of hdf5 1.14.5 to unstable the autopkgtest of fast5 have

regressed on all architectures.

See for instance:
https://ci.debian.net/packages/f/fast5/testing/amd64/55590612/

Please find attached a patch proposal.

Best,
_g.
diff -Nru fast5-0.6.5/debian/changelog fast5-0.6.5/debian/changelog
--- fast5-0.6.5/debian/changelog	2024-08-21 16:53:26.000000000 +0200
+++ fast5-0.6.5/debian/changelog	2024-12-21 22:43:21.000000000 +0100
@@ -1,3 +1,11 @@
+fast5 (0.6.5-8.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * New patch hdf5-1.14.patch: set -DH5_USE_110_API into src/Makefile
+    as well, to fix autopkgtest
+
+ -- Gilles Filippini <p...@debian.org>  Sat, 21 Dec 2024 22:43:21 +0100
+
 fast5 (0.6.5-8) unstable; urgency=medium
 
   * d/control: set CPPFLAGS to add -DH5_USE_110_API.
diff -Nru fast5-0.6.5/debian/patches/hdf5-1.14.patch fast5-0.6.5/debian/patches/hdf5-1.14.patch
--- fast5-0.6.5/debian/patches/hdf5-1.14.patch	1970-01-01 01:00:00.000000000 +0100
+++ fast5-0.6.5/debian/patches/hdf5-1.14.patch	2024-12-21 22:43:21.000000000 +0100
@@ -0,0 +1,13 @@
+Index: fast5-0.6.5/src/Makefile
+===================================================================
+--- fast5-0.6.5.orig/src/Makefile
++++ fast5-0.6.5/src/Makefile
+@@ -24,7 +24,7 @@ EXTRA_TARGETS = f5dump f5pack
+ HPP_FILES := $(addprefix ${FAST5_DIR}/, fast5.hpp fast5/hdf5_tools.hpp fast5/Huffman_Packer.hpp fast5/Bit_Packer.hpp)
+ 
+ CXXFLAGS += -std=c++11 -O0 -g3 -ggdb -fno-eliminate-unused-debug-types -Wall -Wextra -Wpedantic
+-CPPFLAGS += -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR)
++CPPFLAGS += -isystem ${HDF5_INCLUDE_DIR} -I $(FAST5_DIR) -DH5_USE_110_API
+ EXTRA_CPPFLAGS := -isystem ${TCLAP_DIR}/include -I ${HPPTOOLS_DIR}/include
+ LDFLAGS += -L${HDF5_LIB_DIR} -Wl,--rpath=${HDF5_LIB_DIR} -l${HDF5_LIB} -lpthread -lz -ldl
+ 
diff -Nru fast5-0.6.5/debian/patches/series fast5-0.6.5/debian/patches/series
--- fast5-0.6.5/debian/patches/series	2024-08-21 16:53:26.000000000 +0200
+++ fast5-0.6.5/debian/patches/series	2024-12-21 22:43:21.000000000 +0100
@@ -1,3 +1,4 @@
 rpath.patch
 gcc-12.patch
 build-flags.patch
+hdf5-1.14.patch

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