[Debian-med-packaging] Bug#1139615: unifrac-tools: FTBFS against HDF5 2.1.0

Gilles Filippini pini at debian.org
Wed Jun 10 10:28:23 BST 2026 

Source: unifrac-tools
Version: 1.4-3
Severity: important
Tags: ftbfs patch

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Hash: SHA512

Hi,

During a test rebuild of HDF5's reverse dependencies against HDF5 2.1.0
currently in experimental, unifrac-tools FTBFS because its build
toolchain doesn't support this new major release.

The attached patch is a workaround for this issue and supports both
HDF5 1.14.6 in unstable and HDF5 2.1.0 in experimental.

Best,
_g.


- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-44-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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diff -Nru unifrac-tools-1.4/debian/changelog unifrac-tools-1.4/debian/changelog
--- unifrac-tools-1.4/debian/changelog	2023-12-03 13:21:32.000000000 +0100
+++ unifrac-tools-1.4/debian/changelog	2026-06-05 16:37:17.000000000 +0200
@@ -1,3 +1,10 @@
+unifrac-tools (1.4-3.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <pini at debian.org>  Fri, 05 Jun 2026 16:37:17 +0200
+
 unifrac-tools (1.4-3) unstable; urgency=medium
 
   * d/clean: new: clean build artifacts. (Closes: #1048281)
diff -Nru unifrac-tools-1.4/debian/patches/enable_linking_to_shared_hdf5_lib.patch unifrac-tools-1.4/debian/patches/enable_linking_to_shared_hdf5_lib.patch
--- unifrac-tools-1.4/debian/patches/enable_linking_to_shared_hdf5_lib.patch	2023-12-03 13:21:32.000000000 +0100
+++ unifrac-tools-1.4/debian/patches/enable_linking_to_shared_hdf5_lib.patch	2026-06-05 16:37:17.000000000 +0200
@@ -4,25 +4,42 @@
 Description: Enable linking ro shared hdf5 library
 Forwarded: not-needed
 
---- unifrac-tools.orig/src/Makefile
-+++ unifrac-tools/src/Makefile
-@@ -55,7 +55,7 @@
- 	MPFLAG = -fopenmp
+Index: unifrac-tools-1.4/src/Makefile
+===================================================================
+--- unifrac-tools-1.4.orig/src/Makefile
++++ unifrac-tools-1.4/src/Makefile
+@@ -1,6 +1,6 @@
+ .PHONY: all main api test test_binaries install clean rapi_test
+ 
+-CXX := h5c++
++CXX := h5c++ -shlib
+ 
+ PLATFORM := $(shell uname -s)
+ COMPILER := $(shell ($(CXX) -v 2>&1) | tr A-Z a-z )
+@@ -72,7 +72,7 @@ ifndef NOGPU
+ 		    # optional info
+ 		    ACCCPPFLAGS += -Minfo=accel
+                 endif
+-	        LDDFLAGS += -shlib -acc -Bstatic_pgi
++	        LDDFLAGS += -acc -Bstatic_pgi
+ 	        EXEFLAGS += -acc -Bstatic_pgi
+ 	endif
  endif
+@@ -103,14 +103,14 @@ test_api: test_api.cpp tree.o tsv.o test
+ 	$(CXX) $(CPPFLAGS) $(EXEFLAGS) test_api.cpp -o test_api tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
  
--LDDFLAGS += $(MPFLAG)
-+LDDFLAGS += $(MPFLAG) -shlib
- CPPFLAGS += $(MPFLAG)
+ $(SSU): su.cpp tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
+-	$(CXX) $(CPPFLAGS) $(EXEFLAGS) su.cpp -o $(SSU) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
++	$(CXX) $(CPPFLAGS) $(EXEFLAGS) su.cpp -o $(SSU) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
  
- UNIFRAC_FILES = unifrac_internal.o unifrac_cmp_cpu.o
-@@ -109,8 +109,8 @@
- 	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $(FPD) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
+ $(FPD): faithpd.cpp tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
+-	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $(FPD) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
++	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o $(FPD) tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -llz4 $(BLASLIB) -lpthread
  
  lib$(SSU).so: tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
--#	$(CXX) $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(BLASLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
+ #	$(CXX) $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(BLASLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
 -	$(CXX) $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,lib$(SSU).so.0 $(BLASLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
-+#	$(CXX) $(LDDFLAGS) -o lib$(SSU).so tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(BLASLIB) -L$(PREFIX)/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
-+	$(CXX) $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,lib$(SSU).so.0 $(BLASLIB) -L$(PREFIX)/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
++	$(CXX) $(LDDFLAGS) -o lib$(SSU).so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -Wl,-soname,lib$(SSU).so.0 $(BLASLIB)
  	ln -sf lib$(SSU).so.0 lib$(SSU).so
  	# FIXME: Should build static lib as well
  	# $(CXX) $(LDDFLAGS) -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib

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