[med-svn] [Git][med-team/unifrac-tools][master] 2 commits: d/watch: version=5

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Jun 16 21:24:21 BST 2026 


Andreas Tille pushed to branch master at Debian Med / unifrac-tools


Commits:
7989053e by Andreas Tille at 2026-06-16T22:20:14+02:00
d/watch: version=5

- - - - -
cef3a8a1 by Andreas Tille at 2026-06-16T22:23:55+02:00
Fix FTBFS against HDF5 2.1.0 Closes: #1139615

- - - - -


3 changed files:

- debian/changelog
- debian/patches/enable_linking_to_shared_hdf5_lib.patch
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+unifrac-tools (1.4-4) UNRELEASED; urgency=medium
+
+  [ Andreas Tille ]
+  * d/watch: version=5
+
+  [ Gilles Filippini ]
+  * Fix FTBFS against HDF5 2.1.0
+    Closes: #1139615
+
+ -- Andreas Tille <tille at debian.org>  Tue, 16 Jun 2026 22:19:58 +0200
+
 unifrac-tools (1.4-3) unstable; urgency=medium
 
   * d/clean: new: clean build artifacts. (Closes: #1048281)


=====================================
debian/patches/enable_linking_to_shared_hdf5_lib.patch
=====================================
@@ -4,25 +4,42 @@ Origin: https://lists.debian.org/debian-med/2022/07/msg00078.html
 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


=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=4
+Version: 5
 
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-https://github.com/biocore/unifrac-binaries/tags .*/v?@ANY_VERSION@\.tar\.gz
+Template: Github
+Dist: https://github.com/biocore/unifrac-binaries



View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/1adef4e62965ceca8ad07db3d00ebdd81d09a2b4...cef3a8a1153e268a04785cfc043111a1c2650aa6

-- 
View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/1adef4e62965ceca8ad07db3d00ebdd81d09a2b4...cef3a8a1153e268a04785cfc043111a1c2650aa6
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