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 <[email protected]> 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@-$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 You're receiving this email because of your account on salsa.debian.org. 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