[From nobody Thu Jul 2 14:21:04 2026 Received: (at submit) by bugs.debian.org; 10 Jun 2026 09:28:26 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-10.6 required=4.0 tests=BAYES_00,FOURLA, FROMDEVELOPER,FVGT_m_MULTI_ODD,HEADER_FROM_DIFFERENT_DOMAINS, PGPSIGNATURE,SPF_HELO_NONE,SPF_PASS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 113; hammy, 150; neutral, 191; spammy, 0. spammytokens: hammytokens:0.000-+--HTo:N*Debian, 0.000-+--H*Ad:N*Bug, 0.000-+--H*Ad:N*Tracking, 0.000-+--sk:taint_o, 0.000-+--sk:TAINT_O Return-path: <SRS0=a6bP=EG=debian.org=pini@bou-fi.net> Received: from mail.bou-fi.net ([51.255.91.82]:57380) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <SRS0=a6bP=EG=debian.org=pini@bou-fi.net>) id 1wXFEX-00Ea46-32 for submit@bugs.debian.org; Wed, 10 Jun 2026 09:28:26 +0000 Content-Type: multipart/mixed; boundary="===============1546972846141911774==" Authentication-Results: mail.bou-fi.net; auth=pass smtp.mailfrom=pini@debian.org MIME-Version: 1.0 From: Gilles Filippini <pini@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: unifrac-tools: FTBFS against HDF5 2.1.0 Message-ID: <178108370351.25536.1213529281115429015.reportbug@pinibrem14> Date: Wed, 10 Jun 2026 11:28:23 +0200 X-Spamd-Bar: -- Delivered-To: submit@bugs.debian.org This is a multi-part MIME message sent by reportbug. --===============1546972846141911774== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline Source: unifrac-tools Version: 1.4-3 Severity: important Tags: ftbfs patch -----BEGIN PGP SIGNED MESSAGE----- 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 -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAmopLjcACgkQ7+hsbH/+ z4Nk7gf/WJ35CjyKghkkpt8wi9E1NB+MZdYipy9rRMF0H7ErZnII1inYT50JaTKb WThrpfI5Ovoet8x8XFn1JdjfvTaQg/t8Yjo1snUdH+LN0Z5vNjI+2i0Ed/z8crRn IWnAAM9O6Hnu23XzuPPM2jL9vpX7CVIPON9k3MhGdXqO3vRYFL+BOzRpQekKCsTo F4IkUUXAcND5dpnE8o42cllzgTKEKo3fIn0DpyzZr1G7tffleAvqAqkWmi5aYdgR +rKr4OYNobwBndSK9w7aq985WPLRHY58j5it0TrxiUHQATQknbfutya7/RdLOQRQ T2CGpzfZd1rhmqI5tFsmKnEzUI7pcQ== =vp2W -----END PGP SIGNATURE----- --===============1546972846141911774== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="unifrac-tools.debdiff" 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@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 --===============1546972846141911774==-- ]