Michael R. Crusoe pushed to branch master at Debian Med / unifrac-tools
Commits: 5ab28fa7 by Michael R. Crusoe at 2023-08-17T14:49:44+02:00 Adapt baseline patch even further to enable building on non-x86. - - - - - a9525b85 by Michael R. Crusoe at 2023-08-17T14:54:08+02:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/patches/baseline.patch - debian/patches/enable-debug-flag.patch - debian/patches/enable_linking_to_shared_hdf5_lib.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +unifrac-tools (1.3.2-4) unstable; urgency=medium + + * Team upload. + * Adapt baseline patch even further to enable building on non-x86. + + -- Michael R. Crusoe <[email protected]> Thu, 17 Aug 2023 14:54:08 +0200 + unifrac-tools (1.3.2-3) unstable; urgency=medium [ Adrian Bunk ] ===================================== debian/patches/baseline.patch ===================================== @@ -5,9 +5,9 @@ Forwarded: not-needed Last-Update: 2023-07-26 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ---- unifrac-tools-1.3.2.orig/src/Makefile -+++ unifrac-tools-1.3.2/src/Makefile -@@ -44,7 +44,7 @@ ifeq ($(PLATFORM),Darwin) +--- unifrac-tools.orig/src/Makefile ++++ unifrac-tools/src/Makefile +@@ -44,7 +44,7 @@ else AVX2 := $(shell grep "^flags" /proc/cpuinfo | head -n 1 | grep -c avx2) LDDFLAGS = -shared @@ -16,7 +16,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ endif EXEFLAGS = -@@ -77,39 +77,6 @@ ifndef NOGPU +@@ -77,39 +77,6 @@ endif endif @@ -56,3 +56,32 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ifeq (,$(findstring pgi,$(COMPILER))) ifneq ($(PERFORMING_CONDA_BUILD),True) # basically, not gcc +--- unifrac-tools.orig/combined/libssu.c ++++ unifrac-tools/combined/libssu.c +@@ -24,6 +24,8 @@ + + /* Pick the right libssu implementation */ + static const char *ssu_get_lib_name() { ++ const char *ssu = "libssu_nv.so"; ++#if defined (__i386__) || defined (__x86_64__) + __builtin_cpu_init (); + bool has_avx = __builtin_cpu_supports ("avx"); + bool has_avx2 = __builtin_cpu_supports ("avx2"); +@@ -35,7 +37,6 @@ + has_avx2 = false; + } + +- const char *ssu = "libssu_nv.so"; + if (has_avx) { + if ((env_max_cpu!=NULL) && (strcmp(env_max_cpu,"avx")==0)) { + has_avx2 = false; +@@ -52,6 +53,9 @@ + } + ssu="libssu_cpu_basic.so"; + } ++#else ++ ssu="libssu_cpu_basic.so"; ++#endif + + const char* env_cpu_info = getenv("UNIFRAC_CPU_INFO"); + if ((env_cpu_info!=NULL) && (env_cpu_info[0]=='Y')) { ===================================== debian/patches/enable-debug-flag.patch ===================================== @@ -1,9 +1,9 @@ Description: Add debug flag to cppflags Author: Nilesh Patra <[email protected]> Last-Update: 2023-01-05 ---- a/src/Makefile -+++ b/src/Makefile -@@ -118,7 +118,7 @@ ifeq (,$(findstring pgi,$(COMPILER))) +--- unifrac-tools.orig/src/Makefile ++++ unifrac-tools/src/Makefile +@@ -85,7 +85,7 @@ endif ===================================== debian/patches/enable_linking_to_shared_hdf5_lib.patch ===================================== @@ -3,9 +3,9 @@ Date: Wed, 27 Jul 2022 07:44:28 -0400 Origin: https://lists.debian.org/debian-med/2022/07/msg00078.html Description: Enable linking ro shared hdf5 library ---- a/src/Makefile -+++ b/src/Makefile -@@ -55,7 +55,7 @@ else +--- unifrac-tools.orig/src/Makefile ++++ unifrac-tools/src/Makefile +@@ -55,7 +55,7 @@ MPFLAG = -fopenmp endif @@ -14,7 +14,7 @@ Description: Enable linking ro shared hdf5 library CPPFLAGS += $(MPFLAG) UNIFRAC_FILES = unifrac_internal.o unifrac_cmp_cpu.o -@@ -142,8 +142,8 @@ $(FPD): faithpd.cpp tree.o biom.o biom_i +@@ -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 $(BLASLIB) -lpthread lib$(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) View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/699abd4cc76869bd6c0d4467aea94306a8a4266b...a9525b858ee784c610a30557f80964a80f7aae36 -- View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/699abd4cc76869bd6c0d4467aea94306a8a4266b...a9525b858ee784c610a30557f80964a80f7aae36 You're receiving this email because of your account on salsa.debian.org.
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