Michael R. Crusoe pushed to branch master at Debian Med / unifrac-tools
Commits: 5c7db14a by Michael R. Crusoe at 2023-08-17T16:58:32+02:00 Add patch to improve build hardening. - - - - - 6c8284ac by Michael R. Crusoe at 2023-08-17T17:01:48+02:00 routine-update: Ready to upload to unstable - - - - - 8 changed files: - debian/changelog - debian/patches/enable-debug-flag.patch - debian/patches/enable_linking_to_shared_hdf5_lib.patch - + debian/patches/hardening - debian/patches/python3.patch - debian/patches/remove_non-free_headers.patch - debian/patches/series - debian/patches/soname.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +unifrac-tools (1.3.2-5) unstable; urgency=medium + + * Team upload. + * Add patch to improve build hardening. + + -- Michael R. Crusoe <[email protected]> Thu, 17 Aug 2023 17:01:48 +0200 + unifrac-tools (1.3.2-4) unstable; urgency=medium * Team upload. ===================================== debian/patches/enable-debug-flag.patch ===================================== @@ -1,6 +1,7 @@ Description: Add debug flag to cppflags Author: Nilesh Patra <[email protected]> Last-Update: 2023-01-05 +Forwarded: not-needed --- unifrac-tools.orig/src/Makefile +++ unifrac-tools/src/Makefile @@ -85,7 +85,7 @@ ===================================== debian/patches/enable_linking_to_shared_hdf5_lib.patch ===================================== @@ -2,6 +2,7 @@ From: [email protected] (Aaron M. Ucko) 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 +Forwarded: not-needed --- unifrac-tools.orig/src/Makefile +++ unifrac-tools/src/Makefile ===================================== debian/patches/hardening ===================================== @@ -0,0 +1,39 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Use CPPFLAGS, CFLAGS, and LDFLAGS +Forwarded: https://github.com/biocore/unifrac-binaries/pull/46 + +--- unifrac-tools.orig/combined/Makefile ++++ unifrac-tools/combined/Makefile +@@ -13,10 +13,10 @@ + endif + + libssu.o: libssu.c +- $(CC) -c libssu.c -fPIC ++ $(CC) $(CPPFLAGS) $(CFLAGS) -c libssu.c -fPIC + + libssu.so: libssu.o +- $(CC) -shared -o libssu.so libssu.o -fPIC -ldl ++ $(CC) -shared -o libssu.so libssu.o -fPIC -ldl $(LDFLAGS) + + install: libssu.so + rm -f ${PREFIX}/lib//libssu.so; cp libssu.so ${PREFIX}/lib/ +--- unifrac-tools.orig/test/Makefile ++++ unifrac-tools/test/Makefile +@@ -1,8 +1,5 @@ + .PHONY: test_binaries test + +-CFLAGS := +-LDFLAGS := +- + ifeq ($(PREFIX),) + PREFIX := $(CONDA_PREFIX) + endif +@@ -13,7 +10,7 @@ + test_binaries: capi_test + + capi_test: capi_test.c +- $(CC) -std=c99 -O0 -g capi_test.c -I../src -lssu -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib -o capi_test ++ $(CC) $(CFLAGS) -std=c99 -O0 -g capi_test.c -I../src -lssu -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib $(LDFLAGS) -o capi_test + + clean: + -rm -f *.o capi_test ===================================== debian/patches/python3.patch ===================================== @@ -1,6 +1,7 @@ Author: Andreas Tille <[email protected]> Last-Update: Mon, 10 Oct 2022 15:15:26 +0200 Description: Call Python3 +Forwarded: not-needed --- a/ci/crawford_test.sh +++ b/ci/crawford_test.sh ===================================== debian/patches/remove_non-free_headers.patch ===================================== @@ -2,6 +2,7 @@ Author: Andreas Tille <[email protected]> Last-Update: Fri, 18 Feb 2022 12:25:53 +0100 Description: mkl_cblas.h and mkl_lapacke.h are in libmkl-dev but this is non-free. Just removing it here +Forwarded: not-needed --- a/src/skbio_alt.cpp +++ b/src/skbio_alt.cpp ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ baseline.patch enable_linking_to_shared_hdf5_lib.patch enable-debug-flag.patch gcc-13.patch +hardening ===================================== debian/patches/soname.patch ===================================== @@ -1,6 +1,7 @@ Author: Andreas Tille <[email protected]> Last-Update: Tue, 26 Jul 2022 16:46:09 +0200 Description: Create SONAME for libssu +Forwarded: not-needed --- a/src/Makefile +++ b/src/Makefile View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/a9525b858ee784c610a30557f80964a80f7aae36...6c8284acc22812b9d886b88681eb3e8901713ff9 -- View it on GitLab: https://salsa.debian.org/med-team/unifrac-tools/-/compare/a9525b858ee784c610a30557f80964a80f7aae36...6c8284acc22812b9d886b88681eb3e8901713ff9 You're receiving this email because of your account on salsa.debian.org.
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