[med-svn] [Git][med-team/unifrac-tools][master] 2 commits: Add patch to improve build hardening.

[Michael R. Crusoe (@crusoe)]

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 <crusoe at debian.org>  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 <nilesh at debian.org>
 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: ucko at debian.org (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 <crusoe at debian.org>
+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 <tille at debian.org>
 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 <tille at debian.org>
 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 <tille at debian.org>
 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
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