[med-svn] [Git][med-team/primer3][master] 8 commits: d/rules: fix handling of big-endian archs.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jul 9 12:54:51 BST 2022
Étienne Mollier pushed to branch master at Debian Med / primer3
Commits:
ef46d400 by Steve Langasek at 2022-07-09T10:03:34+02:00
d/rules: fix handling of big-endian archs.
Closes: #1014626
- - - - -
32b75b07 by Étienne Mollier at 2022-07-09T10:04:27+02:00
initialize changelog
- - - - -
a9cd2800 by Étienne Mollier at 2022-07-09T10:05:05+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
7a4c8ab1 by Étienne Mollier at 2022-07-09T10:17:46+02:00
routine-update: Ready to upload to unstable
- - - - -
b16eccbb by Étienne Mollier at 2022-07-09T10:32:14+02:00
d/rules: remove executable bit to samples.
- - - - -
cb9aacbb by Étienne Mollier at 2022-07-09T10:33:24+02:00
d/primer3-examples.lintian-overrides: refresh override.
- - - - -
3eaf2558 by Étienne Mollier at 2022-07-09T10:50:07+02:00
Add buildflags.patch: propagate Debian build flags.
- - - - -
be2c2bb4 by Étienne Mollier at 2022-07-09T10:51:49+02:00
update changelog
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/buildflags.patch
- debian/patches/series
- debian/primer3-examples.lintian-overrides
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+primer3 (2.6.1-3) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Steve Langasek ]
+ * d/rules: fix handling of big-endian archs. (Closes: #1014626)
+
+ [ Étienne Mollier ]
+ * Standards-Version: 4.6.1 (routine-update)
+ * d/primer3-examples.lintian-overrides: refresh override.
+ * d/rules: remove executable bit to samples.
+ * Add buildflags.patch: propagate Debian build flags.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 09 Jul 2022 10:50:59 +0200
+
primer3 (2.6.1-2) unstable; urgency=medium
* Run dh_auto_test with --no-parallel
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/primer3
Vcs-Git: https://salsa.debian.org/med-team/primer3.git
Homepage: http://primer3.sourceforge.net
=====================================
debian/patches/buildflags.patch
=====================================
@@ -0,0 +1,169 @@
+Description: propagate Debian standard build flags.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-07-09
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- primer3.orig/src/Makefile
++++ primer3/src/Makefile
+@@ -52,9 +52,9 @@
+ WINMAKE=mingw32-make
+
+ LDLIBS = -lm
+-AR = ar
+-CC = gcc
+-CXX = g++
++AR ?= ar
++CC ?= gcc
++CXX ?= g++
+ O_OPTS = -O2
+ CC_OPTS = -g -Wall
+ P_DEFINES =
+@@ -153,108 +153,108 @@
+ $(RANLIB) $@
+
+ $(LIBOLIGOTM_LIB): oligotm.o
+- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
+
+ $(LIBAMPTM): amplicontm.o
+ $(AR) rv $@ amplicontm.o
+ $(RANLIB) $@
+
+ $(LIBAMPTM_LIB): amplicontm.o
+- $(CC) -shared -W1,-soname,libamplicontm.so.1 -o $(LIBAMPTM_DYN) amplicontm.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libamplicontm.so.1 -o $(LIBAMPTM_DYN) amplicontm.o
+
+ $(LIBDPAL): dpal_primer.o
+ $(AR) rv $@ dpal_primer.o
+ $(RANLIB) $@
+
+ $(LIBDPAL_DYN): dpal_primer.o
+- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
+
+ $(LIBTHAL): thal_primer.o
+ $(AR) rv $@ thal_primer.o
+ $(RANLIB) $@
+
+ $(LIBTHAL_DYN): thal_primer.o
+- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
+
+ $(LIBTHALPARA): thal_parameters.o
+ $(AR) rv $@ thal_parameters.o
+ $(RANLIB) $@
+
+ $(LIBTHALPARA_DYN): thal_parameters.o
+- $(CC) -shared -W1,-soname,libthalpara.so.1 -o $(LIBTHALPARA_DYN_LIB) thal_parameters.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libthalpara.so.1 -o $(LIBTHALPARA_DYN_LIB) thal_parameters.o
+
+ $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
+ $(AR) rv $@ libprimer3.o p3_seq_lib.o
+ $(RANLIB) $@
+
+ $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
+- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
+
+ $(LIBMASKER): masker.o
+ $(AR) rv $@ masker.o
+ $(RANLIB) $@
+
+ $(LIBMASKER_DYN): masker.o
+- $(CC) -shared -W1,-soname,libmasker.so.1 -o $(LIBMASKER_DYN) masker.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libmasker.so.1 -o $(LIBMASKER_DYN) masker.o
+
+ $(PRIMER_EXE): $(PRIMER_OBJECTS)
+- $(CXX) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+
+ libprimer3.o: libprimer3.cc libprimer3.h p3_seq_lib.h dpal.h thal.h thal_parameters.h oligotm.h
+- $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ libprimer3.cc
++ $(CXX) $(CPPFLAGS) -c $(CXXFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ libprimer3.cc
+
+ $(NTDPAL_EXE): ntdpal_main.o dpal.o
+- $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+
+ $(NTTHAL_EXE): thal_main.o thal.o thal_parameters.o
+- $(CC) $(LDFLAGS) -o $@ thal_main.o thal.o thal_parameters.o $(LDLIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ thal_main.o thal.o thal_parameters.o $(LDLIBS)
+
+ $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
+- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
+
+ $(AMPLICONTM_EXE): amplicontm_main.c amplicontm.h $(LIBAMPTM)
+- $(CC) $(CFLAGS) -o $@ amplicontm_main.c $(LIBAMPTM) $(LIBOPTS) $(LDLIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ amplicontm_main.c $(LIBAMPTM) $(LIBOPTS) $(LDLIBS)
+
+ $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
+- $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+
+ $(MASKER_EXE): masker_main.c $(LIBRARIES)
+- $(CXX) $(CXXFLAGS) -lstdc++ -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)
+
+ read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h thal_parameters.h p3_seq_lib.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ read_boulder.c
+
+ print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ print_boulder.c
+
+ dpal.o: dpal.c dpal.h
+- $(CC) -c $(CFLAGS) -o $@ dpal.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ dpal.c
+
+ # We use '-ffloat-store' on windows to prevent undesirable
+ # precision which may lead to differences in floating point results.
+ thal.o: thal.c thal.h thal_parameters.h
+- $(CC) -c $(CFLAGS) -ffloat-store -o $@ thal.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(LDFLAGS) -o $@ thal.c
+
+ thal_parameters.o: thal_parameters.c thal_parameters.h thal.h
+- $(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal_parameters.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(P_DEFINES) $(LDFLAGS) -o $@ thal_parameters.c
+
+ p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
+- $(CC) -c $(CFLAGS) -o $@ p3_seq_lib.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ p3_seq_lib.c
+
+ dpal_primer.o: dpal.c dpal.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ dpal.c
+
+ thal_primer.o: thal.c thal.h thal_parameters.h
+- $(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(P_DEFINES) $(LDFLAGS) -o $@ thal.c
+
+ format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ format_output.c
+
+ ntdpal_main.o: ntdpal_main.c dpal.h
+- $(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(CC_OPTS) $(LDFLAGS) -o $@ ntdpal_main.c
+
+ thal_main.o: thal_main.c thal.h thal_parameters.h
+- $(CC) -c $(CFLAGS) -o $@ thal_main.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ thal_main.c
+ # We use CC_OPTS above rather than CFLAGS because
+ # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
+
+@@ -263,10 +263,10 @@
+ oligotm.o: oligotm.c oligotm.h
+
+ primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h thal_parameters.h oligotm.h format_output.h print_boulder.h read_boulder.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) primer3_boulder_main.c
+
+ masker.o: masker.c masker.h libprimer3.h
+- $(CC) -c $(CFLAGS) $(P_DEFINES) masker.c
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) masker.c
+
+ primer_test: test
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
hardening.patch
primer_thermodynamic_parameters_path_2_etc.patch
set_prefix.patch
+buildflags.patch
=====================================
debian/primer3-examples.lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# The directories are supposed to be empty
-primer3-examples: package-contains-empty-directory usr/share/doc/primer3/examples/test/*_tmp/
+primer3-examples: package-contains-empty-directory [usr/share/doc/primer3/examples/test/*_tmp/]
=====================================
debian/rules
=====================================
@@ -29,9 +29,8 @@ ifneq ($(BUILDARCH),little)
cp -a test/Makefile test/Makefile~
# exclude tests known to fail on big endian
# See README.source for further explanation.
- for tst in $(P3CORE_FAILED_TESTS) ; do sed -i "/$${tst}/d" test/p3test.pl ; done
- sed -i "0,/$(FAILED_TESTS)/s///" test/Makefile
- sed -i "/$(FAILED_TESTS)/,/endif/d" test/Makefile
+ for tst in $(P3CORE_FAILED_TESTS) ; do sed -i "/$${tst}.,/d" test/p3test.pl ; done
+ for tst in $(FAILED_TESTS); do sed -i "/^test:/s/$$tst//" test/Makefile; done
endif
dh_auto_test --no-parallel --sourcedirectory=test
ifneq ($(BUILDARCH),little)
@@ -52,7 +51,8 @@ override_dh_installexamples:
cp -aR ./src/humrep_and_simple.txt $(sampledir)/src;
cp -a settings_files/primer*.txt $(sampledir)/settings_files;
cp -aR ./kmer_lists/*.list $(sampledir)/kmer_lists;
-
- chmod -x $(sampledir)/test/thal*;
+ chmod -x $(sampledir)/test/thal*
+ chmod -x $(sampledir)/test/amplicon3/amplicons.csv
+ chmod -x $(sampledir)/test/primer_windows_newlines_input
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/long_seq_tm_test.pl ;
sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' $(sampledir)/test/vgrep.pl ;
View it on GitLab: https://salsa.debian.org/med-team/primer3/-/compare/87400369b9462300d625d51ac685779de1ca2f04...be2c2bb407d2c85ef056b77fa2707b2dbe3b9b5d
--
View it on GitLab: https://salsa.debian.org/med-team/primer3/-/compare/87400369b9462300d625d51ac685779de1ca2f04...be2c2bb407d2c85ef056b77fa2707b2dbe3b9b5d
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