[med-svn] [abyss] 02/04: Patch to run gtest properly
Andreas Tille
tille at debian.org
Fri Sep 19 21:17:06 UTC 2014
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tille pushed a commit to branch master
in repository abyss.
commit 3c048c3ef64ddd5040f3e65c1cf2203d32035bc4
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 19 22:34:53 2014 +0200
Patch to run gtest properly
---
debian/patches/gtest.patch | 177 +++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 170 insertions(+), 7 deletions(-)
diff --git a/debian/patches/gtest.patch b/debian/patches/gtest.patch
index 4a09c1e..1bf6580 100644
--- a/debian/patches/gtest.patch
+++ b/debian/patches/gtest.patch
@@ -1,16 +1,179 @@
Author: Anthony Raymond <traymond at bcgsc.ca>
-Last-Updated: Tue, 16 Sep 2014 14:13:33 -0700
+Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700
Description: Make sure gtest works properly
I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:
http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test
---- abyss.orig/configure.ac
-+++ abyss/configure.ac
-@@ -195,6 +195,7 @@
+--- a/Unittest/Makefile.am
++++ b/Unittest/Makefile.am
+@@ -1,58 +1,72 @@
++check_LIBRARIES = libgtest.a libgtest_main.a
++
++gtest-all.cc:
++ cp $(GTEST)/src/gtest-all.cc .
++
++gtest_main.cc:
++ cp $(GTEST)/src/gtest_main.cc .
++
++libgtest_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
++libgtest_a_SOURCES = gtest-all.cc
++
++libgtest_main_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
++libgtest_main_a_SOURCES = gtest_main.cc gtest-all.cc
++
+ UNIT_TESTS = common_stringutil
+ check_PROGRAMS = common_stringutil
+ common_stringutil_SOURCES = Common/StringUtilTest.cpp
+ common_stringutil_CPPFLAGS = -I$(top_srcdir)
+-common_stringutil_LDADD = $(GTEST_LIBS)
++common_stringutil_LDADD = libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_histogram
+ check_PROGRAMS += common_histogram
+ common_histogram_SOURCES = Common/HistogramTest.cpp
+ common_histogram_CPPFLAGS = -I$(top_srcdir)
+-common_histogram_LDADD = $(GTEST_LIBS)
++common_histogram_LDADD = libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_bitutil
+ check_PROGRAMS += common_bitutil
+ common_bitutil_SOURCES = Common/BitUtilTest.cpp
+ common_bitutil_CPPFLAGS = -I$(top_srcdir)
+-common_bitutil_LDADD = $(GTEST_LIBS)
++common_bitutil_LDADD = libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_kmer
+ check_PROGRAMS += common_kmer
+ common_kmer_SOURCES = Common/KmerTest.cpp
+ common_kmer_CPPFLAGS = -I$(top_srcdir)
+-common_kmer_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++common_kmer_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_sequence
+ check_PROGRAMS += common_sequence
+ common_sequence_SOURCES = Common/Sequence.cc
+ common_sequence_CPPFLAGS = -I$(top_srcdir)
+-common_sequence_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++common_sequence_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_KmerIterator
+ check_PROGRAMS += common_KmerIterator
+ common_KmerIterator_SOURCES = Common/KmerIteratorTest.cpp
+ common_KmerIterator_CPPFLAGS = -I$(top_srcdir)
+-common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += common_sam
+ check_PROGRAMS += common_sam
+ common_sam_SOURCES = Common/SAM.cc
+ common_sam_CPPFLAGS = -I$(top_srcdir)
+-common_sam_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++common_sam_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += BloomFilter
+ check_PROGRAMS += BloomFilter
+ BloomFilter_SOURCES = Konnector/BloomFilter.cc
+ BloomFilter_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+ BloomFilter_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
+-BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += Konnector_DBGBloom
+ check_PROGRAMS += Konnector_DBGBloom
+ Konnector_DBGBloom_SOURCES = Konnector/DBGBloomTest.cpp
+ Konnector_DBGBloom_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+ Konnector_DBGBloom_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
+-Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += Konnector_DBGBloomAlgorithms
+ check_PROGRAMS += Konnector_DBGBloomAlgorithms
+@@ -61,38 +75,38 @@ Konnector_DBGBloomAlgorithms_CPPFLAGS =
+ Konnector_DBGBloomAlgorithms_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
+ Konnector_DBGBloomAlgorithms_LDADD = \
+ $(top_builddir)/Common/libcommon.a \
+- $(GTEST_LIBS)
++ libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += graph_ConstrainedBFSVisitor
+ check_PROGRAMS += graph_ConstrainedBFSVisitor
+ graph_ConstrainedBFSVisitor_SOURCES = Graph/ConstrainedBFSVisitorTest.cpp
+ graph_ConstrainedBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+-graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += graph_BidirectionalBFS
+ check_PROGRAMS += graph_BidirectionalBFS
+ graph_BidirectionalBFS_SOURCES = Graph/BidirectionalBFSTest.cpp
+ graph_BidirectionalBFS_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+-graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += graph_AllPathsSearch
+ check_PROGRAMS += graph_AllPathsSearch
+ graph_AllPathsSearch_SOURCES = Graph/AllPathsSearchTest.cpp
+ graph_AllPathsSearch_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+-graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += graph_HashGraph
+ check_PROGRAMS += graph_HashGraph
+ graph_HashGraph_SOURCES = Graph/HashGraphTest.cpp
+ graph_HashGraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+-graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += graph_ConstrainedBidiBFSVisitor
+ check_PROGRAMS += graph_ConstrainedBidiBFSVisitor
+ graph_ConstrainedBidiBFSVisitor_SOURCES = \
+ Graph/ConstrainedBidiBFSVisitorTest.cpp
+ graph_ConstrainedBidiBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
+-graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ UNIT_TESTS += Konnector_konnector
+ check_PROGRAMS += Konnector_konnector
+@@ -102,7 +116,7 @@ Konnector_konnector_CPPFLAGS = -I$(top_s
+ Konnector_konnector_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
+ Konnector_konnector_LDADD = \
+ $(top_builddir)/Align/libalign.a \
+- $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
++ $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
+
+ ##Tests for log kmer counting / Counting bloom filter
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -89,10 +89,12 @@ fi
+ # GTest
+ AC_ARG_WITH(gtest, AS_HELP_STRING([--with-gtest=PATH],
+ [specify prefix directory for the installed gtest library]))
++gtest_src="/usr/src/gtest"
+ if test "$with_gtest" -a -d "$with_gtest"; then
+ gtest_cppflags="-I$with_gtest/include"
+- gtest_ldflags="-L$with_gtest/lib"
++ gtest_src="$with_gtest"
+ fi
++AC_SUBST(GTEST, "$gtest_src")
+
+ AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich],
+ [use MPICH (default is to use Open MPI)]))
+@@ -118,7 +120,7 @@ boost_ver=1.55.0
+ boost_ver_dir=boost_1_55_0
+ AC_SUBST(CPPFLAGS,
+ "-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $gtest_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")
+-AC_SUBST(LDFLAGS, "$mpi_ldflags $gtest_ldflags $LDFLAGS")
++AC_SUBST(LDFLAGS, "$mpi_ldflags $LDFLAGS")
+
+ # Check for the MPI parallel computing library.
+ libs="$LIBS"
+@@ -194,8 +196,7 @@ fi
+ libs="$LIBS"
AC_CHECK_HEADERS([gtest/gtest.h])
AC_CHECK_LIB([pthread], [pthread_create])
- AC_CHECK_LIB([gtest_main],[main])
-+AC_CHECK_LIB([gtest],[main])
- AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes])
+-AC_CHECK_LIB([gtest_main],[main])
+-AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes])
++AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes])
AC_SUBST(GTEST_LIBS, "$LIBS")
LIBS=$libs
+
--
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