[med-svn] [pbbam] 03/06: Attempt to build test suite sources
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Sep 8 08:40:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbbam.
commit aa8a991f91fc7a07fd948646ae75f43b47949e4a
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Sep 7 23:57:33 2015 -0700
Attempt to build test suite sources
---
debian/control | 1 +
debian/patches/dont-try-building-gtest | 12 +
debian/patches/gcc5 | 515 +++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/rules | 5 +-
5 files changed, 534 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index e750bd8..db366c0 100644
--- a/debian/control
+++ b/debian/control
@@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9),
cmake,
# swig3.0,
doxygen,
+ libgtest-dev,
libboost-dev (>= 1.54),
zlib1g-dev,
libssl-dev,
diff --git a/debian/patches/dont-try-building-gtest b/debian/patches/dont-try-building-gtest
new file mode 100644
index 0000000..b859a7d
--- /dev/null
+++ b/debian/patches/dont-try-building-gtest
@@ -0,0 +1,12 @@
+--- pbbam.orig/CMakeLists.txt
++++ pbbam/CMakeLists.txt
+@@ -124,9 +124,5 @@
+ add_subdirectory(docs)
+ endif()
+ if(PacBioBAM_build_tests)
+- if (NOT GTEST_SRC_DIR)
+- set(GTEST_SRC_DIR ../gtest)
+- endif()
+- add_subdirectory(${GTEST_SRC_DIR} external/gtest/build)
+ add_subdirectory(tests)
+ endif()
diff --git a/debian/patches/gcc5 b/debian/patches/gcc5
new file mode 100644
index 0000000..e577299
--- /dev/null
+++ b/debian/patches/gcc5
@@ -0,0 +1,515 @@
+Description: Improve ability of test suite sources to build
+ The test suite relies on a hackish CPP trick to redefine "private" as
+ "public". Unfortunately, this fails when including headers from the standard
+ library or other external sources. These patches undo the trick before
+ including external headers. Again unfortunately, this isn't sufficient to
+ allow the test suite to build because the pbbam headers themselves also
+ include external headers. It looks like some refactoring is in order.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-09-07
+--- pbbam.orig/tests/src/test_Accuracy.cpp
++++ pbbam/tests/src/test_Accuracy.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/Accuracy.h>
++#undef private
++#include <gtest/gtest.h>
++
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+ using namespace std;
+--- pbbam.orig/tests/src/test_AlignmentPrinter.cpp
++++ pbbam/tests/src/test_AlignmentPrinter.cpp
+@@ -40,7 +40,6 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+
+ #include "pbbam/AlignmentPrinter.h"
+ #include "pbbam/BamFile.h"
+@@ -48,6 +47,10 @@
+ #include "pbbam/EntireFileQuery.h"
+ #include "pbbam/IndexedFastaReader.h"
+
++#undef private
++
++#include <gtest/gtest.h>
++
+ #include <iostream>
+ #include <sstream>
+ #include <string>
+--- pbbam.orig/tests/src/test_BamFile.cpp
++++ pbbam/tests/src/test_BamFile.cpp
+@@ -40,8 +40,11 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/BamFile.h>
++
++#undef private
++
++#include <gtest/gtest.h>
+ #include <stdexcept>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_BamHeader.cpp
++++ pbbam/tests/src/test_BamHeader.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
++#include <pbbam/BamHeader.h>
++#undef private
++
+ #include <gtest/gtest.h>
+ #include <htslib/sam.h>
+-#include <pbbam/BamHeader.h>
+ #include <iostream>
+ #include <string>
+ #include <utility>
+--- pbbam.orig/tests/src/test_BamRecord.cpp
++++ pbbam/tests/src/test_BamRecord.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecord.h>
+ #include <pbbam/BamTagCodec.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_BamRecordBuilder.cpp
++++ pbbam/tests/src/test_BamRecordBuilder.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecordBuilder.h>
+ #include <pbbam/BamTagCodec.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <chrono>
+ #include <string>
+ using namespace PacBio;
+--- pbbam.orig/tests/src/test_BamRecordClipping.cpp
++++ pbbam/tests/src/test_BamRecordClipping.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecord.h>
+ #include <pbbam/BamTagCodec.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <chrono>
+ #include <string>
+ using namespace PacBio;
+--- pbbam.orig/tests/src/test_BamRecordImplCore.cpp
++++ pbbam/tests/src/test_BamRecordImplCore.cpp
+@@ -39,11 +39,13 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecordImpl.h>
+ #include <pbbam/BamTagCodec.h>
+ #include <pbbam/Tag.h>
+ #include <pbbam/TagCollection.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <algorithm>
+ #include <iostream>
+ #include <iterator>
+--- pbbam.orig/tests/src/test_BamRecordImplTags.cpp
++++ pbbam/tests/src/test_BamRecordImplTags.cpp
+@@ -39,8 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecordImpl.h>
++#undef private
++
++#include <gtest/gtest.h>
++
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+ using namespace std;
+--- pbbam.orig/tests/src/test_BamRecordImplVariableData.cpp
++++ pbbam/tests/src/test_BamRecordImplVariableData.cpp
+@@ -39,12 +39,14 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecordImpl.h>
+ #include <pbbam/BamTagCodec.h>
+ #include <pbbam/SamTagCodec.h>
+ #include <pbbam/Tag.h>
+ #include <pbbam/TagCollection.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <algorithm>
+ #include <iostream>
+ #include <iterator>
+--- pbbam.orig/tests/src/test_BamRecordMapping.cpp
++++ pbbam/tests/src/test_BamRecordMapping.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/BamRecord.h>
+ #include <pbbam/BamTagCodec.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <chrono>
+ #include <string>
+ using namespace PacBio;
+--- pbbam.orig/tests/src/test_BamWriter.cpp
++++ pbbam/tests/src/test_BamWriter.cpp
+@@ -40,12 +40,14 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+-#include <htslib/sam.h>
+ #include <pbbam/BamHeader.h>
+ #include <pbbam/BamRecord.h>
+ #include <pbbam/BamWriter.h>
+ #include <pbbam/EntireFileQuery.h>
++#undef private
++
++#include <gtest/gtest.h>
++#include <htslib/sam.h>
+ #include <chrono>
+ #include <iostream>
+ #include <string>
+--- pbbam.orig/tests/src/test_Cigar.cpp
++++ pbbam/tests/src/test_Cigar.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/Cigar.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_DataSetCore.cpp
++++ pbbam/tests/src/test_DataSetCore.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/DataSet.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_DataSetIO.cpp
++++ pbbam/tests/src/test_DataSetIO.cpp
+@@ -40,9 +40,11 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/DataSet.h>
+ #include <pbbam/internal/DataSetElement.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <stdexcept>
+ #include <sstream>
+ #include <string>
+--- pbbam.orig/tests/src/test_DataSetMetadata.cpp
++++ pbbam/tests/src/test_DataSetMetadata.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/dataset/DataSet.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_EndToEnd.cpp
++++ pbbam/tests/src/test_EndToEnd.cpp
+@@ -41,11 +41,14 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+-#include <htslib/sam.h>
+ #include <pbbam/BamFile.h>
+ #include <pbbam/BamWriter.h>
+ #include <pbbam/EntireFileQuery.h>
++#undef private
++#undef protected
++
++#include <gtest/gtest.h>
++#include <htslib/sam.h>
+ #include <iostream>
+ #include <memory>
+ #include <string>
+--- pbbam.orig/tests/src/test_EntireFileQuery.cpp
++++ pbbam/tests/src/test_EntireFileQuery.cpp
+@@ -40,8 +40,10 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/EntireFileQuery.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_Frames.cpp
++++ pbbam/tests/src/test_Frames.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/Frames.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ #include <vector>
+ using namespace PacBio;
+--- pbbam.orig/tests/src/test_GenomicIntervalQuery.cpp
++++ pbbam/tests/src/test_GenomicIntervalQuery.cpp
+@@ -40,8 +40,10 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/GenomicIntervalQuery.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <iostream>
+ #include <string>
+ using namespace PacBio;
+--- pbbam.orig/tests/src/test_GroupQuery.cpp
++++ pbbam/tests/src/test_GroupQuery.cpp
+@@ -40,9 +40,11 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/ZmwGroupQuery.h>
+ #include <pbbam/GroupQuery.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_IndexedFastaReader.cpp
++++ pbbam/tests/src/test_IndexedFastaReader.cpp
+@@ -44,6 +44,8 @@
+ #include "pbbam/BamRecord.h"
+ #include "pbbam/BamFile.h"
+ #include "pbbam/EntireFileQuery.h"
++#undef private
++
+ #include <gtest/gtest.h>
+ #include <iostream>
+ #include <sstream>
+--- pbbam.orig/tests/src/test_Intervals.cpp
++++ pbbam/tests/src/test_Intervals.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/GenomicInterval.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_PacBioIndex.cpp
++++ pbbam/tests/src/test_PacBioIndex.cpp
+@@ -40,7 +40,6 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/BamFile.h>
+ #include <pbbam/BamWriter.h>
+ #include <pbbam/EntireFileQuery.h>
+@@ -48,6 +47,9 @@
+ #include <pbbam/PbiIndex.h>
+ #include <pbbam/PbiRawData.h>
+ #include <pbbam/internal/PbiIndex_p.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ #include <cstdio>
+ #include <cstdlib>
+--- pbbam.orig/tests/src/test_PolymeraseStitching.cpp
++++ pbbam/tests/src/test_PolymeraseStitching.cpp
+@@ -39,18 +39,19 @@
+ #define private public
+ #endif
+
+-#include <iostream>
+-#include <map>
+-#include <string>
+-
+-#include <gtest/gtest.h>
+-
+ #include "pbbam/virtual/VirtualPolymeraseReader.h"
+ #include "pbbam/BamFile.h"
+ #include "pbbam/BamRecord.h"
+ #include "pbbam/EntireFileQuery.h"
+ #include "pbbam/Frames.h"
+ #include "TestData.h"
++#undef private
++
++#include <iostream>
++#include <map>
++#include <string>
++
++#include <gtest/gtest.h>
+
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_QualityValues.cpp
++++ pbbam/tests/src/test_QualityValues.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/QualityValues.h>
++#undef private
++
++#include <gtest/gtest.h>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+ using namespace std;
+--- pbbam.orig/tests/src/test_ReadGroupInfo.cpp
++++ pbbam/tests/src/test_ReadGroupInfo.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/ReadGroupInfo.h>
++#undef private
++
++#include <gtest/gtest.h>
+ using namespace PacBio::BAM;
+
+
+--- pbbam.orig/tests/src/test_SequenceUtils.cpp
++++ pbbam/tests/src/test_SequenceUtils.cpp
+@@ -39,9 +39,11 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/../../src/SequenceUtils.h>
+ #include <pbbam/../../src/StringUtils.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ #include <vector>
+
+--- pbbam.orig/tests/src/test_Tags.cpp
++++ pbbam/tests/src/test_Tags.cpp
+@@ -39,11 +39,13 @@
+ #define private public
+ #endif
+
+-#include <boost/type_traits/is_convertible.hpp>
+-#include <gtest/gtest.h>
+ #include <pbbam/BamTagCodec.h>
+ #include <pbbam/TagCollection.h>
+ #include <pbbam/SamTagCodec.h>
++#undef private
++
++#include <boost/type_traits/is_convertible.hpp>
++#include <gtest/gtest.h>
+ #include <algorithm>
+ #include <iostream>
+ #include <map>
+--- pbbam.orig/tests/src/test_TimeUtils.cpp
++++ pbbam/tests/src/test_TimeUtils.cpp
+@@ -39,8 +39,10 @@
+ #define private public
+ #endif
+
+-#include <gtest/gtest.h>
+ #include <pbbam/../../src/TimeUtils.h>
++#undef private
++
++#include <gtest/gtest.h>
+
+ using namespace PacBio;
+ using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_UnmappedReadsQuery.cpp
++++ pbbam/tests/src/test_UnmappedReadsQuery.cpp
+@@ -40,10 +40,11 @@
+ //#endif
+
+ //#include "TestData.h"
+-//#include <gtest/gtest.h>
+ //#include <pbbam/EntireFileQuery.h>
+-
+ //#include <pbbam/UnmappedReadsQuery.h>
++//#undef private
++
++//#include <gtest/gtest.h>
+ //#include <string>
+ //using namespace PacBio;
+ //using namespace PacBio::BAM;
+--- pbbam.orig/tests/src/test_ZmwQuery.cpp
++++ pbbam/tests/src/test_ZmwQuery.cpp
+@@ -40,8 +40,10 @@
+ #endif
+
+ #include "TestData.h"
+-#include <gtest/gtest.h>
+ #include <pbbam/ZmwQuery.h>
++#undef private
++
++#include <gtest/gtest.h>
+ #include <string>
+ using namespace PacBio;
+ using namespace PacBio::BAM;
diff --git a/debian/patches/series b/debian/patches/series
index f3a7560..7d5b54a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,4 @@
set-samtools-path
ssl-md5
+dont-try-building-gtest
+gcc5
diff --git a/debian/rules b/debian/rules
index cdf38fc..54a306a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,7 @@ include /usr/share/dpkg/default.mk
override_dh_auto_configure:
dh_auto_configure -- \
-DPacBioBAM_build_shared=ON \
- -DPacBioBAM_build_tests=OFF \
+ -DPacBioBAM_build_tests=ON \
-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \
-DHTSLIB_INCLUDE_DIRS=/usr/include \
-DHTSLIB_LIBRARIES=/usr/lib \
@@ -19,5 +19,8 @@ override_dh_auto_configure:
# -DPacBioBAM_wrap_python=ON \
# -DPacBioBAM_wrap_r=ON
+override_dh_auto_test:
+ cd build && $(MAKE) test
+
override_dh_installchangelogs:
dh_installchangelogs CHANGELOG.md
--
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