[med-svn] [pbbam] 05/12: Update patches
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 5 03:24:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbbam.
commit 7e7dfa066981872b9473da1ee0a2f5047066bb72
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Jul 4 16:20:10 2016 -0700
Update patches
---
...uilding-gtest => dont-try-building-gtest.patch} | 15 +-
debian/patches/gcc5 | 515 ---------------------
debian/patches/series | 6 +-
debian/patches/set-samtools-path | 15 -
debian/patches/{ssl-md5 => ssl-md5.patch} | 6 +-
5 files changed, 16 insertions(+), 541 deletions(-)
diff --git a/debian/patches/dont-try-building-gtest b/debian/patches/dont-try-building-gtest.patch
similarity index 60%
rename from debian/patches/dont-try-building-gtest
rename to debian/patches/dont-try-building-gtest.patch
index bfab654..df4e13f 100644
--- a/debian/patches/dont-try-building-gtest
+++ b/debian/patches/dont-try-building-gtest.patch
@@ -7,13 +7,20 @@ Forwarded: not-needed
Last-Update: 2015-09-07
--- pbbam.orig/CMakeLists.txt
+++ pbbam/CMakeLists.txt
-@@ -124,9 +124,5 @@
- add_subdirectory(docs)
- endif()
+@@ -170,16 +170,6 @@
+
if(PacBioBAM_build_tests)
+
- if (NOT GTEST_SRC_DIR)
-- set(GTEST_SRC_DIR ../gtest)
+- set(PREBUILT_GTEST_SRC ${PacBioBAM_RootDir}/../../../../prebuilt.tmpout/gtest/gtest_1.7.0/)
+- if(EXISTS ${PREBUILT_GTEST_SRC})
+- set(GTEST_SRC_DIR ${PREBUILT_GTEST_SRC})
+- else()
+- set(GTEST_SRC_DIR ../gtest) # keep old fallback behavior for external builds, for now at least
+- endif()
- endif()
+-
- add_subdirectory(${GTEST_SRC_DIR} external/gtest/build)
add_subdirectory(tests)
+
endif()
diff --git a/debian/patches/gcc5 b/debian/patches/gcc5
deleted file mode 100644
index e577299..0000000
--- a/debian/patches/gcc5
+++ /dev/null
@@ -1,515 +0,0 @@
-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 7d5b54a..59337a9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-set-samtools-path
-ssl-md5
-dont-try-building-gtest
-gcc5
+dont-try-building-gtest.patch
+ssl-md5.patch
diff --git a/debian/patches/set-samtools-path b/debian/patches/set-samtools-path
deleted file mode 100644
index aa1819f..0000000
--- a/debian/patches/set-samtools-path
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: Set samtools path
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-09-06
---- pbbam.orig/tests/CMakeLists.txt
-+++ pbbam/tests/CMakeLists.txt
-@@ -2,7 +2,7 @@
-
- # find samtools binary for comparing against 'gold standard' files
- #set(Samtools_Dir "/Users/derek/development/samtools")
--set(Samtools_Dir "${PacBioBAM_RootDir}/../../../../prebuilt.out/samtools/samtools-0.1.19/ubuntu-1404/bin")
-+set(Samtools_Dir "")
- find_program(Samtools_Bin samtools HINTS ${Samtools_Dir})
-
- # ensure tests directory exists
diff --git a/debian/patches/ssl-md5 b/debian/patches/ssl-md5.patch
similarity index 93%
rename from debian/patches/ssl-md5
rename to debian/patches/ssl-md5.patch
index af927ec..f5153a9 100644
--- a/debian/patches/ssl-md5
+++ b/debian/patches/ssl-md5.patch
@@ -13,12 +13,12 @@ Forwarded: no
Last-Update: 2015-09-07
--- pbbam.orig/src/ReadGroupInfo.cpp
+++ pbbam/src/ReadGroupInfo.cpp
-@@ -37,7 +37,7 @@
-
+@@ -42,7 +42,7 @@
#include "pbbam/ReadGroupInfo.h"
+ #include "ChemistryTable.h"
#include "SequenceUtils.h"
-#include <cram/md5.h>
+#include <openssl/md5.h>
- #include <cstdio>
+ #include <iomanip>
#include <set>
#include <sstream>
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbbam.git
More information about the debian-med-commit
mailing list