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commit 7e7dfa066981872b9473da1ee0a2f5047066bb72 Author: Afif Elghraoui <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
