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commit 364b82db6ab13f6a4dba56d7dd005530b4e686ad Author: Afif Elghraoui <[email protected]> Date: Thu Aug 11 20:31:39 2016 -0700 Refresh and update patches --- debian/patches/adjust-include-path.patch | 136 ++----------------------------- debian/patches/compiler-flags.patch | 17 ++-- debian/patches/fix-ftbfs-with-gcc6.patch | 6 +- debian/patches/reproducible.patch | 6 +- 4 files changed, 21 insertions(+), 144 deletions(-) diff --git a/debian/patches/adjust-include-path.patch b/debian/patches/adjust-include-path.patch index 8ad2e35..ad8836b 100644 --- a/debian/patches/adjust-include-path.patch +++ b/debian/patches/adjust-include-path.patch @@ -1,9 +1,9 @@ Description: Adjust #include statements Use angle brackets rather than quotes so that the library headers can be pulled in from prespecified locations. -Author: Afif Elghraoui <[email protected]> +Author: Afif Elghraoui <[email protected]> Forwarded: https://github.com/jts/nanopolish/pull/33 -Last-Update: 2016-01-18 +Last-Update: 2016-08-11 --- nanopolish.orig/src/nanopolish_poremodel.cpp +++ nanopolish/src/nanopolish_poremodel.cpp @@ -11,7 +11,7 @@ @@ -17,10 +17,10 @@ Last-Update: 2016-01-18 { --- nanopolish.orig/src/nanopolish_poremodel.h +++ nanopolish/src/nanopolish_poremodel.h -@@ -13,7 +13,7 @@ - #include "nanopolish_common.h" - #include <inttypes.h> +@@ -15,7 +15,7 @@ #include <string> + #include <map> + #include "nanopolish_model_names.h" -#include "../fast5/src/fast5.hpp" +#include <fast5.hpp> @@ -28,130 +28,12 @@ Last-Update: 2016-01-18 struct PoreModelStateParams --- nanopolish.orig/src/nanopolish_squiggle_read.cpp +++ nanopolish/src/nanopolish_squiggle_read.cpp -@@ -9,7 +9,7 @@ - #include <algorithm> - #include "nanopolish_common.h" +@@ -11,7 +11,7 @@ #include "nanopolish_squiggle_read.h" + #include "nanopolish_pore_model_set.h" + #include "nanopolish_methyltrain.h" -#include "src/fast5.hpp" +#include <fast5.hpp> // - SquiggleRead::SquiggleRead(const std::string& name, const std::string& path) : ---- nanopolish.orig/src/alignment/nanopolish_alignment_db.cpp -+++ nanopolish/src/alignment/nanopolish_alignment_db.cpp -@@ -9,9 +9,9 @@ - #include <assert.h> - #include <algorithm> - #include "nanopolish_alignment_db.h" --#include "htslib/faidx.h" --#include "htslib/hts.h" --#include "htslib/sam.h" -+#include <htslib/faidx.h> -+#include <htslib/hts.h> -+#include <htslib/sam.h> - - // Various file handle and structures - // needed to traverse a bam file ---- nanopolish.orig/src/alignment/nanopolish_anchor.cpp -+++ nanopolish/src/alignment/nanopolish_anchor.cpp -@@ -10,7 +10,7 @@ - #include <string> - #include <stdio.h> - #include <assert.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_common.h" - #include "nanopolish_anchor.h" - #include "nanopolish_squiggle_read.h" ---- nanopolish.orig/src/alignment/nanopolish_anchor.h -+++ nanopolish/src/alignment/nanopolish_anchor.h -@@ -10,8 +10,8 @@ - #define NANOPOLISH_ANCHOR_H - - #include <memory> --#include "htslib/hts.h" --#include "htslib/sam.h" -+#include <htslib/hts.h> -+#include <htslib/sam.h> - #include "nanopolish_common.h" - #include "nanopolish_squiggle_read.h" - #include "nanopolish_fast5_map.h" ---- nanopolish.orig/src/alignment/nanopolish_eventalign.cpp -+++ nanopolish/src/alignment/nanopolish_eventalign.cpp -@@ -19,7 +19,7 @@ - #include <set> - #include <omp.h> - #include <getopt.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_eventalign.h" - #include "nanopolish_iupac.h" - #include "nanopolish_poremodel.h" ---- nanopolish.orig/src/alignment/nanopolish_eventalign.h -+++ nanopolish/src/alignment/nanopolish_eventalign.h -@@ -9,8 +9,8 @@ - #ifndef NANOPOLISH_EVENTALIGN_H - #define NANOPOLISH_EVENTALIGN_H - --#include "htslib/faidx.h" --#include "htslib/sam.h" -+#include <htslib/faidx.h> -+#include <htslib/sam.h> - #include "nanopolish_alphabet.h" - #include "nanopolish_common.h" - ---- nanopolish.orig/src/common/nanopolish_fast5_map.cpp -+++ nanopolish/src/common/nanopolish_fast5_map.cpp -@@ -14,7 +14,7 @@ - #include <sys/stat.h> - #include "nanopolish_fast5_map.h" - #include "nanopolish_common.h" --#include "htslib/kseq.h" -+#include <htslib/kseq.h> - - // - #define FOFN_SUFFIX ".fast5.fofn" ---- nanopolish.orig/src/nanopolish_call_variants.cpp -+++ nanopolish/src/nanopolish_call_variants.cpp -@@ -21,7 +21,7 @@ - #include <set> - #include <omp.h> - #include <getopt.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_poremodel.h" - #include "nanopolish_transition_parameters.h" - #include "nanopolish_matrix.h" ---- nanopolish.orig/src/nanopolish_getmodel.cpp -+++ nanopolish/src/nanopolish_getmodel.cpp -@@ -20,7 +20,7 @@ - #include <set> - #include <omp.h> - #include <getopt.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_poremodel.h" - #include "nanopolish_squiggle_read.h" - #include "profiler.h" ---- nanopolish.orig/src/nanopolish_methyltest.cpp -+++ nanopolish/src/nanopolish_methyltest.cpp -@@ -20,7 +20,7 @@ - #include <set> - #include <omp.h> - #include <getopt.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_eventalign.h" - #include "nanopolish_iupac.h" - #include "nanopolish_poremodel.h" ---- nanopolish.orig/src/nanopolish_methyltrain.cpp -+++ nanopolish/src/nanopolish_methyltrain.cpp -@@ -20,7 +20,7 @@ - #include <set> - #include <omp.h> - #include <getopt.h> --#include "htslib/faidx.h" -+#include <htslib/faidx.h> - #include "nanopolish_methyltrain.h" - #include "nanopolish_eventalign.h" - #include "nanopolish_iupac.h" + SquiggleRead::SquiggleRead(const std::string& name, const std::string& path, const uint32_t flags) : diff --git a/debian/patches/compiler-flags.patch b/debian/patches/compiler-flags.patch index dad91eb..6e32878 100644 --- a/debian/patches/compiler-flags.patch +++ b/debian/patches/compiler-flags.patch @@ -1,9 +1,9 @@ Description: Allow adding settings to standard compiler flags * Use += for CFLAGS/CXXFLAGS * Use LDFLAGS -Author: Afif Elghraoui <[email protected]> +Author: Afif Elghraoui <[email protected]> Forwarded: no -Last-Update: 2016-01-18 +Last-Update: 2016-08-11 --- nanopolish.orig/Makefile +++ nanopolish/Makefile @@ -9,9 +9,9 @@ @@ -18,22 +18,17 @@ Last-Update: 2016-01-18 CXX=g++ CC=gcc HDF5=install -@@ -95,15 +95,15 @@ - $(CXX) -o $@ -c $(CXXFLAGS) $(CPPFLAGS) -fPIC $< - - .c.o: -- $(CC) -o $@ -c $(CFLAGS) -fPIC $< -+ $(CC) -o $@ -c $(CFLAGS) $(CPPFLAGS) -fPIC $< +@@ -108,11 +108,11 @@ # Link main executable - $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) + $(PROGRAM): src/main/nanopolish.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(EIGEN) - $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) -+ $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(LDFLAGS) $(HTS_LIB) $(H5_LIB) $(LIBS) ++ $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS) # Link test executable $(TEST_PROGRAM): src/test/nanopolish_test.o $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) - $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) -+ $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(LDFLAGS) $(HTS_LIB) $(H5_LIB) $(LIBS) ++ $(CXX) -o $@ $(CXXFLAGS) $(CPPFLAGS) -fPIC $< $(CPP_OBJ) $(C_OBJ) $(HTS_LIB) $(H5_LIB) $(LIBS) $(LDFLAGS) test: $(TEST_PROGRAM) ./$(TEST_PROGRAM) diff --git a/debian/patches/fix-ftbfs-with-gcc6.patch b/debian/patches/fix-ftbfs-with-gcc6.patch index 950f620..534261f 100644 --- a/debian/patches/fix-ftbfs-with-gcc6.patch +++ b/debian/patches/fix-ftbfs-with-gcc6.patch @@ -1,8 +1,8 @@ Description: fix build with GCC6 Author: Sascha Steinbiss <[email protected]> ---- a/src/common/nanopolish_variant.cpp -+++ b/src/common/nanopolish_variant.cpp -@@ -24,7 +24,8 @@ +--- nanopolish.orig/src/common/nanopolish_variant.cpp ++++ nanopolish/src/common/nanopolish_variant.cpp +@@ -29,7 +29,8 @@ const std::string& haplotype) { AlnParam par = aln_param_nt2nt; diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch index 91abfc3..a457fa7 100644 --- a/debian/patches/reproducible.patch +++ b/debian/patches/reproducible.patch @@ -2,9 +2,9 @@ Description: make build reproducible This patch enforces stable input file ordering w.r.t. source file gathering via Make's 'wildcard' directive. Author: Sascha Steinbiss <[email protected]> ---- a/Makefile -+++ b/Makefile -@@ -69,8 +69,8 @@ +--- nanopolish.orig/Makefile ++++ nanopolish/Makefile +@@ -78,8 +78,8 @@ # # Find the source files by searching subdirectories -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/nanopolish.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
