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commit cf27ea5fa2a120b7f94b1005efc3d6e24dac5323 Author: Michael R. Crusoe <[email protected]> Date: Tue Apr 18 03:38:09 2017 -0700 New upstream version 3.10.1 refresh patches fix boost bool cast --- debian/changelog | 6 + debian/control | 4 +- debian/patches/0003_accept-system-bwa.patch | 10 +- .../0101_cmake_ignore_removed_python-yaml.patch | 11 +- debian/patches/0103_use-debian-packaged-bwa.patch | 11 +- debian/patches/0110_build_single_thread.patch | 6 +- debian/patches/0111_use_full_config_dirs.patch | 8 +- debian/patches/0114_use_debian_provided_libs.patch | 185 ++++++++++++++------- debian/patches/0115_enable_compiler_messages.patch | 6 +- debian/patches/0116_stable_link_order.patch | 6 +- debian/patches/0117_build_with_debug.patch | 8 +- debian/patches/fix-bool-cast | 13 ++ debian/patches/series | 1 + 13 files changed, 182 insertions(+), 93 deletions(-) diff --git a/debian/changelog b/debian/changelog index dea80e1..940d3ea 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +spades (3.10.1+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version 3.10.1+dfsg + + -- Michael R. Crusoe <[email protected]> Tue, 18 Apr 2017 03:37:47 -0700 + spades (3.9.1+dfsg-1) unstable; urgency=medium * New upstream release. diff --git a/debian/control b/debian/control index e02d81e..832fbb4 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]>, Afif Elghraoui <[email protected]>, - Sascha Steinbiss <[email protected]> + Sascha Steinbiss <[email protected]>, + Michael R. Crusoe <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 9), @@ -23,6 +24,7 @@ Build-Depends: debhelper (>= 9), python-joblib, asciidoctor (>= 1.5.3), bwa, + libbwa-dev, lynx Standards-Version: 3.9.8 Testsuite: autopkgtest diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch index f89d04a..fa2e718 100644 --- a/debian/patches/0003_accept-system-bwa.patch +++ b/debian/patches/0003_accept-system-bwa.patch @@ -13,8 +13,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades In case you consider taking over the patch I'd suggest to take it over into some common import file. ---- a/src/spades_pipeline/support.py -+++ b/src/spades_pipeline/support.py +--- spades.orig/src/spades_pipeline/support.py ++++ spades/src/spades_pipeline/support.py @@ -58,6 +58,22 @@ sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n") sys.stdout.flush() @@ -55,8 +55,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades def check_file_existence(input_filename, message="", log=None, dipspades=False): filename = abspath(expanduser(input_filename)) ---- a/spades.py -+++ b/spades.py +--- spades.orig/spades.py ++++ spades/spades.py @@ -156,6 +156,22 @@ print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ") log.info("") @@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades def fill_cfg(options_to_parse, log, secondary_filling=False): skip_output_dir=secondary_filling -@@ -456,7 +472,11 @@ +@@ -470,7 +486,11 @@ if (not options_storage.only_error_correction) and options_storage.mismatch_corrector: cfg["mismatch_corrector"] = empty_config() cfg["mismatch_corrector"].__dict__["skip-masked"] = None diff --git a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch index 695befc..4dec147 100644 --- a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch +++ b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch @@ -4,8 +4,8 @@ Description: Since we are using Debian packaged python-yaml (see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be excluded ---- a/ext/src/CMakeLists.txt -+++ b/ext/src/CMakeLists.txt +--- spades.orig/ext/src/CMakeLists.txt ++++ spades/ext/src/CMakeLists.txt @@ -4,8 +4,6 @@ add_subdirectory(nlopt) add_subdirectory(python_libs/joblib2) @@ -15,10 +15,3 @@ Description: Since we are using Debian packaged python-yaml add_subdirectory(ConsensusCore) add_subdirectory(bamtools) add_subdirectory(samtools) -@@ -13,4 +11,4 @@ - add_subdirectory(ssw) - add_subdirectory(cityhash) - add_subdirectory(llvm) --add_subdirectory(htrie) -\ No newline at end of file -+add_subdirectory(htrie) diff --git a/debian/patches/0103_use-debian-packaged-bwa.patch b/debian/patches/0103_use-debian-packaged-bwa.patch index 9355359..15a7233 100644 --- a/debian/patches/0103_use-debian-packaged-bwa.patch +++ b/debian/patches/0103_use-debian-packaged-bwa.patch @@ -13,10 +13,17 @@ Description: SPAdes originally contained a code copy of bwa since the version ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades which enables successfull run of the test suite ---- a/ext/tools/CMakeLists.txt -+++ b/ext/tools/CMakeLists.txt +--- spades.orig/ext/tools/CMakeLists.txt ++++ spades/ext/tools/CMakeLists.txt @@ -5,4 +5,3 @@ # See file LICENSE for details. ############################################################################ -add_subdirectory(bwa-0.7.12) +--- spades.orig/ext/src/CMakeLists.txt ++++ spades/ext/src/CMakeLists.txt +@@ -11,4 +11,3 @@ + add_subdirectory(getopt_pp) + add_subdirectory(llvm) + add_subdirectory(htrie) +-add_subdirectory(bwa) diff --git a/debian/patches/0110_build_single_thread.patch b/debian/patches/0110_build_single_thread.patch index 7b2b360..31fd94a 100644 --- a/debian/patches/0110_build_single_thread.patch +++ b/debian/patches/0110_build_single_thread.patch @@ -1,12 +1,12 @@ Description: build in single thread Upstream builds this in 8 threads, which might overwhelm weaker machines. Author: Sascha Steinbiss <[email protected]> ---- a/spades_compile.sh -+++ b/spades_compile.sh +--- spades.orig/spades_compile.sh ++++ spades/spades_compile.sh @@ -20,6 +20,6 @@ set -e cd "$BASEDIR/$BUILD_DIR" - cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $* + cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src" -make -j 8 +make -j 1 make install diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch index 50861da..5524172 100644 --- a/debian/patches/0111_use_full_config_dirs.patch +++ b/debian/patches/0111_use_full_config_dirs.patch @@ -2,9 +2,9 @@ Description: use full config include path This patch makes sure that the config files are not dependent on local directory structure. Author: Sascha Steinbiss <[email protected]> ---- a/src/spades_pipeline/spades_logic.py -+++ b/src/spades_pipeline/spades_logic.py -@@ -180,6 +180,20 @@ +--- spades.orig/src/spades_pipeline/spades_logic.py ++++ spades/src/spades_pipeline/spades_logic.py +@@ -185,6 +185,20 @@ add_configs(command, dst_configs) @@ -25,7 +25,7 @@ Author: Sascha Steinbiss <[email protected]> #print("Calling: " + " ".join(command)) support.sys_call(command, log) -@@ -227,6 +241,19 @@ +@@ -232,6 +246,19 @@ command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name] add_configs(command, dst_configs) log.info(str(command)) diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch index e66a3f8..c48b267 100644 --- a/debian/patches/0114_use_debian_provided_libs.patch +++ b/debian/patches/0114_use_debian_provided_libs.patch @@ -8,8 +8,8 @@ Description: use Debian-packaged jemalloc library does not report the 'stats.cactive_max' mallctl stat anymore. Hence to avoid a NULL dereference the max rss value is logged. Author: Sascha Steinbiss <[email protected]> ---- a/src/cmake/includes.cmake -+++ b/src/cmake/includes.cmake +--- spades.orig/src/cmake/includes.cmake ++++ spades/src/cmake/includes.cmake @@ -3,6 +3,8 @@ set(CMAKE_INCLUDE_CURRENT_DIR ON) set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ") @@ -19,8 +19,8 @@ Author: Sascha Steinbiss <[email protected]> include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR} ${CMAKE_SOURCE_DIR} ${SPADES_MODULES_DIR}) include_directories(SYSTEM "${EXT_DIR}/include") include_directories(SYSTEM "${ZLIB_INCLUDE_DIRS}") ---- a/src/cmake/flags.cmake -+++ b/src/cmake/flags.cmake +--- spades.orig/src/cmake/flags.cmake ++++ spades/src/cmake/flags.cmake @@ -53,3 +53,5 @@ if (SPADES_USE_TCMALLOC) add_compile_options(-fno-omit-frame-pointer) @@ -28,29 +28,54 @@ Author: Sascha Steinbiss <[email protected]> + +add_definitions(-DJEMALLOC_NO_DEMANGLE) \ No newline at end of file ---- a/ext/src/CMakeLists.txt -+++ b/ext/src/CMakeLists.txt -@@ -1,12 +1,8 @@ - # -*- cmake -*- +--- spades.orig/src/common/assembly_graph/CMakeLists.txt ++++ spades/src/common/assembly_graph/CMakeLists.txt +@@ -9,4 +9,4 @@ --add_subdirectory(jemalloc) --add_subdirectory(nlopt) - add_subdirectory(ConsensusCore) --add_subdirectory(bamtools) - add_subdirectory(samtools) -+add_subdirectory(bamtools) - add_subdirectory(cppformat) --add_subdirectory(ssw) - add_subdirectory(cityhash) - add_subdirectory(llvm) --add_subdirectory(htrie) ---- a/src/modules/dev_support/logger/logger_impl.cpp -+++ b/src/modules/dev_support/logger/logger_impl.cpp + add_library(assembly_graph STATIC + components/connected_component.cpp paths/bidirectional_path.cpp paths/bidirectional_path_io/io_support.cpp paths/bidirectional_path_io/bidirectional_path_output.cpp graph_support/scaff_supplementary.cpp ../modules/alignment/edge_index_refiller.cpp graph_support/coverage_uniformity_analyzer.cpp) +-target_link_libraries(assembly_graph hattrie) ++target_link_libraries(assembly_graph hat-trie) +--- spades.orig/src/common/modules/alignment/kmer_map.hpp ++++ spades/src/common/modules/alignment/kmer_map.hpp +@@ -9,7 +9,7 @@ + + #include "sequence/rtseq.hpp" + +-#include <htrie/hat-trie.h> ++#include <hat-trie/hat-trie.h> + #include <boost/iterator/iterator_facade.hpp> + + namespace debruijn_graph { +--- spades.orig/src/common/modules/path_extend/overlap_analysis.hpp ++++ spades/src/common/modules/path_extend/overlap_analysis.hpp +@@ -2,7 +2,7 @@ + + #include "utils/logger/logger.hpp" + #include "utils/range.hpp" +-#include "ssw/ssw_cpp.h" ++#include "ssw_cpp.h" + + namespace debruijn_graph { + using omnigraph::Range; +--- spades.orig/src/common/utils/coverage_model/kmer_coverage_model.cpp ++++ spades/src/common/utils/coverage_model/kmer_coverage_model.cpp +@@ -18,7 +18,7 @@ + #include <boost/math/distributions/geometric.hpp> + #include <boost/math/distributions/pareto.hpp> + +-#include <nlopt/nlopt.hpp> ++#include <nlopt.hpp> + + #include <vector> + +--- spades.orig/src/common/utils/logger/logger_impl.cpp ++++ spades/src/common/utils/logger/logger_impl.cpp @@ -13,6 +13,7 @@ #include <vector> - #include "dev_support/logger/logger.hpp" -+#include "dev_support/memory_limit.hpp" + #include "utils/logger/logger.hpp" ++#include "utils/memory_limit.hpp" #include "config.hpp" @@ -74,8 +99,8 @@ Author: Sascha Steinbiss <[email protected]> } #else void logger::log(level desired_level, const char* file, size_t line_num, const char* source, const char* msg) { ---- a/src/modules/dev_support/memory_limit.hpp -+++ b/src/modules/dev_support/memory_limit.hpp +--- spades.orig/src/common/utils/memory_limit.hpp ++++ spades/src/common/utils/memory_limit.hpp @@ -20,6 +20,7 @@ #include <sys/resource.h> @@ -84,44 +109,86 @@ Author: Sascha Steinbiss <[email protected]> #ifdef SPADES_USE_JEMALLOC ---- a/src/modules/assembly_graph/CMakeLists.txt -+++ b/src/modules/assembly_graph/CMakeLists.txt -@@ -9,4 +9,4 @@ - - add_library(graph_support STATIC - components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp graph_alignment/edge_index_refiller.cpp) --target_link_libraries(graph_support hattrie) -+target_link_libraries(graph_support hat-trie) ---- a/src/modules/assembly_graph/graph_alignment/kmer_map.hpp -+++ b/src/modules/assembly_graph/graph_alignment/kmer_map.hpp -@@ -9,7 +9,7 @@ +--- spades.orig/src/projects/cclean/brute_force_clean.cpp ++++ spades/src/projects/cclean/brute_force_clean.cpp +@@ -12,7 +12,7 @@ + #include <iostream> + + #include "adapter_index.hpp" +-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner ++#include "ssw_cpp.h" // Striped Smith-Waterman aligner + #include "additional.cpp" + #include "output.hpp" + +--- spades.orig/src/projects/cclean/job_wrappers.cpp ++++ spades/src/projects/cclean/job_wrappers.cpp +@@ -13,7 +13,7 @@ + #include "valid_kmer_generator.hpp" + #include "adapter_index.hpp" + #include "output.hpp" +-#include "ssw/ssw_cpp.h" ++#include "ssw_cpp.h" + #include "utils.hpp" - #include "data_structures/sequence/runtime_k.hpp" + using cclean_output::print_alignment; +--- spades.orig/src/projects/cclean/main.cpp ++++ spades/src/projects/cclean/main.cpp +@@ -21,7 +21,7 @@ --#include <htrie/hat-trie.h> -+#include <hat-trie/hat-trie.h> - #include <boost/iterator/iterator_facade.hpp> - - namespace debruijn_graph { ---- a/src/modules/math/kmer_coverage_model.cpp -+++ b/src/modules/math/kmer_coverage_model.cpp -@@ -18,7 +18,7 @@ - #include <boost/math/distributions/geometric.hpp> - #include <boost/math/distributions/pareto.hpp> + #include "valid_kmer_generator.hpp" + #include "io/read_processor.hpp" +-#include "modules/ssw_cpp.h" ++#include "ssw_cpp.h" + #include "additional.cpp" + + #include "job_wrappers.hpp" +--- spades.orig/src/projects/cclean/output.hpp ++++ spades/src/projects/cclean/output.hpp +@@ -14,7 +14,7 @@ + #include <io/read.hpp> + #include <ostream> + #include "comparator.hpp" +-#include "modules/ssw_cpp.h" ++#include "ssw_cpp.h" --#include <nlopt/nlopt.hpp> -+#include <nlopt.hpp> + namespace cclean_output { +--- spades.orig/src/projects/cclean/utils.cpp ++++ spades/src/projects/cclean/utils.cpp +@@ -12,8 +12,7 @@ #include <vector> ---- a/src/modules/algorithms/path_extend/overlap_analysis.hpp -+++ b/src/modules/algorithms/path_extend/overlap_analysis.hpp -@@ -2,7 +2,7 @@ - - #include "dev_support/logger/logger.hpp" - #include "dev_support/range.hpp" --#include "ssw/ssw_cpp.h" -+#include "ssw_cpp.h" + #include "utils.hpp" +-#include <ssw/ssw_cpp.h> +-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner ++#include <ssw_cpp.h> // Striped Smith-Waterman aligner + #include <io/read.hpp> + #include "additional.cpp" + +--- spades.orig/src/projects/cclean/utils.hpp ++++ spades/src/projects/cclean/utils.hpp +@@ -8,7 +8,7 @@ + #ifndef UTILS_HPP + #define UTILS_HPP + +-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner ++#include <ssw_cpp.h> // Striped Smith-Waterman aligner + #include <io/read.hpp> + #include "additional.cpp" + #include "running_modes.hpp" +--- spades.orig/ext/src/CMakeLists.txt ++++ spades/ext/src/CMakeLists.txt +@@ -1,13 +1,9 @@ + # -*- cmake -*- - namespace debruijn_graph { - using omnigraph::Range; +-add_subdirectory(jemalloc) +-add_subdirectory(nlopt) + add_subdirectory(ConsensusCore) + add_subdirectory(bamtools) + add_subdirectory(samtools) + add_subdirectory(cppformat) +-add_subdirectory(ssw) + add_subdirectory(cityhash) + add_subdirectory(getopt_pp) + add_subdirectory(llvm) +-add_subdirectory(htrie) diff --git a/debian/patches/0115_enable_compiler_messages.patch b/debian/patches/0115_enable_compiler_messages.patch index 4a6eef7..3e3aa14 100644 --- a/debian/patches/0115_enable_compiler_messages.patch +++ b/debian/patches/0115_enable_compiler_messages.patch @@ -1,11 +1,11 @@ Description: enable compiler messages Author: Sascha Steinbiss <[email protected]> ---- a/spades_compile.sh -+++ b/spades_compile.sh +--- spades.orig/spades_compile.sh ++++ spades/spades_compile.sh @@ -20,6 +20,6 @@ set -e cd "$BASEDIR/$BUILD_DIR" - cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $* + cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src" -make -j 1 +make -j 1 VERBOSE=1 make install diff --git a/debian/patches/0116_stable_link_order.patch b/debian/patches/0116_stable_link_order.patch index 73e4288..5cc8f95 100644 --- a/debian/patches/0116_stable_link_order.patch +++ b/debian/patches/0116_stable_link_order.patch @@ -1,8 +1,8 @@ Description: use stable sort order for file globbing Author: Sascha Steinbiss <[email protected]> ---- a/ext/src/llvm/CMakeLists.txt -+++ b/ext/src/llvm/CMakeLists.txt -@@ -26,6 +26,7 @@ +--- spades.orig/ext/src/llvm/CMakeLists.txt ++++ spades/ext/src/llvm/CMakeLists.txt +@@ -29,6 +29,7 @@ ${SPADES_BUILT_INCLUDE_DIR}/llvm/Config.h) file(GLOB sources "[a-zA-Z]*.cpp" "[a-zA-Z]*.c") diff --git a/debian/patches/0117_build_with_debug.patch b/debian/patches/0117_build_with_debug.patch index 08d2b83..b1a053f 100644 --- a/debian/patches/0117_build_with_debug.patch +++ b/debian/patches/0117_build_with_debug.patch @@ -1,13 +1,13 @@ Description: enable building with debug symbols Author: Sascha Steinbiss <[email protected]> ---- a/spades_compile.sh -+++ b/spades_compile.sh +--- spades.orig/spades_compile.sh ++++ spades/spades_compile.sh @@ -19,7 +19,7 @@ mkdir -p "$BASEDIR/$BUILD_DIR" set -e cd "$BASEDIR/$BUILD_DIR" --cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $* -+cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $* +-cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src" ++cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src" make -j 1 VERBOSE=1 make install cd $PREFIX diff --git a/debian/patches/fix-bool-cast b/debian/patches/fix-bool-cast new file mode 100644 index 0000000..2421ff3 --- /dev/null +++ b/debian/patches/fix-bool-cast @@ -0,0 +1,13 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Make explicit cast to bool +--- spades.orig/src/common/func/pred.hpp ++++ spades/src/common/func/pred.hpp +@@ -33,7 +33,7 @@ + : data_(std::move(p)) { } + + virtual bool operator()(T x) const override { +- return data_(x); ++ return (bool) data_(x); + } + + P data_; diff --git a/debian/patches/series b/debian/patches/series index f3d6337..4705406 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -16,3 +16,4 @@ 0111_use_full_config_dirs.patch 0116_stable_link_order.patch 0117_build_with_debug.patch +fix-bool-cast -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
