Index: head/biology/jellyfish/Makefile =================================================================== --- head/biology/jellyfish/Makefile (revision 501577) +++ head/biology/jellyfish/Makefile (revision 501578) @@ -1,37 +1,45 @@ # $FreeBSD$ -PORTNAME= jellyfish -PORTVERSION= 2.2.6 +PORTNAME= Jellyfish DISTVERSIONPREFIX= v -PORTREVISION= 4 -CATEGORIES= biology +DISTVERSION= 2.2.10 +PORTREVISION= 5 +CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Fast, memory-efficient counting of k-mers in DNA LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= yaggo:devel/yaggo +LIB_DEPENDS= libhts.so:biology/htslib -GNU_CONFIGURE= yes - USES= autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig USE_LDCONFIG= yes - USE_GITHUB= yes + +GNU_CONFIGURE= yes GH_ACCOUNT= gmarcais -GH_PROJECT= Jellyfish INSTALL_TARGET= install-strip - PLIST_SUB= VER=${PORTVERSION} +OPTIONS_DEFINE= NLS +OPTIONS_SUB= yes + +NLS_USES= gettext +NLS_CONFIGURE_ENABLE= nls + .include # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse +.endif + +.if ${CHOSEN_COMPILER_TYPE} == gcc +CXXFLAGS+= -faligned-new .endif .include Index: head/biology/jellyfish/distinfo =================================================================== --- head/biology/jellyfish/distinfo (revision 501577) +++ head/biology/jellyfish/distinfo (revision 501578) @@ -1,3 +1,3 @@ -TIMESTAMP = 1482069678 -SHA256 (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 800bc60aaec273dc04296ee7493e714457f2fe88551f76693e5d9f9a679dd35e -SIZE (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 660858 +TIMESTAMP = 1557758001 +SHA256 (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 49137356b1cdd014cb70e866f0739fc3fafea6421fa22cc64bcfeba55fc1dc27 +SIZE (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 677009 Index: head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp =================================================================== --- head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp (revision 501577) +++ head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp (revision 501578) @@ -1,35 +1,35 @@ ---- include/jellyfish/file_header.hpp.orig 2015-10-27 14:32:31 UTC +--- include/jellyfish/file_header.hpp.orig 2018-04-16 12:46:09 UTC +++ include/jellyfish/file_header.hpp @@ -21,6 +21,8 @@ #include #include +using std::string; + namespace jellyfish { /// A header with jellyfish hash specific entries: size, matrix, etc. class file_header : public generic_file_header { -@@ -42,7 +44,10 @@ public: +@@ -42,7 +44,10 @@ class file_header : public generic_file_header { (publ RectangularBinaryMatrix matrix(int i = 1) const { std::string name("matrix"); - name += std::to_string((long long int)i); // Cast to make gcc4.4 happy! + char buff[100]; + // name += std::to_string((long long int)i); // Cast to make gcc4.4 happy! + snprintf(buff, 99, "%d", i); + name += buff; const unsigned int r = root_[name]["r"].asUInt(); const unsigned int c = root_[name]["c"].asUInt(); - std::vector raw(c, (uint64_t)0); -@@ -53,7 +58,10 @@ public: + if(root_[name]["identity"].asBool()) +@@ -56,7 +61,10 @@ class file_header : public generic_file_header { (publ void matrix(const RectangularBinaryMatrix& m, int i = 1) { std::string name("matrix"); - name += std::to_string((long long int)i); + char buff[100]; + // name += std::to_string((long long int)i); + snprintf(buff, 99, "%d", i); + name += buff; root_[name].clear(); root_[name]["r"] = m.r(); root_[name]["c"] = m.c(); Index: head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp =================================================================== --- head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp (nonexistent) +++ head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp (revision 501578) @@ -0,0 +1,11 @@ +--- include/jellyfish/hash_counter.hpp.orig 2018-04-16 12:46:09 UTC ++++ include/jellyfish/hash_counter.hpp +@@ -213,7 +213,7 @@ class hash_counter { (protected) + new_ary_ = new array(ary_->size(), ary_->key_len(), ary_->val_len() + 1, + ary_->max_reprobe(), ary_->reprobes()); + } +- } catch(typename array::ErrorAllocation e) { ++ } catch(typename array::ErrorAllocation &e) { + new_ary_ = 0; + } + } Property changes on: head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/files/patch-sub__commands_count__main.cc =================================================================== --- head/biology/jellyfish/files/patch-sub__commands_count__main.cc (nonexistent) +++ head/biology/jellyfish/files/patch-sub__commands_count__main.cc (revision 501578) @@ -0,0 +1,11 @@ +--- sub_commands/count_main.cc.orig 2019-05-13 07:42:50 UTC ++++ sub_commands/count_main.cc +@@ -330,7 +330,7 @@ int count_main(int argc, char *argv[]) + uint64_t max = args.upper_count_given ? args.upper_count_arg : std::numeric_limits::max(); + try { + merge_files(files, args.output_arg, header, min, max); +- } catch(MergeError e) { ++ } catch(MergeError &e) { + err::die(err::msg() << e.what()); + } + if(!args.no_unlink_flag) { Property changes on: head/biology/jellyfish/files/patch-sub__commands_count__main.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/files/patch-sub__commands_merge__main.cc =================================================================== --- head/biology/jellyfish/files/patch-sub__commands_merge__main.cc (nonexistent) +++ head/biology/jellyfish/files/patch-sub__commands_merge__main.cc (revision 501578) @@ -0,0 +1,11 @@ +--- sub_commands/merge_main.cc.orig 2019-05-13 07:46:43 UTC ++++ sub_commands/merge_main.cc +@@ -33,7 +33,7 @@ int merge_main(int argc, char *argv[]) + + try { + merge_files(args.input_arg, args.output_arg, out_header, min, max); +- } catch(MergeError e) { ++ } catch(MergeError &e) { + err::die(err::msg() << e.what()); + } + Property changes on: head/biology/jellyfish/files/patch-sub__commands_merge__main.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/files/patch-sub__commands_query__main.cc =================================================================== --- head/biology/jellyfish/files/patch-sub__commands_query__main.cc (nonexistent) +++ head/biology/jellyfish/files/patch-sub__commands_query__main.cc (revision 501578) @@ -0,0 +1,20 @@ +--- sub_commands/query_main.cc.orig 2019-05-13 07:47:53 UTC ++++ sub_commands/query_main.cc +@@ -60,7 +60,7 @@ void query_from_cmdline(std::vector mers, + if(canonical) + m.canonicalize(); + out << m << " " << db.check(m) << "\n"; +- } catch(std::length_error e) { ++ } catch(std::length_error &e) { + std::cerr << "Invalid mer '" << *it << "'\n"; + } + } +@@ -77,7 +77,7 @@ void query_from_stdin(const Database& db, std::ostream + if(canonical) + m.canonicalize(); + out << db.check(m) << std::endl; // a flush is need for interactive use +- } catch(std::length_error e) { ++ } catch(std::length_error &e) { + std::cerr << "Invalid mer '" << buffer << "'" << std::endl; + } + } Property changes on: head/biology/jellyfish/files/patch-sub__commands_query__main.cc ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/jellyfish/pkg-plist =================================================================== --- head/biology/jellyfish/pkg-plist (revision 501577) +++ head/biology/jellyfish/pkg-plist (revision 501578) @@ -1,55 +1,57 @@ bin/jellyfish include/jellyfish-%%VER%%/jellyfish/allocators_mmap.hpp include/jellyfish-%%VER%%/jellyfish/atomic_bits_array.hpp include/jellyfish-%%VER%%/jellyfish/atomic_field.hpp include/jellyfish-%%VER%%/jellyfish/atomic_gcc.hpp include/jellyfish-%%VER%%/jellyfish/backtrace.hpp include/jellyfish-%%VER%%/jellyfish/binary_dumper.hpp include/jellyfish-%%VER%%/jellyfish/bloom_common.hpp include/jellyfish-%%VER%%/jellyfish/bloom_counter2.hpp include/jellyfish-%%VER%%/jellyfish/bloom_filter.hpp include/jellyfish-%%VER%%/jellyfish/circular_buffer.hpp include/jellyfish-%%VER%%/jellyfish/compare_and_swap.hpp include/jellyfish-%%VER%%/jellyfish/cooperative_pool.hpp include/jellyfish-%%VER%%/jellyfish/cooperative_pool2.hpp include/jellyfish-%%VER%%/jellyfish/cpp_array.hpp include/jellyfish-%%VER%%/jellyfish/divisor.hpp include/jellyfish-%%VER%%/jellyfish/dumper.hpp include/jellyfish-%%VER%%/jellyfish/err.hpp include/jellyfish-%%VER%%/jellyfish/file_header.hpp include/jellyfish-%%VER%%/jellyfish/generator_manager.hpp include/jellyfish-%%VER%%/jellyfish/generic_file_header.hpp include/jellyfish-%%VER%%/jellyfish/hash_counter.hpp include/jellyfish-%%VER%%/jellyfish/int128.hpp include/jellyfish-%%VER%%/jellyfish/jellyfish.hpp include/jellyfish-%%VER%%/jellyfish/json.h include/jellyfish-%%VER%%/jellyfish/large_hash_array.hpp include/jellyfish-%%VER%%/jellyfish/large_hash_iterator.hpp include/jellyfish-%%VER%%/jellyfish/locks_pthread.hpp include/jellyfish-%%VER%%/jellyfish/mapped_file.hpp include/jellyfish-%%VER%%/jellyfish/mer_dna.hpp include/jellyfish-%%VER%%/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish-%%VER%%/jellyfish/mer_heap.hpp include/jellyfish-%%VER%%/jellyfish/mer_iterator.hpp include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish-%%VER%%/jellyfish/mer_qual_iterator.hpp include/jellyfish-%%VER%%/jellyfish/misc.hpp include/jellyfish-%%VER%%/jellyfish/offsets_key_value.hpp +include/jellyfish-%%VER%%/jellyfish/parser_common.hpp include/jellyfish-%%VER%%/jellyfish/rectangular_binary_matrix.hpp +include/jellyfish-%%VER%%/jellyfish/sam_format.hpp include/jellyfish-%%VER%%/jellyfish/simple_circular_buffer.hpp include/jellyfish-%%VER%%/jellyfish/sorted_dumper.hpp include/jellyfish-%%VER%%/jellyfish/stdio_filebuf.hpp include/jellyfish-%%VER%%/jellyfish/storage.hpp include/jellyfish-%%VER%%/jellyfish/stream_iterator.hpp include/jellyfish-%%VER%%/jellyfish/stream_manager.hpp include/jellyfish-%%VER%%/jellyfish/text_dumper.hpp include/jellyfish-%%VER%%/jellyfish/thread_exec.hpp include/jellyfish-%%VER%%/jellyfish/time.hpp include/jellyfish-%%VER%%/jellyfish/token_ring.hpp include/jellyfish-%%VER%%/jellyfish/whole_sequence_parser.hpp lib/libjellyfish-2.0.a lib/libjellyfish-2.0.so lib/libjellyfish-2.0.so.2 lib/libjellyfish-2.0.so.2.0.0 libdata/pkgconfig/jellyfish-2.0.pc man/man1/jellyfish.1.gz