Date: Mon, 13 May 2019 16:23:36 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r501578 - in head/biology/jellyfish: . files Message-ID: <201905131623.x4DGNa6o078017@repo.freebsd.org>
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Author: jwb Date: Mon May 13 16:23:35 2019 New Revision: 501578 URL: https://svnweb.freebsd.org/changeset/ports/501578 Log: biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64 PR: 237868 Submitted by: pkubaj Added: head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp (contents, props changed) head/biology/jellyfish/files/patch-sub__commands_count__main.cc (contents, props changed) head/biology/jellyfish/files/patch-sub__commands_merge__main.cc (contents, props changed) head/biology/jellyfish/files/patch-sub__commands_query__main.cc (contents, props changed) Modified: head/biology/jellyfish/Makefile head/biology/jellyfish/distinfo head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp head/biology/jellyfish/pkg-plist Modified: head/biology/jellyfish/Makefile ============================================================================== --- head/biology/jellyfish/Makefile Mon May 13 15:23:41 2019 (r501577) +++ head/biology/jellyfish/Makefile Mon May 13 16:23:35 2019 (r501578) @@ -1,10 +1,10 @@ # $FreeBSD$ -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 @@ -13,25 +13,33 @@ 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 <bsd.port.pre.mk> # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse +.endif + +.if ${CHOSEN_COMPILER_TYPE} == gcc +CXXFLAGS+= -faligned-new .endif .include <bsd.port.post.mk> Modified: head/biology/jellyfish/distinfo ============================================================================== --- head/biology/jellyfish/distinfo Mon May 13 15:23:41 2019 (r501577) +++ head/biology/jellyfish/distinfo Mon May 13 16:23:35 2019 (r501578) @@ -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 Modified: head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp ============================================================================== --- head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp Mon May 13 15:23:41 2019 (r501577) +++ head/biology/jellyfish/files/patch-include_jellyfish_file__header.hpp Mon May 13 16:23:35 2019 (r501578) @@ -1,4 +1,4 @@ ---- 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 <jellyfish/generic_file_header.hpp> @@ -9,7 +9,7 @@ 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"); @@ -20,8 +20,8 @@ + name += buff; const unsigned int r = root_[name]["r"].asUInt(); const unsigned int c = root_[name]["c"].asUInt(); - std::vector<uint64_t> 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"); Added: head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp Mon May 13 16:23:35 2019 (r501578) @@ -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; + } + } Added: head/biology/jellyfish/files/patch-sub__commands_count__main.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/jellyfish/files/patch-sub__commands_count__main.cc Mon May 13 16:23:35 2019 (r501578) @@ -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<uint64_t>::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) { Added: head/biology/jellyfish/files/patch-sub__commands_merge__main.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/jellyfish/files/patch-sub__commands_merge__main.cc Mon May 13 16:23:35 2019 (r501578) @@ -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()); + } + Added: head/biology/jellyfish/files/patch-sub__commands_query__main.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/jellyfish/files/patch-sub__commands_query__main.cc Mon May 13 16:23:35 2019 (r501578) @@ -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<const char*> 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; + } + } Modified: head/biology/jellyfish/pkg-plist ============================================================================== --- head/biology/jellyfish/pkg-plist Mon May 13 15:23:41 2019 (r501577) +++ head/biology/jellyfish/pkg-plist Mon May 13 16:23:35 2019 (r501578) @@ -35,7 +35,9 @@ include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequen 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
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