svn commit: r501578 - in head/biology/jellyfish: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon May 13 16:23:38 UTC 2019
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 at 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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