From owner-dev-commits-ports-main@freebsd.org Sun Aug 22 17:45:26 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id C5517659D99; Sun, 22 Aug 2021 17:45:26 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Gt2pG5G0Jz3LVQ; Sun, 22 Aug 2021 17:45:26 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 9E1C225204; Sun, 22 Aug 2021 17:45:26 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 17MHjQFT018082; Sun, 22 Aug 2021 17:45:26 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17MHjQoI018081; Sun, 22 Aug 2021 17:45:26 GMT (envelope-from git) Date: Sun, 22 Aug 2021 17:45:26 GMT Message-Id: <202108221745.17MHjQoI018081@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 4952cf637ae5 - main - biology/jellyfish: Update to 2.3.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 4952cf637ae51394337f4ec1c3df17417c171831 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 22 Aug 2021 17:45:26 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=4952cf637ae51394337f4ec1c3df17417c171831 commit 4952cf637ae51394337f4ec1c3df17417c171831 Author: Jason W. Bacon AuthorDate: 2021-08-22 17:44:17 +0000 Commit: Jason W. Bacon CommitDate: 2021-08-22 17:44:17 +0000 biology/jellyfish: Update to 2.3.0 Changelog: https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0 --- biology/jellyfish/Makefile | 3 +-- biology/jellyfish/distinfo | 6 +++--- .../files/patch-include_jellyfish_hash__counter.hpp | 11 ----------- .../files/patch-sub__commands_count__main.cc | 11 ----------- .../files/patch-sub__commands_merge__main.cc | 11 ----------- .../files/patch-sub__commands_query__main.cc | 20 -------------------- 6 files changed, 4 insertions(+), 58 deletions(-) diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile index d84f96e88420..9937ac96c1b2 100644 --- a/biology/jellyfish/Makefile +++ b/biology/jellyfish/Makefile @@ -1,7 +1,6 @@ PORTNAME= Jellyfish DISTVERSIONPREFIX= v -DISTVERSION= 2.2.10 -PORTREVISION= 9 +DISTVERSION= 2.3.0 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/jellyfish/distinfo b/biology/jellyfish/distinfo index 9bea24513108..8e77167cbbfa 100644 --- a/biology/jellyfish/distinfo +++ b/biology/jellyfish/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1557758001 -SHA256 (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 49137356b1cdd014cb70e866f0739fc3fafea6421fa22cc64bcfeba55fc1dc27 -SIZE (gmarcais-Jellyfish-v2.2.10_GH0.tar.gz) = 677009 +TIMESTAMP = 1629646709 +SHA256 (gmarcais-Jellyfish-v2.3.0_GH0.tar.gz) = 23819da9edb579a0cfb8baac9eff473a9477f4f749930cdb754dce1d117495cd +SIZE (gmarcais-Jellyfish-v2.3.0_GH0.tar.gz) = 679144 diff --git a/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp b/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp deleted file mode 100644 index 7410c3edcb71..000000000000 --- a/biology/jellyfish/files/patch-include_jellyfish_hash__counter.hpp +++ /dev/null @@ -1,11 +0,0 @@ ---- 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; - } - } diff --git a/biology/jellyfish/files/patch-sub__commands_count__main.cc b/biology/jellyfish/files/patch-sub__commands_count__main.cc deleted file mode 100644 index b4f2404b6cb2..000000000000 --- a/biology/jellyfish/files/patch-sub__commands_count__main.cc +++ /dev/null @@ -1,11 +0,0 @@ ---- sub_commands/count_main.cc.orig 2018-04-16 12:46:09 UTC -+++ sub_commands/count_main.cc -@@ -360,7 +360,7 @@ 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) { diff --git a/biology/jellyfish/files/patch-sub__commands_merge__main.cc b/biology/jellyfish/files/patch-sub__commands_merge__main.cc deleted file mode 100644 index 0b331da069ff..000000000000 --- a/biology/jellyfish/files/patch-sub__commands_merge__main.cc +++ /dev/null @@ -1,11 +0,0 @@ ---- 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()); - } - diff --git a/biology/jellyfish/files/patch-sub__commands_query__main.cc b/biology/jellyfish/files/patch-sub__commands_query__main.cc deleted file mode 100644 index 243b0df29485..000000000000 --- a/biology/jellyfish/files/patch-sub__commands_query__main.cc +++ /dev/null @@ -1,20 +0,0 @@ ---- 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; - } - }