From nobody Fri Sep 29 18:25:39 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RxzLC6rm7z4vVtR; Fri, 29 Sep 2023 18:25:39 +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 4RxzLC4sNKz3Dp6; Fri, 29 Sep 2023 18:25:39 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1696011939; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=YOLsCqQQ7NVrAMfwYhzVE3cT0ltgLE/ErM8RW+T1fsI=; b=U+VTnRd923mrzI49ZHMNcs4LwIUAqPKOL3N3hXZh2/ubihm1kJ1dhTEGl//hIWqCZ/U2z4 oeiHwZLL0jPj9LJMbMZSN2cewDx8oprJmmu5xKGWn3/eLay35oHMAgaaTKGjWUQBMjEDIN VPUb2J+I64590XTF4MKuEtPX/+GMWsQovrW/3himM47nfUVptpaHjZ6NNvAG/EPArvOLj6 RdOqNnmw5h4E+89a7Zqwk+F6CCV06XXL7r/2iOosTuSzHlvLGUX+UWOtgGhQ5MsR8vv80m acDODed2QQp2cNKtRDmyoMvAej3rm8VnstsQuric+6MtODxjDzAOjw665z7lTw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1696011939; a=rsa-sha256; cv=none; b=tw2B0Ay5g/At95WHGP2T47AsPfvKNvzvcsnX7KBkQhCbMzyKMwyd0/UeVnEN1+Re64HnRl Xd4fhvOlyFKlJd42lwJjbTKxwYBZ4S215/qhduU5mfTdto3dhNV1UR+yWlWjGQ52b3eDH4 JYaWLAFYgNnvK3GVfJfZIdWG+dw253iBLbwvKuDffjx56uOUMNKGvaSgqi/pB/us8Z2r7f 17tnWUjvAfVW9Hhpsg6HgnQ81PKmGYTvZC/40aVLP7/YaqHkcAOBTnGoP/dSa+bfH5zKGW WGePXSGDe+BKgDynf1GwvCKFSR3V8rur/fgI5WVzUAxa0Kg1EWkD+P+ov14JVg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1696011939; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=YOLsCqQQ7NVrAMfwYhzVE3cT0ltgLE/ErM8RW+T1fsI=; b=AIIBj6b5cwce0g0JShKpPCsOxhnq28Db/yj9d0Fpi3umYNyrWaq5CGih0BA/a1u5ock6Ks RxumERBxlFZ5PDimFD4ZddqqP8mptg0t63xWzoCj86NylsDCR5Cbj6ZdW6u1F5cmhcVuBu AKvN+kffLEnJZGIfe1aOlDkt/MHWRcWL2Yhw2jc8Gm89lc9CHOBoqNDszvflBlZyspCe51 IEj6mzZaT7ZmJhclmh+8IGC09iJ5pHSYs/19rD0j2ohVnL3cFf+4bzsQL8+unHEe/6LJEY HnZmE4gfVD8UWKtuZ/w7mJzmTKMkfUVQw8HBjqf4YKtpO9iUrR1dAvBjJENEmQ== 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 4RxzLC3zF5ztp; Fri, 29 Sep 2023 18:25:39 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 38TIPdLH067849; Fri, 29 Sep 2023 18:25:39 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 38TIPd62067846; Fri, 29 Sep 2023 18:25:39 GMT (envelope-from git) Date: Fri, 29 Sep 2023 18:25:39 GMT Message-Id: <202309291825.38TIPd62067846@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: f3576d9ad821 - main - biology/wfa2-lib: Update to 2.3.4 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org 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: f3576d9ad8210076b1f2e81f0bea81f48947f234 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=f3576d9ad8210076b1f2e81f0bea81f48947f234 commit f3576d9ad8210076b1f2e81f0bea81f48947f234 Author: Jason W. Bacon AuthorDate: 2023-09-29 18:24:07 +0000 Commit: Jason W. Bacon CommitDate: 2023-09-29 18:24:07 +0000 biology/wfa2-lib: Update to 2.3.4 A few bug fixes Changes: https://github.com/smarco/WFA2-lib/releases Reported by: portscout --- biology/wfa2-lib/Makefile | 3 +-- biology/wfa2-lib/distinfo | 6 +++--- biology/wfa2-lib/files/patch-CMakeLists.txt | 2 +- .../files/patch-wavefront_wavefront__extend__kernels.c | 11 +++++++++++ biology/wfa2-lib/pkg-plist | 9 ++++++++- 5 files changed, 24 insertions(+), 7 deletions(-) diff --git a/biology/wfa2-lib/Makefile b/biology/wfa2-lib/Makefile index 2300f379ec6f..a8a95a8229d4 100644 --- a/biology/wfa2-lib/Makefile +++ b/biology/wfa2-lib/Makefile @@ -1,7 +1,6 @@ PORTNAME= wfa2-lib DISTVERSIONPREFIX= v -DISTVERSION= 2.3.2 -PORTREVISION= 1 +DISTVERSION= 2.3.4 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/wfa2-lib/distinfo b/biology/wfa2-lib/distinfo index 09a5d3555324..ab50e1352a95 100644 --- a/biology/wfa2-lib/distinfo +++ b/biology/wfa2-lib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1675088499 -SHA256 (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 310e3886506ab57d04205cdf5fed3ef31969ce39e9c6d341fd5c8a0d4aa0830b -SIZE (smarco-WFA2-lib-v2.3.2_GH0.tar.gz) = 4150874 +TIMESTAMP = 1695995337 +SHA256 (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23 +SIZE (smarco-WFA2-lib-v2.3.4_GH0.tar.gz) = 4224505 diff --git a/biology/wfa2-lib/files/patch-CMakeLists.txt b/biology/wfa2-lib/files/patch-CMakeLists.txt index 8b71ad656f0a..5be0031f15f4 100644 --- a/biology/wfa2-lib/files/patch-CMakeLists.txt +++ b/biology/wfa2-lib/files/patch-CMakeLists.txt @@ -1,4 +1,4 @@ ---- CMakeLists.txt.orig 2023-01-31 15:02:27 UTC +--- CMakeLists.txt.orig 2023-09-29 13:47:52 UTC +++ CMakeLists.txt @@ -55,7 +55,7 @@ if(NOT CMAKE_BUILD_TYPE) endif() diff --git a/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c new file mode 100644 index 000000000000..c46271b7a21e --- /dev/null +++ b/biology/wfa2-lib/files/patch-wavefront_wavefront__extend__kernels.c @@ -0,0 +1,11 @@ +--- wavefront/wavefront_extend_kernels.c.orig 2023-09-29 17:25:17 UTC ++++ wavefront/wavefront_extend_kernels.c +@@ -29,7 +29,7 @@ + * DESCRIPTION: WFA module for the "extension" of exact matches + */ + +-#include ++#include + + #include "wavefront_extend_kernels.h" + #include "wavefront_termination.h" diff --git a/biology/wfa2-lib/pkg-plist b/biology/wfa2-lib/pkg-plist index 235ff54015ca..2fa4ac482adc 100644 --- a/biology/wfa2-lib/pkg-plist +++ b/biology/wfa2-lib/pkg-plist @@ -3,6 +3,7 @@ include/wfa2lib/alignment/affine_penalties.h include/wfa2lib/alignment/cigar.h include/wfa2lib/alignment/linear_penalties.h include/wfa2lib/alignment/score_matrix.h +include/wfa2lib/bindings/cpp/WFAligner.hpp include/wfa2lib/system/mm_allocator.h include/wfa2lib/system/mm_stack.h include/wfa2lib/system/profiler_counter.h @@ -12,7 +13,6 @@ include/wfa2lib/utils/commons.h include/wfa2lib/utils/dna_text.h include/wfa2lib/utils/heatmap.h include/wfa2lib/utils/sequence_buffer.h -include/wfa2lib/utils/string_padded.h include/wfa2lib/utils/vector.h include/wfa2lib/wavefront/wavefront.h include/wfa2lib/wavefront/wavefront_align.h @@ -32,15 +32,22 @@ include/wfa2lib/wavefront/wavefront_compute_linear.h include/wfa2lib/wavefront/wavefront_debug.h include/wfa2lib/wavefront/wavefront_display.h include/wfa2lib/wavefront/wavefront_extend.h +include/wfa2lib/wavefront/wavefront_extend_kernels.h +include/wfa2lib/wavefront/wavefront_extend_kernels_avx.h include/wfa2lib/wavefront/wavefront_heuristic.h include/wfa2lib/wavefront/wavefront_offset.h include/wfa2lib/wavefront/wavefront_pcigar.h include/wfa2lib/wavefront/wavefront_penalties.h include/wfa2lib/wavefront/wavefront_plot.h +include/wfa2lib/wavefront/wavefront_sequences.h include/wfa2lib/wavefront/wavefront_slab.h +include/wfa2lib/wavefront/wavefront_termination.h include/wfa2lib/wavefront/wavefront_unialign.h include/wfa2lib/wavefront/wfa.h include/wfa2lib/wavefront/wfa.hpp lib/libwfa2.a lib/libwfa2.so lib/libwfa2.so.0 +lib/libwfa2cpp.a +lib/libwfa2cpp.so +lib/libwfa2cpp.so.0