From nobody Thu Aug 17 16:05:07 2023 X-Original-To: dev-commits-ports-main@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 4RRVFv4tzZz4mMRv; Thu, 17 Aug 2023 16:05:07 +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 4RRVFv4Fylz3Bvl; Thu, 17 Aug 2023 16:05:07 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1692288307; 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=X9mikWEn3PrvlquygMXDBJ89hPGW9A3PclRZvvo6LQM=; b=YcEYpl0Zo1SrI9K9hIsyQD/RzccdA802QdmnmFcih5I4Z2OBP/AhXWruCYEJpAgJMRoFMj 5q1Q8hKppEYtX7CAf69BegTnqnS2V80Ye+s0OJiKbnFVAFJ2JCaMepMvySp17iOuvqSg+U sOq4SFb3H3XsuaJulleK4gtrsDA/QIWRAt5ckLTt8gH6JQj17KCeW1uU+PleWe9vmWkXCA cFLT2UUrPQSF8mmhkiwOhPPUfb6co52mzZPHOFtMSkHEmBWu2awKEC8w4gBYY0yNWoLCYE vPNikCqCP04bOaPeeoZ9fpX9LezRgC827y/JHM581U0nw3DKHQRQgh7iFXUHYg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1692288307; 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=X9mikWEn3PrvlquygMXDBJ89hPGW9A3PclRZvvo6LQM=; b=hN0vv4ws6UnV8ZJFhwyfJc/BM/aq0rhZgO8kGDL562RWfRcY2GYWN3pNR87RVRj3CyJLlt hdSQYWZ8VnjttARkTH25yRUOzxmJUpey8NZMJHc6jtv75maSzXrIj8OKl/HeyS7GUxlRIa +bkL8bmeeBnnHMbFi06z1x3719e1RXifdkYu/9qc52xhPfL+lbtHIb60eBmCTzI7YzvDuJ ScbWKEXg8MKmxTZmo/rhTq9KPYOBKGBQisgek9ZhbwdRUPEpxVcD+rXKm5OPisspR8QyBd +XQWCN3iieE0Nmg5yg97y+G4JSND0du9280ynTGImE1whI0jl9Tjjww8rJZCjw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1692288307; a=rsa-sha256; cv=none; b=A5tx4WQ/FgSbiINJzyNz0MMDv/IsBVrUGjVTXs8v684oc1l8AotHUgQ+6f4k+Kc2mp4VlG 4p+oVx4KkbIDhXHp/nQOGT8dYb8DSzcfasvhi1ytJf4PpKfWwBuecMg7y4YUB5kL5gRlBh t4JgbvuKUy3/TPoHrRlprtrn6vUd41ydXRq8tJW/yzoxnlRd9g7YtAcr4rUJetjI5lrgn3 2KZrfm6kJY9BYFORroYUfLaWKP9paZryYsY0OE45NPJvfB9w5gquaoGJn6iSvnjr6Hn1v2 iLU95voLXn/zpij9Zhwxus3NBHFAScg8RolHadrSkXmC+bickhVLbkPJEy6Diw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4RRVFv31ThzgGK; Thu, 17 Aug 2023 16:05:07 +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 37HG57V7096473; Thu, 17 Aug 2023 16:05:07 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 37HG57qF096470; Thu, 17 Aug 2023 16:05:07 GMT (envelope-from git) Date: Thu, 17 Aug 2023 16:05:07 GMT Message-Id: <202308171605.37HG57qF096470@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: a382bcefaf86 - main - biology/star: Update to 2.7.11a List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@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: a382bcefaf863b6a253ea49758b67de6995e9ca2 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a382bcefaf863b6a253ea49758b67de6995e9ca2 commit a382bcefaf863b6a253ea49758b67de6995e9ca2 Author: Jason W. Bacon AuthorDate: 2023-08-17 16:01:09 +0000 Commit: Jason W. Bacon CommitDate: 2023-08-17 16:01:09 +0000 biology/star: Update to 2.7.11a A few bug fixes and new features Add USE_GCC as a temporary hack for input read issue This was also an issue in 2.7.10b Changes: https://github.com/alexdobin/STAR/releases --- biology/star/Makefile | 5 ++++- biology/star/distinfo | 6 +++--- biology/star/files/patch-SpliceGraph.cpp | 10 ---------- biology/star/files/patch-opal_opal.cpp | 13 ------------- 4 files changed, 7 insertions(+), 27 deletions(-) diff --git a/biology/star/Makefile b/biology/star/Makefile index fc32ddebc58b..dd8137dee91f 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,5 +1,5 @@ PORTNAME= STAR -DISTVERSION= 2.7.10b +DISTVERSION= 2.7.11a CATEGORIES= biology PKGNAMEPREFIX= rna- @@ -16,9 +16,12 @@ NOT_FOR_ARCHS_REASON= Requires 64-bit processor BROKEN= requires OpenMP support that is missing on this architecture .endif +BUILD_DEPENDS= xxd:sysutils/xxd LIB_DEPENDS= libhts.so:biology/htslib USES= compiler:c++11-lang gmake localbase:ldflags +# FIXME: When built with clang, number of input reads = 0 +USE_GCC= yes USE_GITHUB= yes GH_ACCOUNT= alexdobin diff --git a/biology/star/distinfo b/biology/star/distinfo index 6f7048071c63..395c98a981c1 100644 --- a/biology/star/distinfo +++ b/biology/star/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1689939622 -SHA256 (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5 -SIZE (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 12443703 +TIMESTAMP = 1692285897 +SHA256 (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a +SIZE (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 12463429 diff --git a/biology/star/files/patch-SpliceGraph.cpp b/biology/star/files/patch-SpliceGraph.cpp deleted file mode 100644 index b839bfe7e802..000000000000 --- a/biology/star/files/patch-SpliceGraph.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- SpliceGraph.cpp.orig 2023-07-21 15:27:26 UTC -+++ SpliceGraph.cpp -@@ -1,7 +1,6 @@ - /* - * Created by Fahimeh Mirhaj on 6/10/19. - */ --using namespace std; - - #include "SpliceGraph.h" - #include "GTF.h" diff --git a/biology/star/files/patch-opal_opal.cpp b/biology/star/files/patch-opal_opal.cpp deleted file mode 100644 index dcda064df27a..000000000000 --- a/biology/star/files/patch-opal_opal.cpp +++ /dev/null @@ -1,13 +0,0 @@ ---- opal/opal.cpp.orig 2021-11-26 16:14:46 UTC -+++ opal/opal.cpp -@@ -5,10 +5,8 @@ - #include - #include - --extern "C" { - #define SIMDE_ENABLE_NATIVE_ALIASES - #include // AVX2 and lower --} - - #include "opal.h" -