From nobody Fri Oct 18 11:39:16 2024 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 4XVN5d17M0z5Z5wL; Fri, 18 Oct 2024 11:39:17 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XVN5d0Nypz4Bkm; Fri, 18 Oct 2024 11:39:17 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1729251557; 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=qKQWuUtQEdOaaiNt4IndFWBau+BvcOFTYcTuqz6DGVg=; b=p0OAJM8b/s0aQiX3aozFKTM9CrMHab33T4w7KjBPRDYCaLGsc7pzRjbDQ9527nhct5obXR Amt/9tiP0K/gcIRzxKh7LceZk3wUG4HfxWewFv499igypCgikbO7Oi0LCdS6/MhUbkGPPN 9enks5lc6FpIhERM0MMiyFiX113jOncucfq5+hagPNGe7r4VUlujBuM2af/a/tvhffBj3W pd59CjWzfDnwZOoO5ghKJbaJJdEK487upTYLvqMUw5aED0K9R7Nt82+/kMkL51MFLYK0LY 8LWWARGiskAISsDudWY9j8C+8UGE7l2oxYoI82DT6hjWyAduFjDx4IO5tYudfQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1729251557; 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=qKQWuUtQEdOaaiNt4IndFWBau+BvcOFTYcTuqz6DGVg=; b=kg+rYJQDVt6dcQ9T96EHpzkBLaWvzXfSAfRB4epFl1m5magfDHBj8FlV6AziNImbPZpS0P C5BMLTQoxK4Ai1KEJsi2IxTwm9oTXg130p2YdGAlFCPXMou+T8ihjZCEGe12vzFDXbXPu+ JLDdI//HUg4BNE78dkVqnBAbjamLlT1WPqSuIMxUoKpumRaQSjSPLW1ZomQ6ufi27nIyH5 bRAC2w7nxDVITaf5HloJJA6EuboaV9KH91IQ5n6k7gAZ2FPnWmIfeShmJpIglwptSQ8wXR +cB5hS4joPOsSA/Xppqa9hPFfT58lAfhxvz74UXQX0ELM/DBY4pBaa4Cswxkcg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1729251557; a=rsa-sha256; cv=none; b=Y1fvR7FM4vCzRBuos8AiIUR6IgDMh6qzQKkLq7ZCdZpQFGdmhkj1tHoOYrHHQwDlAfQSJa vEaHnSh9sTYT7kwfFYHIknJd0YnIcZGNEFpn1oC/ZwN36DpDu01VVvG2/xLXe4c8ObQQ0x 1H3X4xtVBdltQ5NquxJg0xnOdlmVHq0RtE1g5IhPSX6rA2rsRWjwq2kAnCsBexUvZ64DaN Qlvl0GkZn8nAVjHqjucfcB0s51xGqNIL8IBZNacT5Eo2hX863bpEhsXca3ZTKsPNcLAl75 bG3ZUjdGNoP8yrFP0qTGh/umU69N+ZUI9zGDWDTYlo1UagrlrFoarRwgkVYDuA== 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 4XVN5c6wgBzY78; Fri, 18 Oct 2024 11:39:16 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 49IBdGfm078271; Fri, 18 Oct 2024 11:39:16 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 49IBdG1a078268; Fri, 18 Oct 2024 11:39:16 GMT (envelope-from git) Date: Fri, 18 Oct 2024 11:39:16 GMT Message-Id: <202410181139.49IBdG1a078268@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: 0ece2dbac79c - main - biology/trimadap: Update to 0.1.4 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: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-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: 0ece2dbac79cc447af3d8385ff6ab867134cccb7 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0ece2dbac79cc447af3d8385ff6ab867134cccb7 commit 0ece2dbac79cc447af3d8385ff6ab867134cccb7 Author: Jason W. Bacon AuthorDate: 2024-10-18 11:37:12 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-18 11:37:12 +0000 biology/trimadap: Update to 0.1.4 Update to latest commit, with new MIT license Add support for other architectures using SIMDE Reported by: fuz Reviewed by: fuz Differential Revision: https://reviews.freebsd.org/D47129 --- biology/trimadap/Makefile | 11 +++++------ biology/trimadap/distinfo | 6 +++--- biology/trimadap/files/patch-ksw.c | 13 +++++++++++++ 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/biology/trimadap/Makefile b/biology/trimadap/Makefile index 800b2a18d6fe..7d5d5a58e05f 100644 --- a/biology/trimadap/Makefile +++ b/biology/trimadap/Makefile @@ -1,18 +1,17 @@ PORTNAME= trimadap -DISTVERSION= 0.1-3 -DISTVERSIONSUFFIX= -gddfef21 -PORTREVISION= 1 +DISTVERSION= 0.1-4 +DISTVERSIONSUFFIX= -gec5a764 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Trim adapter sequences from Illumina data using heuristic rules WWW= https://github.com/lh3/trimadap -LICENSE= GPLv2 +LICENSE= MIT -ONLY_FOR_ARCHS= amd64 i386 powerpc64le -ONLY_FOR_ARCHS_REASON= uses hard-coded SSE instructions +BUILD_DEPENDS= simde>0:devel/simde +USES= localbase USE_GITHUB= yes GH_ACCOUNT= lh3 diff --git a/biology/trimadap/distinfo b/biology/trimadap/distinfo index 99e06ce2a75b..59177ee4abda 100644 --- a/biology/trimadap/distinfo +++ b/biology/trimadap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1522773176 -SHA256 (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = c2c42a3257d37b12be3523ed0d4415bddd401d72b99b05ba4ae33afaa3c3f373 -SIZE (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = 13138 +TIMESTAMP = 1729109026 +SHA256 (lh3-trimadap-0.1-4-gec5a764_GH0.tar.gz) = fa842c705028054e13dc5be6aab5feb621b0ac54c2ca5bee3ab9eb9046a55ac4 +SIZE (lh3-trimadap-0.1-4-gec5a764_GH0.tar.gz) = 13268 diff --git a/biology/trimadap/files/patch-ksw.c b/biology/trimadap/files/patch-ksw.c new file mode 100644 index 000000000000..e82692c1ee80 --- /dev/null +++ b/biology/trimadap/files/patch-ksw.c @@ -0,0 +1,13 @@ +--- ksw.c.orig 2024-10-16 19:52:35 UTC ++++ ksw.c +@@ -26,7 +26,9 @@ + #include + #include + #include +-#include ++// #include ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include + #include "ksw.h" + + #ifdef __GNUC__