From nobody Sat Dec 18 19:37:08 2021 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 AE97A18FFB90; Sat, 18 Dec 2021 19:37:08 +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 4JGbhh1tQ7z3GFX; Sat, 18 Dec 2021 19:37:08 +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 1D00815051; Sat, 18 Dec 2021 19:37:08 +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 1BIJb8xZ040571; Sat, 18 Dec 2021 19:37:08 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1BIJb8tY040570; Sat, 18 Dec 2021 19:37:08 GMT (envelope-from git) Date: Sat, 18 Dec 2021 19:37:08 GMT Message-Id: <202112181937.1BIJb8tY040570@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: 02105a9bc95c - main - biology/seqtk: Update to 1.3 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: 02105a9bc95c5771fac5452e1cf8176a1b591c88 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1639856228; 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=fzx2P7coo4OjRd8GuZXv+bGDhK7aDuruTLMkEHNP9I8=; b=tJZGcRfFrAM0RoGm670mJR+m/UczbY2AzQs7sngbmY9z2zodu93Pku8x5ti0GyRhcl24MB JQcYQb3df1DxpXce8WX4dsRSJWpU3VSnnk705GnvaRqGXOhiNq18+fGyyfKqp+H08qdKIg d1Aj6WlDk3ji4H9fr7txU9XKDV8EcBR1GSN2GUeG85DMJBZiVInkKYnlE3v5y9oIvpkLn1 vHf/l26WcwdxKIPF/YadqpQCWTCc6L1VAdbBS4X9nRS3t5088o9U6kF6G2g2gx3A7k8sz5 S4GsdjNkSexig/+N0ws73ieER3x1CdQVEFkGriKLEfHgxCau1GJ43CScjQt6AQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1639856228; a=rsa-sha256; cv=none; b=YWYp0nBc4vIlbJ3jAxn/KedBLOH3Q68XNH6163AREe7X0hul1e0vvcGB+1H0pkHcZjbSme MUPUNUzcWQZG7hLCWGaJirxJVfHe9Nqpmx17hTP/HXOtMLqhPsgPL2bX5Efv0yTZRrrvg/ wmDCmYg9u5f6WTXJcnQVvjngE5mBZ+Qudj4X2ECll9kZinGqAaG/qWtqvYpx9ylqVmSteU /1QGCuQwTaYepc2tYUL6ioE/Qv6b/gSLKBjDdpU3ZNLgOnpLiJl+eIvLG87TB8C/vrevaj F0NAgJqLq4YRn6PjsCNnpfO9b56urFeVQLB5DQ0p73I1mQd0T013V1AFNOYcdw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=02105a9bc95c5771fac5452e1cf8176a1b591c88 commit 02105a9bc95c5771fac5452e1cf8176a1b591c88 Author: Jason W. Bacon AuthorDate: 2021-12-18 19:35:28 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-18 19:37:06 +0000 biology/seqtk: Update to 1.3 A few minor fixes and enhancements Changes: https://github.com/lh3/seqtk/tags --- biology/seqtk/Makefile | 11 ++++------- biology/seqtk/distinfo | 6 +++--- biology/seqtk/files/patch-Makefile | 29 ++++++++++++++++++++++------- 3 files changed, 29 insertions(+), 17 deletions(-) diff --git a/biology/seqtk/Makefile b/biology/seqtk/Makefile index 820432492ed8..c4b0dd5ecab6 100644 --- a/biology/seqtk/Makefile +++ b/biology/seqtk/Makefile @@ -1,7 +1,7 @@ -PORTNAME= seqtk -DISTVERSION= 1.2-8 -DISTVERSIONSUFFIX= -gd210c57 -CATEGORIES= biology +PORTNAME= seqtk +DISTVERSIONPREFIX= v +DISTVERSION= 1.3 +CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tool for processing sequences in FASTA/FASTQ format @@ -13,7 +13,4 @@ GH_ACCOUNT= lh3 PLIST_FILES= bin/seqtk -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/seqtk ${STAGEDIR}${PREFIX}/bin - .include diff --git a/biology/seqtk/distinfo b/biology/seqtk/distinfo index 430869c941bf..f44856371472 100644 --- a/biology/seqtk/distinfo +++ b/biology/seqtk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1522780777 -SHA256 (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 557317aab7f8cc306a98cd1148449f1e2edd7cd7c78ad5254ba955dfee518fa0 -SIZE (lh3-seqtk-1.2-8-gd210c57_GH0.tar.gz) = 21166 +TIMESTAMP = 1639855187 +SHA256 (lh3-seqtk-v1.3_GH0.tar.gz) = 5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563 +SIZE (lh3-seqtk-v1.3_GH0.tar.gz) = 21196 diff --git a/biology/seqtk/files/patch-Makefile b/biology/seqtk/files/patch-Makefile index 6d8f5ee8535d..ab373642a46e 100644 --- a/biology/seqtk/files/patch-Makefile +++ b/biology/seqtk/files/patch-Makefile @@ -1,20 +1,35 @@ ---- Makefile.orig 2017-11-07 19:42:14 UTC +--- Makefile.orig 2018-06-18 00:15:09 UTC +++ Makefile -@@ -1,10 +1,11 @@ +@@ -1,14 +1,23 @@ -CC=gcc -CFLAGS=-g -Wall -O2 -Wno-unused-function -+CC ?= gcc -+CFLAGS ?= -g -Wall -O2 -Wno-unused-function -+LDFLAGS += -lz -lm +-BINDIR=/usr/local/bin -all:seqtk -+all: seqtk ++# Respect user's build environment by using ?= to set defaults for variables ++# not set in the env or make arguments. Use += to add essential args. -seqtk:seqtk.c khash.h kseq.h - $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function ++LDFLAGS += -lz -lm ++PREFIX ?= /usr/local ++MKDIR ?= mkdir ++INSTALL ?= install ++# DESTDIR is empty by default to install straight to PREFIX + +-install:all +- install seqtk $(BINDIR) ++all: seqtk + +seqtk: seqtk.c khash.h kseq.h + $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) - ++ ++install: all ++ $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin ++ $(INSTALL) -c -m 0755 seqtk $(DESTDIR)$(PREFIX)/bin ++ clean: - rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session* + rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*