From nobody Fri Feb 24 23:31:46 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 4PNmPZ6cDjz3v4wd; Fri, 24 Feb 2023 23:31:46 +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 4PNmPZ5sCDz4Jr7; Fri, 24 Feb 2023 23:31:46 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677281506; 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=HfWR96sbxPNjo7r3Egsmg0qDtDy5NsTjQhPQdep0hYE=; b=jvJyglKwW9AsDrPeFxmZSfnY+YgYBAAC/wXynVpKJz2VHjgjaoeo2LZZzWS25/WFXKrJTQ sQx7M7LFC5oGb8cnKL4LhEhZZZhi02QjD6A1dcwewB4kMlb5Eyo8xG2Cga3LZ+y4GmX63U LWoyPto58L9SBAG9dJh3D9/Btz3d4fEevcQd1obcO8avzzh3vT6yGrcj2jI4gQU2zcYT2d JslXNPOy0UU1wxDBlq6jXmjqItBNkHLpaJZbmWxxbRaYvyDiDFN/Xwxzpo+WQfyOHAo/vy a3YOVGrzw3AIL8pQqN1WWi4/uLdTDAbAKBHtrFnDBihq57DfBX57s6HUmIXoxA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677281506; 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=HfWR96sbxPNjo7r3Egsmg0qDtDy5NsTjQhPQdep0hYE=; b=Hcp6sHg9EqabHFd83Mp/stAweBGgLXHjNlg3WISL8g7XplUuw2tZJmbqtzk6jUQxbYQJch YI75j1TVo8wLQGLCqvsbrGcEVR44oF2dTQZVmGOn+yS1Z7n0SDl4VqYg5W4MPJNWLMIfXD TNgLS2Ghw4sBlUzL67YwbhIKg/11PpKTyWNMmAad6zbSHtlS4tsVkzkhvYzhHeJBep6tAm GuCnyGGvhlezb+C8UCupCiQrVSqtbj/spHiMx0aCoRV0RoVhwWDKjJbGwPcetRjjpZGSYt fYH3QwoBGQ3IYmjJuxuHXKV7pGwVEooQntGYVsNEGgiMHUqgtAGI/0Hr0THi9Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1677281506; a=rsa-sha256; cv=none; b=Nf7bl4sddSEUf8M86pZYI4UjwcUF+D0ReLXGeoHIhRBRld/HV/dBoBg7TUJcCG/gYYe2JF 0mYiDzXlA4B33oySqtR24YvjhYeJP03+LuwfIYTk4NSTGU6Xapkxht7S0Ad7OhKdveYE6z 8hTHa3i/CrAMCusXAr68UV6Kvci6zaEzlL7Ntq4Jun2GfGYPweCCMict8VPz4NED9GTY+l tVESFn0bb2uccBwTqgoYFQSWz/3+i/1ZbeEY0pNo9q1MzpoBMY5YBZj8k/FWaiHo0RzWdB rk8LVUSxld462LpnrtN8EJyK8+B4S1+2l+uvad9XtqnXaJtjuF+fwdQJrVCrMw== 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 4PNmPZ4wg3zhh6; Fri, 24 Feb 2023 23:31:46 +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 31ONVkho059420; Fri, 24 Feb 2023 23:31:46 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 31ONVkQA059419; Fri, 24 Feb 2023 23:31:46 GMT (envelope-from git) Date: Fri, 24 Feb 2023 23:31:46 GMT Message-Id: <202302242331.31ONVkQA059419@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: 5ce41514802c - main - biology/htslib: Update to 1.17 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: 5ce41514802cd442c01388c30a97e1fde16d836f Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=5ce41514802cd442c01388c30a97e1fde16d836f commit 5ce41514802cd442c01388c30a97e1fde16d836f Author: Jason W. Bacon AuthorDate: 2023-02-24 23:23:25 +0000 Commit: Jason W. Bacon CommitDate: 2023-02-24 23:23:25 +0000 biology/htslib: Update to 1.17 Numerous enhancements and fixes Changes: https://github.com/samtools/htslib/releases Reported by: portscout --- biology/htslib/Makefile | 2 +- biology/htslib/distinfo | 6 +++--- biology/htslib/files/patch-Makefile | 37 +++++++++---------------------------- 3 files changed, 13 insertions(+), 32 deletions(-) diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index 383f90e08114..9f85da45917a 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -1,5 +1,5 @@ PORTNAME= htslib -DISTVERSION= 1.16 +DISTVERSION= 1.17 CATEGORIES= biology devel # Github generated distfiles are incomplete, so use custom tarball MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo index 88b848aeb2fb..24c398cacc3c 100644 --- a/biology/htslib/distinfo +++ b/biology/htslib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1672094487 -SHA256 (htslib-1.16.tar.bz2) = 606b7c7aff73734cf033ecd156f40529fa5792f54524952a28938ca0890d7924 -SIZE (htslib-1.16.tar.bz2) = 4466776 +TIMESTAMP = 1677245487 +SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f +SIZE (htslib-1.17.tar.bz2) = 4619884 diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile index 7f91465d2ccd..eb6fb7f85901 100644 --- a/biology/htslib/files/patch-Makefile +++ b/biology/htslib/files/patch-Makefile @@ -1,33 +1,14 @@ ---- Makefile.orig 2021-03-20 15:53:14 UTC +--- Makefile.orig 2023-02-24 13:35:28 UTC +++ Makefile -@@ -53,13 +53,14 @@ man5dir = $(mandir)/man5 - man7dir = $(mandir)/man7 - pkgconfigdir= $(prefix)/libdata/pkgconfig - --MKDIR_P = mkdir -p --INSTALL = install -p --INSTALL_DATA = $(INSTALL) -m 644 --INSTALL_DIR = $(MKDIR_P) -m 755 --INSTALL_LIB = $(INSTALL_DATA) --INSTALL_MAN = $(INSTALL_DATA) +@@ -60,9 +60,9 @@ INSTALL = install -p + INSTALL_DATA = $(INSTALL) -m 644 + INSTALL_DIR = $(MKDIR_P) -m 755 + LIB_PERM = 644 +-INSTALL_LIB = $(INSTALL) -m $(LIB_PERM) ++INSTALL_LIB = $(BSD_INSTALL_LIB) + INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set -+MKDIR_P = mkdir -p -+INSTALL = install -p -+INSTALL_DATA = ${BSD_INSTALL_DATA} -+INSTALL_DIR = $(MKDIR_P) -+INSTALL_LIB = ${BSD_INSTALL_LIB} -+INSTALL_MAN = ${BSD_INSTALL_MAN} -+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_PROGRAM = $(BSD_INSTALL_PROGRAM) # Set by config.mk if plugins are enabled plugindir = -@@ -102,7 +103,7 @@ BUILT_THRASH_PROGRAMS = \ - test/thrash_threads6 \ - test/thrash_threads7 - --all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \ -+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \ - htslib_static.mk htslib-uninstalled.pc - - ALL_CPPFLAGS = -I. $(CPPFLAGS)