From nobody Wed Oct 09 22:23:11 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 4XP6pl53Q3z5Z40n; Wed, 09 Oct 2024 22:23:11 +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 4XP6pl4Rwfz4dnR; Wed, 9 Oct 2024 22:23:11 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512591; 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=EeGciUJxF9mYkME3fpkl1ISK0wdeMY8UnRpMPb4h9BE=; b=yrJ6hmc2WinmUy+O9TnUpBBKbdZun6+AJB9gE2/g9aPbRLDgxX0Wd5/k7l5oy1fqY1W2jz O6+pAEMHG0P6786Wjrc4RV0adKOe1FcsN6YPcG6hcyR9TWPYjioFq6Cj56e4aYsBuG7i7c 8atOFVWixW4LJggkYjwwoT/rpjl8IAGq7mC5XZvSt1WyW1me2mHyhRyRm2GohCLuhXJ0bo 4CPr3pPJ28xshX1W4kFpL8KRivYmn9gkV5kayCBdDjfcR8VKCa5zXAzevlJjgQQ85pzusB GbH3Yr7vWSPlkwJzXeW/Sxdtb4K77wn2imBIIPjE8Z8e0Tx/wPl/YqkySzfVlg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1728512591; 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=EeGciUJxF9mYkME3fpkl1ISK0wdeMY8UnRpMPb4h9BE=; b=BpFl4Xf9CacIU5WU2a4P/wzJr1CWPc3bJA3kDKyAhEuGLL1Dn/9WMykjGXWsTCblxF+Vki 1d15s/JMIlxw+tnXoZKtyjx+S6yzwhUJYX75wsseWewjXUlwobj3VV6l0XFG99GGDMzVBW XQR4flSaJhB44K44XAj/UeK90pWuV76VwN0Gno9tnpfNvK7Wz9glQX3ZVfskDrZpu6sLd7 PfiLK4rKQLu05Ycpnmp7ohkuRN2QlgdWUmxIoHQ+LvlOJgW6M0UGL9iCMDhogPDRoGccBs vzo6QfWsRyC+AOyVNbWy+dbzfAwwCyVKsHdQLkV7zHs9bVD3S6fKIv7xC++xnA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1728512591; a=rsa-sha256; cv=none; b=MBfZNSxfGIBRV6Y36tOn/z2NQDpnVwORsEp0DFOoAZ50Ho4GwIcDNyQhrDol+cdRnVPeCd /bLGEn79I+bVufp0fn1F5ywD8vd9DxH4DEWdJqtmQMxQS58wbNUX0xOz/2GG4yv77u3bk0 oDeHldv6AdqbxCwnPLv24tbZ0VGo8QUlcuW+Fq3IGJvpRQgPPpueTu1ktqP7XfdaBJcxcx 8BtGAoqzQ/zb77VSyg0/omsOU1INKLAuRdYtACYugObjWks5SyYkxtxpwJKh2YFpxWytSB CWo7yZ6OvAV0Yvi9OR5OEf8HV7ca+i7Q4HT/2sC6/6WZbih4cybtZWEpi3xuhg== 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 4XP6pl43JZzXMs; Wed, 9 Oct 2024 22:23:11 +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 499MNBLk059702; Wed, 9 Oct 2024 22:23:11 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 499MNBAu059699; Wed, 9 Oct 2024 22:23:11 GMT (envelope-from git) Date: Wed, 9 Oct 2024 22:23:11 GMT Message-Id: <202410092223.499MNBAu059699@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: aafe5d31c5f3 - main - biology/htslib: Update to 1.21 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: aafe5d31c5f3afdaad0f6345bee06e7a3e2c5ced Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=aafe5d31c5f3afdaad0f6345bee06e7a3e2c5ced commit aafe5d31c5f3afdaad0f6345bee06e7a3e2c5ced Author: Jason W. Bacon AuthorDate: 2024-10-09 22:06:24 +0000 Commit: Jason W. Bacon CommitDate: 2024-10-09 22:23:08 +0000 biology/htslib: Update to 1.21 Numerous bug fixes and enhancements since 1.17 Changes: https://github.com/samtools/htslib/releases Reported by: portscout --- biology/htslib/Makefile | 5 ++--- biology/htslib/distinfo | 6 +++--- .../files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c | 6 +++--- .../htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c | 8 ++++---- biology/htslib/pkg-plist | 2 ++ 5 files changed, 14 insertions(+), 13 deletions(-) diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index 5a844cef433c..3d39f202a887 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -1,6 +1,5 @@ PORTNAME= htslib -DISTVERSION= 1.17 -PORTREVISION= 1 +DISTVERSION= 1.21 CATEGORIES= biology devel # Github generated distfiles are incomplete, so use custom tarball MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ @@ -24,7 +23,7 @@ GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX=${PREFIX}/share MAKE_ARGS_armv6= HTS_HAVE_NEON= MAKE_ARGS_armv7= HTS_HAVE_NEON= -MAKE_ARGS= $(MAKE_ARGS_$(ARCH)) +MAKE_ARGS= ${MAKE_ARGS_${ARCH}} PATHFIX_MAKEFILEIN= Makefile SHEBANG_FILES= test/*.pl diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo index 24c398cacc3c..f035bfd3f3d0 100644 --- a/biology/htslib/distinfo +++ b/biology/htslib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1677245487 -SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f -SIZE (htslib-1.17.tar.bz2) = 4619884 +TIMESTAMP = 1727437235 +SHA256 (htslib-1.21.tar.bz2) = 84b510e735f4963641f26fd88c8abdee81ff4cb62168310ae716636aac0f1823 +SIZE (htslib-1.21.tar.bz2) = 4781943 diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c index 577a3d651321..434edf03f411 100644 --- a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c +++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c @@ -1,11 +1,11 @@ ---- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2023-04-17 21:11:08 UTC +--- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2024-10-09 21:43:35 UTC +++ htscodecs/htscodecs/rANS_static32x16pr_neon.c @@ -32,7 +32,7 @@ */ #include "config.h" --#ifdef __ARM_NEON -+#if defined(__ARM_NEON) && defined(__aarch64__) +-#if defined(__ARM_NEON) && defined(__aarch64__) ++#if defined(__ARM_NEON) #include #include diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c index 8f3e883eec42..3eaebe7ae36d 100644 --- a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c +++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c @@ -1,11 +1,11 @@ ---- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2023-04-17 21:13:50 UTC +--- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2024-10-09 21:44:38 UTC +++ htscodecs/htscodecs/rANS_static4x16pr.c -@@ -1006,7 +1006,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order) +@@ -1030,7 +1030,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order) } } --#elif defined(__ARM_NEON) -+#elif defined(__ARM_NEON) && defined(__aarch64__) +-#elif defined(__ARM_NEON) && defined(__aarch64__) ++#elif defined(__ARM_NEON) #if defined(__linux__) || defined(__FreeBSD__) #include diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist index 8c97aa84399c..1d4e538f1e47 100644 --- a/biology/htslib/pkg-plist +++ b/biology/htslib/pkg-plist @@ -1,3 +1,4 @@ +bin/annot-tsv bin/bgzip bin/htsfile bin/tabix @@ -34,6 +35,7 @@ lib/libhts.so lib/libhts.so.%%PORTVERSION%% lib/libhts.so.3 libdata/pkgconfig/htslib.pc +share/man/man1/annot-tsv.1.gz share/man/man1/bgzip.1.gz share/man/man1/htsfile.1.gz share/man/man1/tabix.1.gz