From nobody Wed Dec 1 14:57:35 2021 X-Original-To: dev-commits-ports-all@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 8D4AA18A63A8; Wed, 1 Dec 2021 14:57:35 +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 4J42Hz29nsz4vCG; Wed, 1 Dec 2021 14:57:35 +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 2B0303B22; Wed, 1 Dec 2021 14:57:35 +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 1B1EvZbC038875; Wed, 1 Dec 2021 14:57:35 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 1B1EvZpL038874; Wed, 1 Dec 2021 14:57:35 GMT (envelope-from git) Date: Wed, 1 Dec 2021 14:57:35 GMT Message-Id: <202112011457.1B1EvZpL038874@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: c74d9767d204 - main - biology/bwa: Unbreak on most non-x86 platforms using simde List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: c74d9767d204035f671225a70227a2b24ecb2491 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1638370655; 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=KR4MdhLqZWBr4XfONU7xLolAtdkHmYNmRDNabEvb2Ck=; b=mU3BYzQfoSLfGyQu61QXAmpnAb+M8ThfiPZieWCRHxhaq5J20kW57kp8oHKN/pR9X3KbyR BwNOJvlnE1S2m/eEHkUeqz237msWLpE+tA4I26QVYrBwMZTHXK0vXjk4vXZw5GNnTsLvnI xHE4LdXLN6o772NABB7OxlU4sMerh+74Z80/9DbL6Yrs+r97cZm31VAJgECv6TKNu0iUJx lpDBuZDA2AHLTQM2sb3rOeL3jk3ye2RH+q6ueK2BZFztlVZKc2VeapHsnY/VHbK1HgmbCJ 52gk/qnHfZR0Y5QMC4sSppBNDcFEGL+OTZBQ9n8UHpwiIoUy4lzyqtM0FeeCrQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1638370655; a=rsa-sha256; cv=none; b=T7d78xKS2w8zyz5aOFoXmPD3WwIKK/IRrbysA4YPlaPZhYO+nXi6mKFqKAWJWWTxMxPmOp yBz/M65Pckv7MJqQEhaZz3ETWCRtihm3Jj5L/ihe1F4oCpCN+AIUjhqW/SVsvzFImeblPW ljnBNWNXfaxGN0oVnmlXLMKWoCWqOJ0IArwLbJcirV2GaRh5MItXvc51m6oLKAGVuHdKYv AfMDwfuG+I+U9NzAzbYvBPMIjT2nReSGqzcf0JtZ3Gg17zigwrYg1DQlq/ueq08Jv3WrkI CJ/CJFCa8oi5kRvVe9sEvls48+AGqQ8EVGGCbBUDD/iqvxfDlPbzmkFkCUkH1g== 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=c74d9767d204035f671225a70227a2b24ecb2491 commit c74d9767d204035f671225a70227a2b24ecb2491 Author: Jason W. Bacon AuthorDate: 2021-12-01 14:55:49 +0000 Commit: Jason W. Bacon CommitDate: 2021-12-01 14:56:30 +0000 biology/bwa: Unbreak on most non-x86 platforms using simde --- biology/bwa/Makefile | 11 ++++------- biology/bwa/files/patch-ksw.c | 13 +++++++++++++ 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index a6302394411c..5075bda611bc 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -1,6 +1,7 @@ PORTNAME= bwa PORTVERSION= 0.7.17 DISTVERSIONPREFIX=v +PORTREVISION= 1 CATEGORIES= biology PATCH_SITES= https://github.com/lh3/bwa/commit/ @@ -11,16 +12,12 @@ COMMENT= Burrows-Wheeler sequence aligner LICENSE= GPLv3 -# From 0.7.9a: Recheck for 0.7.17. -BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type -BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type -BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type BROKEN_mips= fails to compile: cc1: unrecognized command line option "-msse2" BROKEN_mips64= fails to compile: cc1: unrecognized command line option "-msse2" -BROKEN_powerpc64= fails to compile: ksw.c: emmintrin.h: No such file or directory -BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type -USES= gmake perl5 shebangfix tar:bzip2 +BUILD_DEPENDS= simde>0:devel/simde + +USES= gmake localbase perl5 shebangfix tar:bzip2 SHEBANG_FILES= qualfa2fq.pl xa2multi.pl USE_PERL5= run diff --git a/biology/bwa/files/patch-ksw.c b/biology/bwa/files/patch-ksw.c new file mode 100644 index 000000000000..c86cabf2e497 --- /dev/null +++ b/biology/bwa/files/patch-ksw.c @@ -0,0 +1,13 @@ +--- ksw.c.orig 2021-12-01 13:48:35 UTC ++++ ksw.c +@@ -26,7 +26,9 @@ + #include + #include + #include +-#include ++// #include ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include + #include "ksw.h" + + #ifdef USE_MALLOC_WRAPPERS