From nobody Sun Jul 16 13:20:21 2023 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 4R3m6Y6qJPz4n230; Sun, 16 Jul 2023 13:20:21 +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 4R3m6Y5ycxz3qGv; Sun, 16 Jul 2023 13:20:21 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689513621; 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=niwL4G8R6gEYddGCHuUMeDOkPX1/7pLoN+0fsQefWTM=; b=W+u6CMekEDX41a1c7HiBM5mpOdifnl5DhorFJxZYouFZxnWgePw+Ti/If3upwxSnmdF2E5 gG7QpVABhRKiBOIND4QnuZkw3SbwOMdTS6O6J2vJGUSSpxP+pEMxp3FemahpnDqj0szX7t qwErh9pRnGwrsANfpoLaHmkbu4JkCzALhT1zFfFd3kmIt3O6oBmZdsiSwHgZjiJEUK3vj9 GlbniQc802rZVwJscgcjp/1yhd/7b110+e0SOyU2HxZkV8OpRUeamLhLI4eJH1Sxf5Bi1k AjL+AyO2F13Ivge9v47gzwWSEt5z9b6A5erEGbIFKxQ3W6IHzp2D11iHwA4RwA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1689513621; 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=niwL4G8R6gEYddGCHuUMeDOkPX1/7pLoN+0fsQefWTM=; b=MTw791zFXPJzI9bt0Balua9P2vpWO8lioomdsvXwYaxbGoMCS8huMtHeXzpk0n6qAwBnrg VxkmAKoFOvyGIhpB4LeNOc76qAWdCnZxx4fnfg4MikqeJMxfMKvL5IdcYREn45yKO2NmfU L9T1j921j399fJoJU9o6LWyKt5MpwqSksAm8Qaoh6xkJ46bIvO1LIxq4OtHoeUoJJDFg0z BrnbqqnezmRden8amNYEcKwmDquGBllWJXQ8ZOEkJNTjPUed0oAYjLaEGtLlX5hWcSuOHT 78Dypqc9ezkwnhv4ZCLDeuFFRMEoZTnO3MCLEMigzR/TOERoFpXAfzwxDRTqFQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1689513621; a=rsa-sha256; cv=none; b=f1j00lnIP7Fs2JryH3g9jkdO9hMlamxDEKJnWXDp6jjs4dxuNvsWwA9zRysrEtsZvaI9ji 9EsFQhAmxR6x10BJlAFeMr8GoB38UfDOnw5DhuWtD6VjTdbk0lZFcUhs2HAVRVqBmLuwd+ mAHqNbrtn6OjrII5/xwc0H2xz/FjAVzuINNWZy8er38Jykk3IxJRD+4qjn9CIqc8FqY/hJ 77Mx+wuJsDBwsCOeuaI8Wk5RmoWG0CLEDaP41Ojz6gCEe5NcefoH586fZsNee/SWKYbrXv +i6VqTZedtnWFuwgGwSaOUlyYRIIV4c5uN61NU+SWqyLYF6mfIgS9IrpqW4D2Q== 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 4R3m6Y4zG5zjq1; Sun, 16 Jul 2023 13:20:21 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 36GDKLmI058036; Sun, 16 Jul 2023 13:20:21 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 36GDKLHF058035; Sun, 16 Jul 2023 13:20:21 GMT (envelope-from git) Date: Sun, 16 Jul 2023 13:20:21 GMT Message-Id: <202307161320.36GDKLHF058035@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: 63e5ba4396f4 - main - biology/bcf-score: Unbreak build with clang 16 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: 63e5ba4396f40d97df99b2856113afcb7623d7c9 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=63e5ba4396f40d97df99b2856113afcb7623d7c9 commit 63e5ba4396f40d97df99b2856113afcb7623d7c9 Author: Jason W. Bacon AuthorDate: 2023-07-16 13:19:06 +0000 Commit: Jason W. Bacon CommitDate: 2023-07-16 13:19:06 +0000 biology/bcf-score: Unbreak build with clang 16 Patch function pointer assignments that went from warning to error with the compiler upgrade Reported by: pkg-fallout --- biology/bcf-score/Makefile | 1 + biology/bcf-score/files/patch-plugins_munge.c | 11 +++++++++++ biology/bcf-score/files/patch-plugins_score.c | 11 +++++++++++ 3 files changed, 23 insertions(+) diff --git a/biology/bcf-score/Makefile b/biology/bcf-score/Makefile index 96207e1f8f84..f183641f4a4f 100644 --- a/biology/bcf-score/Makefile +++ b/biology/bcf-score/Makefile @@ -1,5 +1,6 @@ PORTNAME= bcf-score DISTVERSION= 1.16 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/score/ DISTFILES+= score_${DISTVERSION}-20221221.tar.gz diff --git a/biology/bcf-score/files/patch-plugins_munge.c b/biology/bcf-score/files/patch-plugins_munge.c new file mode 100644 index 000000000000..8906f57a0a73 --- /dev/null +++ b/biology/bcf-score/files/patch-plugins_munge.c @@ -0,0 +1,11 @@ +--- plugins/munge.c.orig 2023-07-16 07:57:54 UTC ++++ plugins/munge.c +@@ -120,7 +120,7 @@ int tsv_read_string(tsv_t *tsv, bcf1_t *rec, void *usr + return 0; + } + +-static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP ++static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP + tsv_setter_pos_flexible, // BP + tsv_setter_chrom_flexible, // CHR + tsv_read_allele, // A1 diff --git a/biology/bcf-score/files/patch-plugins_score.c b/biology/bcf-score/files/patch-plugins_score.c new file mode 100644 index 000000000000..c90a66f313b6 --- /dev/null +++ b/biology/bcf-score/files/patch-plugins_score.c @@ -0,0 +1,11 @@ +--- plugins/score.c.orig 2023-07-16 08:04:54 UTC ++++ plugins/score.c +@@ -140,7 +140,7 @@ static int tsv_read_allele(tsv_t *tsv, bcf1_t *rec, vo + return 0; + } + +-static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP ++static int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP + tsv_setter_pos_flexible, // BP + tsv_setter_chrom_flexible, // CHR + tsv_read_allele, // A1