From nobody Tue Oct 11 20:13:02 2022 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 4Mn6R30HXFz4fKty; Tue, 11 Oct 2022 20:13:03 +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 4Mn6R26nLPz3RBH; Tue, 11 Oct 2022 20:13:02 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1665519183; 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=s1CNKjlUDceFcyAc86Uk5rY3MkXJT23USHxK3Ql0CMI=; b=E69vtc7lWiCuzzrNtb3IxlvU71YbnQh9KaHfE4emni0TQMk0jl280NxeANRV8NHJ1dEJdM ezlmH6cP+230mLdUTnZ/OwrklF5tUfYmOCqaomxxNQaDDqSOTX9BVFGK8+awSIwV1He8Pu 7p4cVYSJZvsL/yYZ1Rit3r4Vi/EEG2iWOrg7HmkCKX6VFA9wa0O4zIbg3TDh9yHCIl4D1h yE8fwIq18lh8lDz9dBnyWk134tE+hHbP7Am5km+8UvcuuJTwJg8v74Syy1t5TAyoRjfyGD 7/ecqvvyl/9MebNTz1MMMtqVPFY2+d9Rpx2BoOcCeJBfE5aaT4NP3eZTyHzjHQ== 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 4Mn6R25p4Mz14bP; Tue, 11 Oct 2022 20:13:02 +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 29BKD2Au074830; Tue, 11 Oct 2022 20:13:02 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 29BKD22l074829; Tue, 11 Oct 2022 20:13:02 GMT (envelope-from git) Date: Tue, 11 Oct 2022 20:13:02 GMT Message-Id: <202210112013.29BKD22l074829@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: b532c5dd966e - main - biology/hmmer: Update to 3.3.2 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: b532c5dd966eb638a5616fc7819657f007c08848 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1665519183; 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=s1CNKjlUDceFcyAc86Uk5rY3MkXJT23USHxK3Ql0CMI=; b=wGyJWHu6LWYbI1lQuEM2BH33ZV0FR3MWPX5/6SS/1nWtihjmHj1SLDuc/VjhOJxZ7yflzi yyjX+Bb9j0T1k+CPq96QkXEMpql1n9Soa7NoJhGydYHi0jhmybnUdCIKMrVaEPZj6oaUJ+ cbRP3x9rxTrUVcvKbfo8cKq7L3UJPrdNl2H9i34MSaf0pLnY61bw451sLQrzNzMQmjh5gu 3s/xKXkEs+lTHqeD/ixKmy08e08Vix8ma6lN8XaVqZa9bmmJ+FKAW0qxsTe4NwfxQhq+e9 tQM/iuahSrF5M8nqIInY++7+rwCqizy3yvpW6QsqyUcNAQ1xubvoIZrkkaKwgA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1665519183; a=rsa-sha256; cv=none; b=aIswjP5o/mJpNBCUPbou2mGZkZLDIvsv8jE8/DxlHNxUcQRmK5jrcuVD9Kg5pSI0Si/JD9 h5prXj3r7C6zTUXDK1k8oi1TjVNRvU1BdhkjzPahkrfGjfqU+5PYzRPm+tE/tM6S0vCgZs AFXwoKd9pmJrMCSOO9WXG6reKhgU140jRf3wHcKpW4wSooXBXFTadVZXz7GVUK5DuPMcxN wyHGmAm18C2IHipnPd25p6k42RsZhqyuZ7+INj+OFBfw2VyYXSodxt1AEAlj/7QUrQuj3g 6zHj0VxKGrVunG6tFaU+/648rnM4d+cn1eXTfFrSjax0vCK7388VfN4JNA884A== 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=b532c5dd966eb638a5616fc7819657f007c08848 commit b532c5dd966eb638a5616fc7819657f007c08848 Author: Jason W. Bacon AuthorDate: 2022-10-11 18:58:39 +0000 Commit: Jason W. Bacon CommitDate: 2022-10-11 20:13:01 +0000 biology/hmmer: Update to 3.3.2 No release notes. See commits for changes: https://github.com/EddyRivasLab/hmmer PR: 266968 Reported by: mzaki@e-mail.ne.jp --- biology/hmmer/Makefile | 16 ++++++++-------- biology/hmmer/distinfo | 6 +++--- biology/hmmer/files/patch-src_hmmc2.c | 11 ----------- 3 files changed, 11 insertions(+), 22 deletions(-) diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile index 3773440431c7..21a16114e1d5 100644 --- a/biology/hmmer/Makefile +++ b/biology/hmmer/Makefile @@ -1,5 +1,5 @@ PORTNAME= hmmer -PORTVERSION= 3.3 +PORTVERSION= 3.3.2 CATEGORIES= biology MASTER_SITES= http://eddylab.org/software/hmmer/ @@ -14,14 +14,14 @@ ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions USES= compiler:c11 gmake perl5 python:3.5+,test shebangfix +USE_PERL5= test +SHEBANG_FILES= easel/devkit/* +SHEBANG_GLOB= *.pl *.py GNU_CONFIGURE= yes MAKE_ARGS= V=1 TEST_TARGET= check -USE_PERL5= test -SHEBANG_GLOB= *.pl *.py -SHEBANG_FILES= easel/devkit/* OPTIONS_DEFINE= DOCS EXAMPLES TEST @@ -30,14 +30,11 @@ EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \ Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \ globins4.hmm globins4.sto globins45.fa -TEST_VARS= use_perl5=build TEST_BUILD_DEPENDS= ${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX} +TEST_VARS= use_perl5=build post-build-TEST-on: pre-test do-test -pre-test: - ${FIND} ${WRKSRC} -type f \( -name Makefile -or -name sqc \) -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /' - post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* @@ -49,4 +46,7 @@ post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR} +pre-test: + ${FIND} ${WRKSRC} -type f \( -name Makefile -or -name sqc \) -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /' + .include diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo index 4af97cebbada..edb75ddf6465 100644 --- a/biology/hmmer/distinfo +++ b/biology/hmmer/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1578579116 -SHA256 (hmmer-3.3.tar.gz) = 0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c -SIZE (hmmer-3.3.tar.gz) = 18614771 +TIMESTAMP = 1665491511 +SHA256 (hmmer-3.3.2.tar.gz) = 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69 +SIZE (hmmer-3.3.2.tar.gz) = 18213049 diff --git a/biology/hmmer/files/patch-src_hmmc2.c b/biology/hmmer/files/patch-src_hmmc2.c deleted file mode 100644 index 8d16156a130c..000000000000 --- a/biology/hmmer/files/patch-src_hmmc2.c +++ /dev/null @@ -1,11 +0,0 @@ ---- src/hmmc2.c.orig 2019-11-18 13:23:12 UTC -+++ src/hmmc2.c -@@ -334,7 +334,7 @@ int main(int argc, char *argv[]) - n = sizeof(sstatus); - total += n; - if ((size = readn(sock, &sstatus, n)) == -1) { -- if(errno == 104 || errno == 0){ -+ if(errno == ECONNRESET || errno == 0){ - // connection was reset, usually because server exited - fprintf(stderr, "Daemon exited, shutting down\n"); - exit(0);