From nobody Wed Oct 12 10:16:06 2022 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 4MnT7q18K6z4dyM0; Wed, 12 Oct 2022 10:16:07 +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 4MnT7q0dmJz3lq4; Wed, 12 Oct 2022 10:16:07 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1665569767; 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=lVA1XlM3p6w6ZWjkL6H+t9XNN6cicUsrt3MbpqFmNj4=; b=Bjt5ZNA7F7sM4Y51f5PmFeY6HFFBTb6pefIg3nAUMqBuUYXpyu3902GJDcFBjEAdACFyaD ay8iXtdiT/4wSra+oa9i91IXKDWL55yqfuuE9Oc1pL9W1TUZEeHXNJ0K+u4YYSpMx0t7bS FPiM9+lmzsNJFb7zHRh+fs/mGjxoi+ZLlohZlwEpNaXFFOb1gfjJXCMUS8GoDUR9/Z7HDG mSltgr42E6GPJphwCBNz4VBgUtve1E/8y0sComnzeUrW+DCqQouZg/pVMUbUT7dUp2oHlh S5jWnd7sJH18QnXWPSqFqDUCK0XW6Rsu1OrHPF+5+wIBHKbhCkp2ecvxu4WT9w== 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 4MnT7p6pzqz1H83; Wed, 12 Oct 2022 10:16:06 +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 29CAG659019886; Wed, 12 Oct 2022 10:16:06 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 29CAG6fT019885; Wed, 12 Oct 2022 10:16:06 GMT (envelope-from git) Date: Wed, 12 Oct 2022 10:16:06 GMT Message-Id: <202210121016.29CAG6fT019885@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Nuno Teixeira Subject: git: 95b2e3a08855 - main - biology/infernal: Update to 1.1.4 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: eduardo X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 95b2e3a08855793600b2587fc598eb23ef83f388 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1665569767; 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=lVA1XlM3p6w6ZWjkL6H+t9XNN6cicUsrt3MbpqFmNj4=; b=kqngXLpIkz/BakQmAFEhxyuM9Ye18JaiqzsJ/AbDK6H/glCj9AjAjqMV0qx7ujeg/IPLJD s6y5EXPIlviDj4OAbJAqvHO+PvL/4oSQsJugq0Uoxe/WJU5XIs8zxLbDACEO88wwtwlzgZ RspJgnlXMrIdGhcl4ZFe/wnJgosQpM6W/pTgxUVa8DVK1+crK4fyzP+viGO5xIBffrhhse 4mkOvIrjYYGjjJEJeqk8rT8d8lmTLuJFH2rLaa031QqxlCylMWYmMwFfDzZwolIfAbzoG1 rL9v4XtL40mErR/J/LbBF0iTyNNVQOqoJKnvpzFt6h+hGL0B07KIdmw1r7jxeg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1665569767; a=rsa-sha256; cv=none; b=x4Usfd3s12NO8jgC9xDIltw0LwGALs29Dig8Wv2KF1bOf7X2fBS7ASi+xp2pd/pd7pctIc k/5WuI9m071oSUoIlMz0TB5I4tjoOY0Z4lridgutYppf6lgCtWxee6ZvrwVEjUHjTyuDZ6 O6RSQOraXWssj3SsyugKf6+R5SoDbvHcaxWlZjo3JueuHbbiuweTiErQbr8rcMMLfxNHdU 4GyxAWgNc6FlvTmqND9itdEQeHXRldKCVTQr2UWQjcK7t7Hl0bpq1qs/9zjJOdAVMDzokh Ohyjyv8Jo4UEXSf2La7pJyxtLLa8lI0t8NaHl32ywyjYrJmcCqHm9gBSbATuqA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=95b2e3a08855793600b2587fc598eb23ef83f388 commit 95b2e3a08855793600b2587fc598eb23ef83f388 Author: Motomichi Matsuzaki AuthorDate: 2022-10-12 10:06:23 +0000 Commit: Nuno Teixeira CommitDate: 2022-10-12 10:15:54 +0000 biology/infernal: Update to 1.1.4 ChangeLog: http://eddylab.org/infernal/RELEASE-1.1.4.md PR: 266967 --- biology/infernal/Makefile | 16 ++++++++-------- biology/infernal/distinfo | 6 +++--- biology/infernal/files/patch-hmmer_src_hmmc2.c | 11 ----------- biology/infernal/files/patch-src_Makefile.in | 19 ------------------- 4 files changed, 11 insertions(+), 41 deletions(-) diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile index 528494dbb63a..af7f5630d313 100644 --- a/biology/infernal/Makefile +++ b/biology/infernal/Makefile @@ -1,5 +1,5 @@ PORTNAME= infernal -PORTVERSION= 1.1.3 +PORTVERSION= 1.1.4 CATEGORIES= biology MASTER_SITES= http://eddylab.org/infernal/ @@ -14,14 +14,14 @@ ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 powerpc64le powerpcspe 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 @@ -34,14 +34,11 @@ EXAMPLES= 5S_rRNA.c.cm 5S_rRNA.sto \ tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \ tRNA5-noss.sto tRNA5.c.cm tRNA5.sto -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/* @@ -53,4 +50,7 @@ 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/infernal/distinfo b/biology/infernal/distinfo index 9f362448abc8..80865c942e66 100644 --- a/biology/infernal/distinfo +++ b/biology/infernal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1578660730 -SHA256 (infernal-1.1.3.tar.gz) = 3b98a6a3a0e7b01aa077a0caf1e958223c4d8f80a69a4eb602ca59a3475da85e -SIZE (infernal-1.1.3.tar.gz) = 29910035 +TIMESTAMP = 1665487539 +SHA256 (infernal-1.1.4.tar.gz) = f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc +SIZE (infernal-1.1.4.tar.gz) = 29499238 diff --git a/biology/infernal/files/patch-hmmer_src_hmmc2.c b/biology/infernal/files/patch-hmmer_src_hmmc2.c deleted file mode 100644 index 5bd86cf55247..000000000000 --- a/biology/infernal/files/patch-hmmer_src_hmmc2.c +++ /dev/null @@ -1,11 +0,0 @@ ---- hmmer/src/hmmc2.c.orig 2019-11-19 19:30:04 UTC -+++ hmmer/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); diff --git a/biology/infernal/files/patch-src_Makefile.in b/biology/infernal/files/patch-src_Makefile.in deleted file mode 100644 index 7afaa0ab41ea..000000000000 --- a/biology/infernal/files/patch-src_Makefile.in +++ /dev/null @@ -1,19 +0,0 @@ ---- src/Makefile.in.orig 2019-11-19 19:28:55 UTC -+++ src/Makefile.in -@@ -27,6 +27,7 @@ CC = @CC@ - CFLAGS = @CFLAGS@ - PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ - PIC_CFLAGS = @PIC_CFLAGS@ -+SIMD_CFLAGS = @SSE_CFLAGS@ @VMX_CFLAGS@ - CPPFLAGS = @CPPFLAGS@ - LDFLAGS = @LDFLAGS@ - DEFS = @DEFS@ -@@ -200,7 +201,7 @@ ${PROGS}: % : %.o libinfernal.a ../${HMM - ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS} - - .c.o: -- ${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $< -+ ${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $< - - ${ITESTS}: % : %.o libinfernal.a ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a ${HDRS} config.h - ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}