From owner-freebsd-ports-bugs@FreeBSD.ORG Sun Nov 24 18:10:09 2013 Return-Path: Delivered-To: freebsd-ports-bugs@smarthost.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 1C9E2401 for ; Sun, 24 Nov 2013 18:10:09 +0000 (UTC) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:1900:2254:206c::16:87]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 01B662CFF for ; Sun, 24 Nov 2013 18:10:09 +0000 (UTC) Received: from freefall.freebsd.org (localhost [127.0.0.1]) by freefall.freebsd.org (8.14.7/8.14.7) with ESMTP id rAOIA8Wa047014 for ; Sun, 24 Nov 2013 18:10:08 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.7/8.14.7/Submit) id rAOIA8iR047013; Sun, 24 Nov 2013 18:10:08 GMT (envelope-from gnats) Resent-Date: Sun, 24 Nov 2013 18:10:08 GMT Resent-Message-Id: <201311241810.rAOIA8iR047013@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 7C0EC28A for ; Sun, 24 Nov 2013 18:00:21 +0000 (UTC) Received: from omta01.auone-net.jp (mail-or2-f145.auone-net.jp [111.87.219.145]) by mx1.freebsd.org (Postfix) with ESMTP id 3E4142C47 for ; Sun, 24 Nov 2013 18:00:21 +0000 (UTC) Received: from coppermine.my.domain (ZT030024.ppp.dion.ne.jp [59.128.30.24]) by omta01.auone-net.jp (au one net mail) with ESMTP id C20F7980038 for ; Mon, 25 Nov 2013 03:00:12 +0900 (JST) Message-Id: <20131125025010.6e5b12f9432d96b76a95a48a@yahoo.com> Date: Mon, 25 Nov 2013 02:50:10 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/184245: biology/blat: Update to version 35 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.16 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 24 Nov 2013 18:10:09 -0000 >Number: 184245 >Category: ports >Synopsis: biology/blat: Update to version 35 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sun Nov 24 18:10:08 UTC 2013 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 8.4-RELEASE-p4 i386 >Organization: >Environment: >Description: - Update to version 35 >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/blat/Makefile biology/blat/Makefile --- /usr/ports/biology/blat/Makefile 2013-11-13 17:50:18.000000000 +0900 +++ biology/blat/Makefile 2013-11-25 00:00:00.000000000 +0900 @@ -2,45 +2,68 @@ # $FreeBSD: head/biology/blat/Makefile 333628 2013-11-12 22:02:02Z bapt $ PORTNAME= blat -PORTVERSION= 34 +PORTVERSION= 35 CATEGORIES= biology -MASTER_SITES= http://www.soe.ucsc.edu/~kent/src/ +MASTER_SITES= http://hgwdev.cse.ucsc.edu/~kent/src/ \ + http://users.soe.ucsc.edu/~kent/src/ DISTNAME= ${PORTNAME}Src${PORTVERSION} +EXTRACT_SUFX= .zip MAINTAINER= ports@FreeBSD.org COMMENT= Fast tool for local sequence similarity searches +LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png + +OPTIONS_DEFINE= DOCS + +WRKSRC= ${WRKDIR}/${PORTNAME}Src + USES= gmake -EXTRACT_SUFX= .zip +USE_OPENSSL= yes MAKEFILE= makefile -WRKSRC= ${WRKDIR}/${PORTNAME}Src -MAKE_ENV+= HOME="${WRKSRC}/${BINDIR}" MACHTYPE="${ARCH}" +MAKE_ENV= MACHTYPE="${ARCH}" HOME="${WRKSRC}/${BINDIR}" STRIP="${TRUE}" + +CPPFLAGS+= $$(libpng-config --cflags) +LDFLAGS+= $$(libpng-config --ldflags) SUB_FILES= pkg-message +PORTDOCS= README +PLIST_FILES= ${EXECUTABLES:S,^,bin/,} \ + lib/blat/webBlat/webBlat \ + lib/blat/webBlat/install.txt +PLIST_DIRS= lib/blat/webBlat \ + lib/blat + EXECUTABLES= blat faToNib faToTwoBit gfClient gfServer nibFrag \ pslPretty pslReps pslSort twoBitInfo twoBitToFa -PLIST_FILES+= ${EXECUTABLES:S,^,bin/,} -PORTDOCS= README -PORTDATA= * - -OPTIONS_DEFINE= DOCS +.include post-patch: @${MKDIR} ${WRKSRC}/bin/${ARCH} @${MKDIR} ${WRKSRC}/lib/${ARCH} - @${REINPLACE_CMD} -E 's,^(CC|CFLAGS)=,\1 ?=,g;s,-Werror,,g' \ - ${WRKSRC}/inc/common.mk + @${FIND} ${WRKSRC} -name "makefile" | ${XARGS} ${REINPLACE_CMD} -e \ + 's|$${DESTDIR}||g' + @${REINPLACE_CMD} -e \ + 's|cd |$$(MAKE) -C | ; \ + s| &&.*||' ${WRKSRC}/makefile + @${REINPLACE_CMD} -e \ + 's|^CC=|CC?=| ; \ + s|^COPT=.*|COPT=$${CPPFLAGS}| ; \ + s|^L=.*|L=$${LDFLAGS}|' ${WRKSRC}/inc/common.mk do-install: .for exe in ${EXECUTABLES} - ${INSTALL_PROGRAM} ${WRKSRC}/bin/${ARCH}/${exe} ${STAGEDIR}${PREFIX}/bin + (cd ${WRKSRC}/bin/${ARCH} && ${INSTALL_PROGRAM} ${exe} \ + ${STAGEDIR}${PREFIX}/bin) .endfor - @${MKDIR} ${STAGEDIR}${DATADIR}/webBlat - ${INSTALL_PROGRAM} ${WRKSRC}/webBlat/webBlat ${STAGEDIR}${DATADIR}/webBlat - ${INSTALL_DATA} ${WRKSRC}/webBlat/install.txt ${STAGEDIR}${DATADIR}/webBlat + @${MKDIR} ${STAGEDIR}${PREFIX}/lib/blat/webBlat + (cd ${WRKSRC}/webBlat && ${INSTALL_PROGRAM} webBlat \ + ${STAGEDIR}${PREFIX}/lib/blat/webBlat) + (cd ${WRKSRC}/webBlat && ${INSTALL_DATA} install.txt \ + ${STAGEDIR}${PREFIX}/lib/blat/webBlat) @${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/README ${STAGEDIR}${DOCSDIR} + (cd ${WRKSRC} && ${INSTALL_DATA} README ${STAGEDIR}${DOCSDIR}) .include diff -urN /usr/ports/biology/blat/distinfo biology/blat/distinfo --- /usr/ports/biology/blat/distinfo 2013-11-06 22:05:44.000000000 +0900 +++ biology/blat/distinfo 2013-11-25 00:00:00.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 -SIZE (blatSrc34.zip) = 2142975 +SHA256 (blatSrc35.zip) = 06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620 +SIZE (blatSrc35.zip) = 1886214 diff -urN /usr/ports/biology/blat/files/pkg-message.in biology/blat/files/pkg-message.in --- /usr/ports/biology/blat/files/pkg-message.in 2013-11-06 22:05:44.000000000 +0900 +++ biology/blat/files/pkg-message.in 2013-11-25 00:00:00.000000000 +0900 @@ -3,6 +3,6 @@ A CGI script (webBlat) and instructions on how to set up a BLAT web server have been installed in - %%DATADIR%% + %%PREFIX%%/lib/blat =============================================================================== diff -urN /usr/ports/biology/blat/pkg-descr biology/blat/pkg-descr --- /usr/ports/biology/blat/pkg-descr 2013-11-06 22:05:44.000000000 +0900 +++ biology/blat/pkg-descr 2013-11-25 00:00:00.000000000 +0900 @@ -1,9 +1,9 @@ -BLAT is a bioinformatics software tool which performs rapid mRNA/DNA -and cross-species protein alignments. BLAT is more accurate and 500 -times faster than popular existing tools for mRNA/DNA alignments and 50 -times faster for protein alignments at sensitivity settings typically -used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT --- The BLAST-Like Alignment Tool. Genome Research 4: 656-664. +BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and +cross-species protein alignments. BLAT is more accurate and 500 times +faster than popular existing tools for mRNA/DNA alignments and 50 times +faster for protein alignments at sensitivity settings typically used +when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT -- +The BLAST-Like Alignment Tool. Genome Research 4: 656-664. http://dx.doi.org/10.1101/gr.229202) BLAT is not BLAST. DNA BLAT works by keeping an index of the entire @@ -11,4 +11,4 @@ bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box. -WWW: http://www.genomeblat.com +WWW: http://users.soe.ucsc.edu/~kent/ >Release-Note: >Audit-Trail: >Unformatted: