- Update to version 35
State Changed From-To: open->feedback Hello. You define DOCS in options but you don't use PORTS_OPTIONS:MDOCS. USE_ZIP is better than EXTRACT_SUFX and pkg-descr should terminate with a newline. Regards
Responsible Changed From-To: freebsd-ports-bugs->culot I'll take it.
jadawin@FreeBSD.org wrote: > Hello. You define DOCS in options but you don't use PORTS_OPTIONS:MDOCS. > USE_ZIP is better than EXTRACT_SUFX and pkg-descr should terminate with > a newline. Regards It's unclear to me what is the advantage of external unzip package about extracting normal Zip archive over bsdtar.
On Thu, 28 Nov 2013, KATO Tsuguru wrote: > jadawin@FreeBSD.org wrote: > > > Hello. You define DOCS in options but you don't use PORTS_OPTIONS:MDOCS. > > USE_ZIP is better than EXTRACT_SUFX and pkg-descr should terminate with > > a newline. Regards > > It's unclear to me what is the advantage of external unzip package > about extracting normal Zip archive over bsdtar. Have a look to Mk/bsd.port.mk.
jadawin@FreeBSD.org wrote: > Have a look to Mk/bsd.port.mk. The only thing bsd.port.mk tells me is USE_ZIP needs Info-ZIP's unzip as dependency. There seems to be no information about which one is superior to the other. If standard equipment and optional package have same function under the same condition, it would be difficult for anybody to find a reason to give higher priority to optional one.
Responsible Changed From-To: culot->freebsd-ports-bugs Already hold this PR too long, I prefer reassigning it to the heap as I don't have enough time to test it properly. My apologies for that.
Responsible Changed From-To: freebsd-ports-bugs->miwi I'll take it.
State Changed From-To: feedback->closed Committed. Thanks!
Author: miwi Date: Thu Feb 27 11:46:11 2014 New Revision: 346318 URL: http://svnweb.freebsd.org/changeset/ports/346318 QAT: https://qat.redports.org/buildarchive/r346318/ Log: - Update to 35 PR: 184245 Modified: head/biology/blat/Makefile head/biology/blat/distinfo head/biology/blat/files/pkg-message.in head/biology/blat/pkg-descr Modified: head/biology/blat/Makefile ============================================================================== --- head/biology/blat/Makefile Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/Makefile Thu Feb 27 11:46:11 2014 (r346318) @@ -2,45 +2,68 @@ # $FreeBSD$ 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+= ${EXECUTABLES:S,^,bin/,} -PORTDOCS= README -PORTDATA= * - -OPTIONS_DEFINE= DOCS +.include <bsd.port.options.mk> post-patch: @${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 <bsd.port.mk> Modified: head/biology/blat/distinfo ============================================================================== --- head/biology/blat/distinfo Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/distinfo Thu Feb 27 11:46:11 2014 (r346318) @@ -1,2 +1,2 @@ -SHA256 (blatSrc34.zip) = b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 -SIZE (blatSrc34.zip) = 2142975 +SHA256 (blatSrc35.zip) = 06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620 +SIZE (blatSrc35.zip) = 1886214 Modified: head/biology/blat/files/pkg-message.in ============================================================================== --- head/biology/blat/files/pkg-message.in Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/files/pkg-message.in Thu Feb 27 11:46:11 2014 (r346318) @@ -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 =============================================================================== Modified: head/biology/blat/pkg-descr ============================================================================== --- head/biology/blat/pkg-descr Thu Feb 27 11:45:26 2014 (r346317) +++ head/biology/blat/pkg-descr Thu Feb 27 11:46:11 2014 (r346318) @@ -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 @@ genome (but not the genome itself) in me 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/ _______________________________________________ svn-ports-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/svn-ports-all To unsubscribe, send any mail to "svn-ports-all-unsubscribe@freebsd.org"