From owner-svn-ports-all@freebsd.org Sun Jul 31 14:19:11 2016 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 1FEB8BA979E; Sun, 31 Jul 2016 14:19:11 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id D80281BB3; Sun, 31 Jul 2016 14:19:10 +0000 (UTC) (envelope-from pi@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u6VEJA37092138; Sun, 31 Jul 2016 14:19:10 GMT (envelope-from pi@FreeBSD.org) Received: (from pi@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u6VEJ9Ei092134; Sun, 31 Jul 2016 14:19:09 GMT (envelope-from pi@FreeBSD.org) Message-Id: <201607311419.u6VEJ9Ei092134@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: pi set sender to pi@FreeBSD.org using -f From: Kurt Jaeger Date: Sun, 31 Jul 2016 14:19:09 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r419380 - head/biology/seqtools X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.22 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 31 Jul 2016 14:19:11 -0000 Author: pi Date: Sun Jul 31 14:19:09 2016 New Revision: 419380 URL: https://svnweb.freebsd.org/changeset/ports/419380 Log: biology/seqtools: 4.42.1 -> 4.43.0 ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html - Mark broken on 9.x: Fails to build due to C++ std issues Modified: head/biology/seqtools/Makefile head/biology/seqtools/distinfo head/biology/seqtools/pkg-plist Modified: head/biology/seqtools/Makefile ============================================================================== --- head/biology/seqtools/Makefile Sun Jul 31 14:16:55 2016 (r419379) +++ head/biology/seqtools/Makefile Sun Jul 31 14:19:09 2016 (r419380) @@ -1,7 +1,7 @@ # $FreeBSD$ PORTNAME= seqtools -PORTVERSION= 4.42.1 +PORTVERSION= 4.43.0 CATEGORIES= biology MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/ @@ -11,12 +11,16 @@ COMMENT= Tools for visualising sequence LICENSE= GPLv3 LIB_DEPENDS= libcurl.so:ftp/curl \ - libsqlite3.so:databases/sqlite3 + libsqlite3.so:databases/sqlite3 \ + libfontconfig.so:x11-fonts/fontconfig \ + libfreetype.so:print/freetype2 -USES= compiler:c++14-lang execinfo libtool pkgconfig +BROKEN_FreeBSD_9= Fails to build due to C++ std issues + +USES= compiler:c++14-lang execinfo gettext libtool pkgconfig GNU_CONFIGURE= yes -#USE_GCC= any -USE_GNOME= gtk20 +USE_GNOME= cairo gdkpixbuf2 gtk20 +USE_XORG= x11 CFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -lexecinfo -lcurl -lsqlite3 -lm MAKE_JOBS_UNSAFE= yes Modified: head/biology/seqtools/distinfo ============================================================================== --- head/biology/seqtools/distinfo Sun Jul 31 14:16:55 2016 (r419379) +++ head/biology/seqtools/distinfo Sun Jul 31 14:19:09 2016 (r419380) @@ -1,2 +1,3 @@ -SHA256 (seqtools-4.42.1.tar.gz) = 5b3f7f5f213f47d72c7b2070ff94d0e5ca31a5be8b4558492d45e7dbbfad774b -SIZE (seqtools-4.42.1.tar.gz) = 5847308 +TIMESTAMP = 1469510431 +SHA256 (seqtools-4.43.0.tar.gz) = 01861098451eab001d49a039e60ddc6df22a61a7472924c850942ffdae396c8b +SIZE (seqtools-4.43.0.tar.gz) = 6862548 Modified: head/biology/seqtools/pkg-plist ============================================================================== --- head/biology/seqtools/pkg-plist Sun Jul 31 14:16:55 2016 (r419379) +++ head/biology/seqtools/pkg-plist Sun Jul 31 14:19:09 2016 (r419380) @@ -1,13 +1,3 @@ -bin/belvu -bin/blixem -bin/blixemh -bin/dotter -include/gbtools/gbtools.hpp -include/gbtools/gbtoolsCurl.hpp -include/gbtools/gbtoolsGUI.hpp -include/gbtools/gbtoolsPfetch.hpp -include/gbtools/gbtoolsUtils.hpp -lib/libgbtools.a %%PORTDOCS%%%%DOCSDIR%%/Belvu_manual.pdf %%PORTDOCS%%%%DOCSDIR%%/Blixem_manual.pdf %%PORTDOCS%%%%DOCSDIR%%/Dotter_manual.pdf @@ -19,3 +9,218 @@ lib/libgbtools.a %%PORTDOCS%%%%DOCSDIR%%/dotter_usage.txt %%PORTDOCS%%%%DOCSDIR%%/release_notes.html %%PORTDOCS%%%%DOCSDIR%%/todo.html +bin/belvu +bin/blixem +bin/blixemh +bin/dotter +include/blatSrc/ace.h +include/blatSrc/aliType.h +include/blatSrc/annoAssembly.h +include/blatSrc/annoFilter.h +include/blatSrc/annoFormatTab.h +include/blatSrc/annoFormatter.h +include/blatSrc/annoGrateWig.h +include/blatSrc/annoGrator.h +include/blatSrc/annoGratorQuery.h +include/blatSrc/annoOption.h +include/blatSrc/annoRow.h +include/blatSrc/annoStreamBigBed.h +include/blatSrc/annoStreamBigWig.h +include/blatSrc/annoStreamTab.h +include/blatSrc/annoStreamVcf.h +include/blatSrc/annoStreamer.h +include/blatSrc/apacheLog.h +include/blatSrc/asParse.h +include/blatSrc/axt.h +include/blatSrc/bPlusTree.h +include/blatSrc/bamFile.h +include/blatSrc/bandExt.h +include/blatSrc/base64.h +include/blatSrc/basicBed.h +include/blatSrc/bbiFile.h +include/blatSrc/bigBed.h +include/blatSrc/bigWig.h +include/blatSrc/binRange.h +include/blatSrc/bits.h +include/blatSrc/blastParse.h +include/blatSrc/boxClump.h +include/blatSrc/boxLump.h +include/blatSrc/bwgInternal.h +include/blatSrc/cda.h +include/blatSrc/cgi_build_rules.mk +include/blatSrc/chain.h +include/blatSrc/chainBlock.h +include/blatSrc/chainConnect.h +include/blatSrc/chainToAxt.h +include/blatSrc/chainToPsl.h +include/blatSrc/cheapcgi.h +include/blatSrc/cirTree.h +include/blatSrc/codebias.h +include/blatSrc/common.h +include/blatSrc/common.mk +include/blatSrc/correlate.h +include/blatSrc/crTree.h +include/blatSrc/crudeali.h +include/blatSrc/diGraph.h +include/blatSrc/diGraph.h.97 +include/blatSrc/dlist.h +include/blatSrc/dnaLoad.h +include/blatSrc/dnaMarkov.h +include/blatSrc/dnaMotif.h +include/blatSrc/dnaseq.h +include/blatSrc/dnautil.h +include/blatSrc/dtdParse.h +include/blatSrc/dyOut.h +include/blatSrc/dystring.h +include/blatSrc/elmTree.h +include/blatSrc/emblParse.h +include/blatSrc/ens.h +include/blatSrc/errAbort.h +include/blatSrc/errCatch.h +include/blatSrc/fa.h +include/blatSrc/fieldedTable.h +include/blatSrc/filePath.h +include/blatSrc/flydna.h +include/blatSrc/fof.h +include/blatSrc/fq.h +include/blatSrc/fuzzyFind.h +include/blatSrc/gapCalc.h +include/blatSrc/gdf.h +include/blatSrc/genoFind.h +include/blatSrc/genomeRangeTree.h +include/blatSrc/gfClientLib.h +include/blatSrc/gfPcrLib.h +include/blatSrc/gfWebLib.h +include/blatSrc/gff.h +include/blatSrc/gff3.h +include/blatSrc/gfxPoly.h +include/blatSrc/gifLabel.h +include/blatSrc/hacTree.h +include/blatSrc/hash.h +include/blatSrc/hex.h +include/blatSrc/hgGene.h +include/blatSrc/hgap.h +include/blatSrc/hgdb.h +include/blatSrc/histogram.h +include/blatSrc/hmac.h +include/blatSrc/hmmPfamParse.h +include/blatSrc/hmmstats.h +include/blatSrc/htmlPage.h +include/blatSrc/htmshell.h +include/blatSrc/https.h +include/blatSrc/intValTree.h +include/blatSrc/internet.h +include/blatSrc/itsa.h +include/blatSrc/iupac.h +include/blatSrc/jointalign.h +include/blatSrc/jpegSize.h +include/blatSrc/jsonParse.h +include/blatSrc/jsonWrite.h +include/blatSrc/keys.h +include/blatSrc/knetUdc.h +include/blatSrc/kxTok.h +include/blatSrc/linefile.h +include/blatSrc/localEnvironment.mk +include/blatSrc/localmem.h +include/blatSrc/log.h +include/blatSrc/longToList.h +include/blatSrc/maDbRep.h +include/blatSrc/maToFf.h +include/blatSrc/maf.h +include/blatSrc/mailViaPipe.h +include/blatSrc/md5.h +include/blatSrc/memalloc.h +include/blatSrc/memgfx.h +include/blatSrc/meta.h +include/blatSrc/metaWig.h +include/blatSrc/mime.h +include/blatSrc/net.h +include/blatSrc/nib.h +include/blatSrc/nibTwo.h +include/blatSrc/nt4.h +include/blatSrc/obscure.h +include/blatSrc/oldGff.h +include/blatSrc/oligoTm.h +include/blatSrc/ooc.h +include/blatSrc/options.h +include/blatSrc/pairDistance.h +include/blatSrc/pairHmm.h +include/blatSrc/paraFetch.h +include/blatSrc/patSpace.h +include/blatSrc/peakCluster.h +include/blatSrc/phyloTree.h +include/blatSrc/pipeline.h +include/blatSrc/portable.h +include/blatSrc/psGfx.h +include/blatSrc/psPoly.h +include/blatSrc/pscmGfx.h +include/blatSrc/psl.h +include/blatSrc/pslTbl.h +include/blatSrc/pslTransMap.h +include/blatSrc/pthreadDoList.h +include/blatSrc/pthreadWrap.h +include/blatSrc/qa.h +include/blatSrc/quickHeap.h +include/blatSrc/quotedP.h +include/blatSrc/ra.h +include/blatSrc/raToStruct.h +include/blatSrc/rainbow.h +include/blatSrc/rangeTree.h +include/blatSrc/rbTree.h +include/blatSrc/regexHelper.h +include/blatSrc/repMask.h +include/blatSrc/rle.h +include/blatSrc/rnautil.h +include/blatSrc/rql.h +include/blatSrc/rudp.h +include/blatSrc/scoreWindow.h +include/blatSrc/seg.h +include/blatSrc/seqOut.h +include/blatSrc/seqStats.h +include/blatSrc/shaRes.h +include/blatSrc/sig.h +include/blatSrc/slog.h +include/blatSrc/snof.h +include/blatSrc/snofmake.h +include/blatSrc/spaceSaver.h +include/blatSrc/spacedColumn.h +include/blatSrc/spacedSeed.h +include/blatSrc/splatAli.h +include/blatSrc/splix.h +include/blatSrc/sqlList.h +include/blatSrc/sqlNum.h +include/blatSrc/subText.h +include/blatSrc/sufa.h +include/blatSrc/sufx.h +include/blatSrc/supStitch.h +include/blatSrc/synQueue.h +include/blatSrc/tabRow.h +include/blatSrc/textOut.h +include/blatSrc/tokenizer.h +include/blatSrc/trans3.h +include/blatSrc/trix.h +include/blatSrc/twoBit.h +include/blatSrc/udc.h +include/blatSrc/unfin.h +include/blatSrc/userApp.mk +include/blatSrc/vGfx.h +include/blatSrc/vcf.h +include/blatSrc/vcfBits.h +include/blatSrc/verbose.h +include/blatSrc/wormdna.h +include/blatSrc/xAli.h +include/blatSrc/xa.h +include/blatSrc/xap.h +include/blatSrc/xenalign.h +include/blatSrc/xmlEscape.h +include/blatSrc/xp.h +include/blatSrc/zlibFace.h +include/gbtools/gbtools.hpp +include/gbtools/gbtoolsCurl.hpp +include/gbtools/gbtoolsGUI.hpp +include/gbtools/gbtoolsPfetch.hpp +include/gbtools/gbtoolsTrackhub.hpp +include/gbtools/gbtoolsUtils.hpp +include/json/json-forwards.h +include/json/json.h +lib/libgbtools.a