Date: Thu, 4 Jul 2002 22:42:55 +0200 (CEST) From: Tilman Linneweh <tilman@arved.de> To: FreeBSD-gnats-submit@FreeBSD.org Cc: wjv@FreeBSD.org Subject: ports/40198: Updated port biology/emboss 2.20 -> 2.4.1 Message-ID: <200207042042.g64KgtCa016303@sauna.arved.de>
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>Number: 40198 >Category: ports >Synopsis: Updated port biology/emboss 2.20 -> 2.4.1 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Thu Jul 04 13:50:01 PDT 2002 >Closed-Date: >Last-Modified: >Originator: Tilman Linneweh >Release: FreeBSD 4.6-RC i386 >Organization: BSD Usergroup Austria >Environment: System: FreeBSD sauna.arved.de 4.6-RC FreeBSD 4.6-RC #4: Wed Jun 5 00:48:18 CEST 2002 tilman@sauna.arved.de:/usr/obj/usr/src/sys/SAUNA i386 >Description: [ Maintainer, wjv@ CCed] >How-To-Repeat: >Fix: #cvs diff -u . cvs diff: Diffing . Index: Makefile =================================================================== RCS file: /home/ncvs/ports/biology/emboss/Makefile,v retrieving revision 1.27 diff -u -r1.27 Makefile --- Makefile 17 May 2002 09:24:32 -0000 1.27 +++ Makefile 4 Jul 2002 19:38:54 -0000 @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 2.2.0 +PORTVERSION= 2.4.1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ @@ -18,8 +18,6 @@ MAINTAINER= wjv@FreeBSD.org LIB_DEPENDS= gd.2:${PORTSDIR}/graphics/gd - -BROKEN= "Incorrect checksums" USE_SUBMAKE= yes USE_GMAKE= yes Index: distinfo =================================================================== RCS file: /home/ncvs/ports/biology/emboss/distinfo,v retrieving revision 1.20 diff -u -r1.20 distinfo --- distinfo 18 Jan 2002 14:04:03 -0000 1.20 +++ distinfo 4 Jul 2002 19:54:55 -0000 @@ -1,7 +1,7 @@ -MD5 (emboss/EMBOSS-2.2.0.tar.gz) = c6d755f98f558f9f98649c1d1cca44a6 -MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66 -MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21 -MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c -MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9 -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084 -MD5 (emboss/TOPO-0.1.tar.gz) = 96fced0b0979157e344fd9b08dc2aa64 +MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad +MD5 (emboss/EMNU-1.0.5.tar.gz) = 628f28b24762e75a9546b608cc60f179 +MD5 (emboss/HMMER-2.1.1.tar.gz) = 1bce29d9f215076c90d2b95b9ba6942f +MD5 (emboss/MEME-2.3.1.tar.gz) = 6961f0308b122d170a5e8d27f02edbc3 +MD5 (emboss/MSE-0.0.4.tar.gz) = 067952daa34ce4af71e88d9e87136257 +MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4e69bc86f429d95f99b5e9d3f83036ab +MD5 (emboss/TOPO-0.1.tar.gz) = 8ca248a5cf0ad230d3959fbcce013942 Index: pkg-plist =================================================================== RCS file: /home/ncvs/ports/biology/emboss/pkg-plist,v retrieving revision 1.17 diff -u -r1.17 pkg-plist --- pkg-plist 18 Jan 2002 14:04:03 -0000 1.17 +++ pkg-plist 4 Jul 2002 20:29:46 -0000 @@ -188,7 +188,6 @@ bin/preg bin/prettyplot bin/prettyseq -bin/primer3 bin/primersearch bin/printsextract bin/profit @@ -210,9 +209,6 @@ bin/seealso bin/seqmatchall bin/seqret -bin/seqretall -bin/seqretallfeat -bin/seqretset bin/seqretsplit bin/showalign bin/showdb @@ -320,6 +316,7 @@ share/EMBOSS/acd/emowse.acd share/EMBOSS/acd/entrails.acd share/EMBOSS/acd/entret.acd +share/EMBOSS/acd/eprimer3.acd share/EMBOSS/acd/equicktandem.acd share/EMBOSS/acd/est2genome.acd share/EMBOSS/acd/etandem.acd @@ -339,6 +336,7 @@ share/EMBOSS/acd/iep.acd share/EMBOSS/acd/infoalign.acd share/EMBOSS/acd/infoseq.acd +share/EMBOSS/acd/interface.acd share/EMBOSS/acd/isochore.acd share/EMBOSS/acd/lindna.acd share/EMBOSS/acd/listor.acd @@ -365,6 +363,7 @@ share/EMBOSS/acd/patmatdb.acd share/EMBOSS/acd/patmatmotifs.acd share/EMBOSS/acd/patmattest.acd +share/EMBOSS/acd/pdbtosp.acd share/EMBOSS/acd/pepcoil.acd share/EMBOSS/acd/pepinfo.acd share/EMBOSS/acd/pepnet.acd @@ -379,7 +378,6 @@ share/EMBOSS/acd/prettyplot.acd share/EMBOSS/acd/prettyseq.acd share/EMBOSS/acd/prima.acd -share/EMBOSS/acd/primer3.acd share/EMBOSS/acd/primers.acd share/EMBOSS/acd/primersearch.acd share/EMBOSS/acd/printsextract.acd @@ -397,16 +395,19 @@ share/EMBOSS/acd/restrict.acd share/EMBOSS/acd/revseq.acd share/EMBOSS/acd/scopalign.acd +share/EMBOSS/acd/scopparse.acd share/EMBOSS/acd/scope.acd share/EMBOSS/acd/seealso.acd share/EMBOSS/acd/seqinfo.acd share/EMBOSS/acd/seqmatchall.acd +share/EMBOSS/acd/seqnr.acd share/EMBOSS/acd/seqret.acd share/EMBOSS/acd/seqretall.acd share/EMBOSS/acd/seqretallfeat.acd share/EMBOSS/acd/seqretset.acd share/EMBOSS/acd/seqretsingle.acd share/EMBOSS/acd/seqretsplit.acd +share/EMBOSS/acd/seqsort.acd share/EMBOSS/acd/showalign.acd share/EMBOSS/acd/showdb.acd share/EMBOSS/acd/showfeat.acd @@ -429,16 +430,20 @@ share/EMBOSS/acd/tfm.acd share/EMBOSS/acd/tfscan.acd share/EMBOSS/acd/tmap.acd +share/EMBOSS/acd/tranalign.acd share/EMBOSS/acd/transeq.acd share/EMBOSS/acd/treetypedisplay.acd share/EMBOSS/acd/trimest.acd share/EMBOSS/acd/trimseq.acd +share/EMBOSS/acd/union.acd share/EMBOSS/acd/vectorstrip.acd share/EMBOSS/acd/water.acd +share/EMBOSS/acd/whichdb.acd share/EMBOSS/acd/wobble.acd share/EMBOSS/acd/wordcount.acd share/EMBOSS/acd/wordmatch.acd share/EMBOSS/acd/wossname.acd +share/EMBOSS/acd/yank.acd share/EMBOSS/data/CODONS/Eacc.cut share/EMBOSS/data/CODONS/Eadenovirus5.cut share/EMBOSS/data/CODONS/Eadenovirus7.cut @@ -721,6 +726,7 @@ share/EMBOSS/data/REBASE/dummyfile share/EMBOSS/data/embossre.equ share/EMBOSS/emboss.default.template +share/EMBOSS/jemboss/README share/EMBOSS/jemboss/LICENSE share/EMBOSS/jemboss/api/allclasses-frame.html share/EMBOSS/jemboss/api/deprecated-list.html @@ -791,79 +797,6 @@ share/EMBOSS/jemboss/api/packages.html 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-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoACD.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAnnotate.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAppList.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthException.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPopup.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPrompt.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoException.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoFrame.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupList.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupTree.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelp.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelpView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoJList.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoListFile.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoMakeFileSafe.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoParams.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPendingResults.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPrivateRequest.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPublicRequest.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResList.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResListView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResSave.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResult.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoRun.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoServiceDesc.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoShowDB.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoStartup.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoTreeCellRenderer.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoUtils.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFile.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileGet.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileLaunch.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileList.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileListView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileMgr.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileNode.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFilePut.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRequest.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRoots.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileSave.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTree.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTreePanel.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileViewPanel.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalGet.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalRoots.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTree.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTreePanel.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalView.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalViewPanel.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/FileNode.html -share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/WindowsAltFileSystemView.html -share/EMBOSS/jemboss/embreo/cgi-bin/soap.cgi -share/EMBOSS/jemboss/embreo/embreo-full.jar share/EMBOSS/jemboss/images/Backward_arrow_button.gif share/EMBOSS/jemboss/images/Forward_arrow_button.gif share/EMBOSS/jemboss/images/Go_button.gif @@ -874,7 +807,6 @@ share/EMBOSS/jemboss/images/Job_manager_button.gif share/EMBOSS/jemboss/images/Refresh_button.gif share/EMBOSS/jemboss/images/Refresh_button2.gif -share/EMBOSS/jemboss/interface.html share/EMBOSS/jemboss/lib/README share/EMBOSS/jemboss/lib/activation.jar share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar @@ -882,9 +814,13 @@ share/EMBOSS/jemboss/lib/mail.jar share/EMBOSS/jemboss/lib/soap.jar share/EMBOSS/jemboss/lib/xerces.jar +share/EMBOSS/jemboss/lib/jcert.jar +share/EMBOSS/jemboss/lib/jnet.jar +share/EMBOSS/jemboss/lib/jsse.jar share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss.java share/EMBOSS/jemboss/org/emboss/jemboss/JembossLogo.java share/EMBOSS/jemboss/org/emboss/jemboss/JembossParams.java +share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/LaunchJalView.java @@ -893,6 +829,9 @@ share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowResultSet.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/SwingWorker.java +share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceData.java +share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceList.java +share/EMBOSS/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java @@ -929,6 +868,8 @@ share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/Application.java share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java +share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java +share/EMBOSS/jemboss/org/emboss/jemboss/parser/AjaxUtil.java share/EMBOSS/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java share/EMBOSS/jemboss/org/emboss/jemboss/programs/JembossProcess.java share/EMBOSS/jemboss/org/emboss/jemboss/programs/ListFile.java @@ -936,6 +877,12 @@ share/EMBOSS/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java share/EMBOSS/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossThread.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthServer.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthThread.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java +share/EMBOSS/jemboss/org/emboss/jemboss/server/TestPublicServer.java share/EMBOSS/jemboss/org/emboss/jemboss/soap/AuthPopup.java share/EMBOSS/jemboss/org/emboss/jemboss/soap/CallAjax.java share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetWossname.java @@ -943,13 +890,25 @@ share/EMBOSS/jemboss/org/emboss/jemboss/soap/JembossSoapException.java share/EMBOSS/jemboss/org/emboss/jemboss/soap/PendingResults.java share/EMBOSS/jemboss/org/emboss/jemboss/soap/PrivateRequest.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/ServerSetup.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileRoots.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileList.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/PublicRequest.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetACD.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetHelp.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/ShowDB.java +share/EMBOSS/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java +share/EMBOSS/jemboss/utils/install-jemboss-server.sh +share/EMBOSS/jemboss/utils/keys.sh +share/EMBOSS/jemboss/utils/makeJNLP.sh +share/EMBOSS/jemboss/utils/template.html +share/EMBOSS/jemboss/utils/README +share/EMBOSS/jemboss/utils/makeJar.csh share/EMBOSS/jemboss/readme.html share/EMBOSS/jemboss/resources/jemboss.properties share/EMBOSS/jemboss/resources/readme.txt share/EMBOSS/jemboss/resources/version share/EMBOSS/jemboss/runJemboss.csh -share/EMBOSS/jemboss/setup.html -share/EMBOSS/jemboss/utils/makeJar.csh share/EMBOSS/plstnd5.fnt share/EMBOSS/plxtnd5.fnt share/EMBOSS/test/data/aligna.dna @@ -1005,25 +964,79 @@ share/EMBOSS/test/data/prot.ncbi share/EMBOSS/test/data/prot.swiss share/EMBOSS/test/data/prot.text +share/EMBOSS/test/data/tranalign.pep +share/EMBOSS/test/data/tranalign.seq share/EMBOSS/test/data/z83307.seq share/EMBOSS/test/embl/acnum.hit share/EMBOSS/test/embl/acnum.trg +share/EMBOSS/test/embl/des.hit +share/EMBOSS/test/embl/des.trg share/EMBOSS/test/embl/division.lkp share/EMBOSS/test/embl/entrynam.idx share/EMBOSS/test/embl/est.dat share/EMBOSS/test/embl/fun.dat share/EMBOSS/test/embl/hum1.dat share/EMBOSS/test/embl/inv.dat +share/EMBOSS/test/embl/keyword.hit +share/EMBOSS/test/embl/keyword.trg share/EMBOSS/test/embl/pln.dat share/EMBOSS/test/embl/pro.dat share/EMBOSS/test/embl/rod.dat +share/EMBOSS/test/embl/seqvn.hit +share/EMBOSS/test/embl/seqvn.trg share/EMBOSS/test/embl/sts.dat +share/EMBOSS/test/embl/taxon.hit +share/EMBOSS/test/embl/taxon.trg share/EMBOSS/test/embl/vrl.dat share/EMBOSS/test/embl/vrt.dat +share/EMBOSS/test/genbank/acnum.hit +share/EMBOSS/test/genbank/acnum.trg +share/EMBOSS/test/genbank/division.lkp +share/EMBOSS/test/genbank/entrynam.idx +share/EMBOSS/test/genbank/seqvn.hit +share/EMBOSS/test/genbank/seqvn.trg +share/EMBOSS/test/genbank/des.hit +share/EMBOSS/test/genbank/des.trg +share/EMBOSS/test/genbank/keyword.hit +share/EMBOSS/test/genbank/keyword.trg +share/EMBOSS/test/genbank/taxon.hit +share/EMBOSS/test/genbank/taxon.trg +share/EMBOSS/test/genbank/gbbct1.seq +share/EMBOSS/test/genbank/gbest1.seq +share/EMBOSS/test/genbank/gbinv1.seq +share/EMBOSS/test/genbank/gbpln1.seq +share/EMBOSS/test/genbank/gbpln2.seq +share/EMBOSS/test/genbank/gbpri1.seq +share/EMBOSS/test/genbank/gbrod1.seq +share/EMBOSS/test/genbank/gbsts1.seq +share/EMBOSS/test/genbank/gbvrl1.seq +share/EMBOSS/test/genbank/gbvrt.seq +share/EMBOSS/test/gb/acnum.hit +share/EMBOSS/test/gb/acnum.trg +share/EMBOSS/test/gb/division.lkp +share/EMBOSS/test/gb/entrynam.idx +share/EMBOSS/test/gb/seqvn.hit +share/EMBOSS/test/gb/seqvn.trg +share/EMBOSS/test/gb/des.hit +share/EMBOSS/test/gb/des.trg +share/EMBOSS/test/gb/keyword.hit +share/EMBOSS/test/gb/keyword.trg +share/EMBOSS/test/gb/taxon.hit +share/EMBOSS/test/gb/taxon.trg +share/EMBOSS/test/gb/ba.ref +share/EMBOSS/test/gb/ba.seq +share/EMBOSS/test/gb/htg.ref +share/EMBOSS/test/gb/htg.seq share/EMBOSS/test/pir/acnum.hit share/EMBOSS/test/pir/acnum.trg +share/EMBOSS/test/pir/des.hit +share/EMBOSS/test/pir/des.trg share/EMBOSS/test/pir/division.lkp share/EMBOSS/test/pir/entrynam.idx +share/EMBOSS/test/pir/keyword.hit +share/EMBOSS/test/pir/keyword.trg +share/EMBOSS/test/pir/taxon.hit +share/EMBOSS/test/pir/taxon.trg share/EMBOSS/test/pir/pir1.header share/EMBOSS/test/pir/pir1.names share/EMBOSS/test/pir/pir1.numbers @@ -1053,6 +1066,14 @@ share/EMBOSS/test/swiss/division.lkp share/EMBOSS/test/swiss/entrynam.idx share/EMBOSS/test/swiss/seq.dat +share/EMBOSS/test/swiss/seqvn.hit +share/EMBOSS/test/swiss/seqvn.trg +share/EMBOSS/test/swiss/des.hit +share/EMBOSS/test/swiss/des.trg +share/EMBOSS/test/swiss/keyword.hit +share/EMBOSS/test/swiss/keyword.trg +share/EMBOSS/test/swiss/taxon.hit +share/EMBOSS/test/swiss/taxon.trg share/EMBOSS/test/swnew/acnum.hit share/EMBOSS/test/swnew/acnum.trg share/EMBOSS/test/swnew/division.lkp @@ -1060,11 +1081,21 @@ share/EMBOSS/test/swnew/new_seq.dat share/EMBOSS/test/swnew/upd_ann.dat share/EMBOSS/test/swnew/upd_seq.dat +share/EMBOSS/test/swnew/seqvn.hit +share/EMBOSS/test/swnew/seqvn.trg +share/EMBOSS/test/swnew/des.hit +share/EMBOSS/test/swnew/des.trg +share/EMBOSS/test/swnew/keyword.hit +share/EMBOSS/test/swnew/keyword.trg +share/EMBOSS/test/swnew/taxon.hit +share/EMBOSS/test/swnew/taxon.trg share/EMBOSS/test/wormpep/acnum.hit share/EMBOSS/test/wormpep/acnum.trg share/EMBOSS/test/wormpep/division.lkp share/EMBOSS/test/wormpep/entrynam.idx share/EMBOSS/test/wormpep/wormpep +share/EMBOSS/test/wormpep/des.hit +share/EMBOSS/test/wormpep/des.trg share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt share/doc/EMBOSS/manuals/admin.aux share/doc/EMBOSS/manuals/admin.dvi @@ -1272,8 +1303,6 @@ share/doc/EMBOSS/programs/html/prettyplot3.gif share/doc/EMBOSS/programs/html/prettyplot4.gif share/doc/EMBOSS/programs/html/prettyseq.html -share/doc/EMBOSS/programs/html/prima.html -share/doc/EMBOSS/programs/html/primer3.html share/doc/EMBOSS/programs/html/primersearch.html share/doc/EMBOSS/programs/html/printsextract.html share/doc/EMBOSS/programs/html/profit.html @@ -1350,6 +1379,20 @@ share/doc/EMBOSS/programs/html/wordcount.html share/doc/EMBOSS/programs/html/wordmatch.html share/doc/EMBOSS/programs/html/wossname.html +share/doc/EMBOSS/programs/html/pdbtosp.html +share/doc/EMBOSS/programs/html/psiblasts.html +share/doc/EMBOSS/programs/html/scopparse.html +share/doc/EMBOSS/programs/html/seqnr.html +share/doc/EMBOSS/programs/html/seqsort.html +share/doc/EMBOSS/programs/html/tranalign.html +share/doc/EMBOSS/programs/html/union.html +share/doc/EMBOSS/programs/html/whichdb.html +share/doc/EMBOSS/programs/html/yank.html +share/doc/EMBOSS/programs/html/alignwrap.html +share/doc/EMBOSS/programs/html/dichet.html +share/doc/EMBOSS/programs/html/eprimer3.html +share/doc/EMBOSS/programs/html/interface.html +share/doc/EMBOSS/programs/html/jembossctl.html share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt share/doc/EMBOSS/programs/text/abiview.txt share/doc/EMBOSS/programs/text/ajtest.txt @@ -1497,8 +1540,6 @@ share/doc/EMBOSS/programs/text/preg.txt share/doc/EMBOSS/programs/text/prettyplot.txt share/doc/EMBOSS/programs/text/prettyseq.txt -share/doc/EMBOSS/programs/text/prima.txt -share/doc/EMBOSS/programs/text/primer3.txt share/doc/EMBOSS/programs/text/primersearch.txt share/doc/EMBOSS/programs/text/printsextract.txt share/doc/EMBOSS/programs/text/profit.txt @@ -1559,6 +1600,20 @@ share/doc/EMBOSS/programs/text/wordcount.txt share/doc/EMBOSS/programs/text/wordmatch.txt share/doc/EMBOSS/programs/text/wossname.txt +share/doc/EMBOSS/programs/text/jembossctl.txt +share/doc/EMBOSS/programs/text/pdbtosp.txt +share/doc/EMBOSS/programs/text/psiblasts.txt +share/doc/EMBOSS/programs/text/scopparse.txt +share/doc/EMBOSS/programs/text/seqnr.txt +share/doc/EMBOSS/programs/text/seqsort.txt +share/doc/EMBOSS/programs/text/tranalign.txt +share/doc/EMBOSS/programs/text/union.txt +share/doc/EMBOSS/programs/text/whichdb.txt +share/doc/EMBOSS/programs/text/yank.txt +share/doc/EMBOSS/programs/text/alignwrap.txt +share/doc/EMBOSS/programs/text/dichet.txt +share/doc/EMBOSS/programs/text/eprimer3.txt +share/doc/EMBOSS/programs/text/interface.txt share/doc/EMBOSS/tutorials/biblio.bib share/doc/EMBOSS/tutorials/dottup.ps.gz share/doc/EMBOSS/tutorials/emboss-gcg.ppt @@ -1580,6 +1635,8 @@ @dirrm share/EMBOSS/test/swnew @dirrm share/EMBOSS/test/swiss @dirrm share/EMBOSS/test/pir +@dirrm share/EMBOSS/test/genbank +@dirrm share/EMBOSS/test/gb @dirrm share/EMBOSS/test/embl @dirrm share/EMBOSS/test/data @dirrm share/EMBOSS/test @@ -1600,16 +1657,6 @@ @dirrm share/EMBOSS/jemboss/org @dirrm share/EMBOSS/jemboss/lib @dirrm share/EMBOSS/jemboss/images -@dirrm share/EMBOSS/jemboss/embreo/cgi-bin -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac -@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk -@dirrm share/EMBOSS/jemboss/embreo/api-docs -@dirrm share/EMBOSS/jemboss/embreo/Modules -@dirrm share/EMBOSS/jemboss/embreo @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd cvs diff: Diffing files >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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