Hello,
I am having some issues installing the program oligoMatch. Can you please help me troubleshoot the issue. I am trying to install it on my Unix system which has ubuntu. Following are the specs of my Unix environment: Linux name 2.6.32-24-server #39-Ubuntu SMP Wed Jul 28 06:21:40 UTC 2010 x86_64 GNU/Linux As per the README instructions (see attachment to this email), I followed the instructions after unzipping the jksrc.zip and placing it in my machine. See below the steps I have run: >echo $MACHTYPE >x86_64 mkdir ~/bin/x86_64 cd ~/Programs/jksrc/kent/src/lib make SHOWING PART OF THE MAKE THAT WAS PRINTED ON STDOUT ormat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o zlibFace.o -c zlibFace.c ar rcus x86_64/jkweb.a aliType.o apacheLog.o asParse.o axt.o axtAffine.o base64.o basicBed.o bbiRead.o bbiWrite.o bigBed.o binRange.o bits.o blastOut.o blastParse.o boxClump.o boxLump.o bPlusTree.o bwgCreate.o bwgQuery.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o chainToPsl.o cheapcgi.o cirTree.o codebias.o colHash.o common.o correlate.o crTree.o dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o dnautil.o dtdParse.o dystring.o emblParse.o errCatch.o errabort.o fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o gifcomp.o gifdecomp.o gifread.o gifwrite.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o https.o intExp.o intValTree.o internet.o itsa.o jointalign.o jpegSize.o keys.o kxTok.o linefile.o localmem.o log.o maf.o mafFromAxt.o mafScore.o md5.o memalloc.o memgfx.o metaWig.o mgCircle.o mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o numObscure.o obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o peakCluster.o phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rbTree.o rangeTree.o repMask.o rle.o rnautil.o rqlEval.o rqlParse.o rudp.o scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o splatAli.o sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o tabRow.o textOut.o tokenizer.o trix.o twoBit.o udc.o vGfx.o vGif.o vPng.o verbose.o wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o cd ~/Programs/jksrc/kent/src/jkOwnLib make SHOWING PART OF THE MAKE THAT WAS PRINTED ON STDOUT gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xenbig.o -c xenbig.c gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o xensmall.o -c xensmall.c ar rcus ../lib/x86_64/jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o splix.o supStitch.o trans3.o xenbig.o xensmall.o cd ~/Programs/jksrc/kent/src/hg/utils/oligoMatch >make THE ERROR I GET WHILE INSTALLING oligoMatch cd ~/Programs/jksrc/kent/src/hg/utils/oligoMatch > make gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_PNG -DCOLOR32 -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o oligoMatch.o -c oligoMatch.c make: *** No rule to make target `../../../lib/x86_64/jkhgap.a', needed by `compile'. Stop. When I did make on fixCR as mentioned in the README it installed properly. I have attached the README file I followed with this email. I am not sure what else I need to do, to make this work. Thanks Manisha Brahmachary,PhD. Department of Genetics and Genomic Sciences Prof. Andrew J. SHARP laboratory Mount Sinai School of Medicine Icahn Medical Institute, Room L14-02 1425 Madison Avenue, Box 1498 NY-10029, NEW-YORK, USA Phone:+1-212-659-9777 Email:[email protected]
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