Yes, i used blatSrc34.zip. Let me try the latest version. Thank you Galt. ________________________________________ From: Galt Barber [[email protected]] Sent: Monday, October 25, 2010 7:38 PM To: Li, Yongjin Cc: [email protected] Subject: Re: [Genome] "fuzzyFind.c:1049: error" in BLAT installation
Hi, Yongjin >proto.score = 0; This was fixed by Jim Kent on 2009-08-20 Where did you download blatSrc from? e.g. http://users.soe.ucsc.edu/~kent/src/ Which file did you use? e.g. blatSrc34.zip ? If you want the latest version of the kent source you can get it from here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip This will contain more than just blat, but the latest blat will be in there. There are some pre-compiled blat binaries that might work for you: http://genome-test.cse.ucsc.edu/~kent/exe/ -Galt 10/25/2010 5:13 PM, Li, Yongjin: > Hi, > I got the following errors when installing BLAT on linux. > > : yong...@silver blatSrc; make > cd lib&& make > make[1]: Entering directory > `/net/zz/bi/u9/yxl101820/Downloads/SoftWares/blatSrc/lib' > ar rcus x86_64/jkweb.a aliType.o apacheLog.o asParse.o axt.o axtAffine.o > base64.o bits.o binRange.o blastOut.o blastParse.o boxClump.o boxLump.o > browserGfx.o cda.o chain.o chainBlock.o chainConnect.o chainToAxt.o > chainToPsl.o cheapcgi.o codebias.o colHash.o common.o correlate.o dgRange.o > diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaseq.o dnautil.o dnaMotif.o > dtdParse.o dystring.o emblParse.o errabort.o errCatch.o fa.o ffAli.o > ffScore.o filePath.o fixColor.o flydna.o fof.o fuzzyShow.o gapCalc.o gdf.o > gemfont.o gfNet.o gff.o gfxPoly.o gifcomp.o gifdecomp.o gifLabel.o gifread.o > gifwrite.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o > internet.o intExp.o jointalign.o jpegSize.o keys.o kxTok.o linefile.o > localmem.o log.o maf.o mafFromAxt.o mafScore.o md5.o mgTinyFont.o > mgSmallFont.o mgMediumFont.o mgLargeFont.o mgHugeFont.o memalloc.o memgfx.o > mgCircle.o mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o obscure.o oldGff.o > oligoTm.o options.o osunix.o pairHmm.o ph yloTree.o pipeline.o portimpl.o pscmGfx.o psGfx.o psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o psPoly.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rangeTree.o rbTree.o repMask.o rle.o rnautil.o rudp.o scoreWindow.o seqOut.o seqStats.o servBrcMcw.o servcis.o servCrunx.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o snofmake.o snofsig.o spacedColumn.o spacedSeed.o spaceSaver.o sqlNum.o sqlList.o subText.o synQueue.o tabRow.o textOut.o tokenizer.o trix.o twoBit.o verbose.o vGfx.o vGif.o wildcmp.o wormdna.o xa.o xAli.o xap.o xenshow.o xmlEscape.o xp.o > make[1]: Leaving directory > `/net/zz/bi/u9/yxl101820/Downloads/SoftWares/blatSrc/lib' > cd jkOwnLib&& make > make[1]: Entering directory > `/net/zz/bi/u9/yxl101820/Downloads/SoftWares/blatSrc/jkOwnLib' > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc > -I../../../../inc -I../../../../../inc -o bandExt.o -c bandExt.c > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc > -I../../../../inc -I../../../../../inc -o crudeali.o -c crudeali.c > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc > -I../../../../inc -I../../../../../inc -o ffAliHelp.o -c ffAliHelp.c > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc > -I../../../../inc -I../../../../../inc -o ffSeedExtend.o -c ffSeedExtend.c > gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE > -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc > -I../../../../inc -I../../../../../inc -o fuzzyFind.o -c fuzzyFind.c > cc1: warnings being treated as errors > fuzzyFind.c: In function ‘lumpHits’: > fuzzyFind.c:1049: error: ‘proto.score’ may be used uninitialized in this > function > make[1]: *** [fuzzyFind.o] Error 1 > make[1]: Leaving directory > `/net/zz/bi/u9/yxl101820/Downloads/SoftWares/blatSrc/jkOwnLib' > make: *** [all] Error 2 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
