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Old 03-30-2011, 12:15 AM   #1
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default blat installation problem


I've a problem in the installation of blat. I'm on a Linux Mint 9 x86_64.

I follow the README file but here's when I try to do "make"

cd lib && make
make[1]: entrant dans le répertoire « /home/nicolas/programme/blatSrc/lib »
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o aliType.o -c aliType.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o apacheLog.o -c apacheLog.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o asParse.o -c asParse.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o axt.o -c axt.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o axtAffine.o -c axtAffine.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o base64.o -c base64.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o bits.o -c bits.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o binRange.o -c binRange.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o blastOut.o -c blastOut.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o blastParse.o -c blastParse.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o boxClump.o -c boxClump.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o boxLump.o -c boxLump.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o browserGfx.o -c browserGfx.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o cda.o -c cda.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chain.o -c chain.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chainBlock.o -c chainBlock.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chainConnect.o -c chainConnect.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chainToAxt.o -c chainToAxt.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chainToPsl.o -c chainToPsl.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o cheapcgi.o -c cheapcgi.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o codebias.o -c codebias.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o colHash.o -c colHash.c
gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o common.o -c common.c
cc1: warnings being treated as errors
common.c: In function ‘firstWordInFile’:
common.c:1695: error: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
make[1]: *** [common.o] Erreur 1
make[1]: quittant le répertoire « /home/nicolas/programme/blatSrc/lib »
I don't understand where's the problem


NicoBxl is offline   Reply With Quote
Old 11-11-2015, 07:41 PM   #2
Junior Member
Location: wuhan

Join Date: Nov 2015
Posts: 2

I have the problem as below :

cd lib && make
make[1]: Entering directory `/analysis/software_han/blatSrc/lib'
ar rcus x86_64/jkweb.a aliType.o annoAssembly.o annoFilter.o annoFormatter.o annoFormatTab.o annoGrator.o annoGrateWig.o annoGratorQuery.o annoOption.o annoRow.o annoStreamer.o annoStreamBigBed.o annoStreamBigWig.o annoStreamTab.o annoStreamVcf.o apacheLog.o asParse.o axt.o axtAffine.o bamFile.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 bwgValsOnChrom.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 dyOut.o dystring.o elmTree.o emblParse.o errCatch.o errAbort.o fa.o ffAli.o ffScore.o fieldedTable.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 font/mgMenlo12.o fq.o fuzzyShow.o gapCalc.o gdf.o gemfont.o genomeRangeTree.o gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o hacTree.o hash.o hex.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o hmac.o https.o intExp.o intValTree.o internet.o itsa.o iupac.o jointalign.o jpegSize.o jsonParse.o jsonWrite.o keys.o knetUdc.o kxTok.o linefile.o lineFileOnBigBed.o localmem.o log.o longToList.o maf.o mafFromAxt.o mafScore.o mailViaPipe.o md5.o memalloc.o memgfx.o meta.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 pairDistance.o paraFetch.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 pthreadDoList.o pthreadWrap.o qa.o quickHeap.o quotedP.o ra.o rainbow.o raToStruct.o rbTree.o rangeTree.o regexHelper.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 vcf.o vcfBits.o vGfx.o vPng.o verbose.o wildcmp.o wormdna.o xAli.o xa.o xap.o xenshow.o xmlEscape.o xp.o zlibFace.o
make[1]: Leaving directory `/analysis/software_han/blatSrc/lib'
cd jkOwnLib && make
make[1]: Entering directory `/analysis/software_han/blatSrc/jkOwnLib'
make[1]: `../lib/x86_64/jkOwnLib.a' is up to date.
make[1]: Leaving directory `/analysis/software_han/blatSrc/jkOwnLib'
cd blat && make
make[1]: Entering directory `/analysis/software_han/blatSrc/blat'
gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o /home/myshu/bin/x86_64/blat blat.o ../lib/x86_64/jkOwnLib.a ../lib/x86_64/jkweb.a -pthread -L/usr/lib/x86_64-linux-gnu -lpng12 -lm
true /home/myshu/bin/x86_64/blat
make[1]: Leaving directory `/analysis/software_han/blatSrc/blat'
cd gfClient && make
make[1]: Entering directory `/analysis/software_han/blatSrc/gfClient'
gcc -O -g -o /home/myshu/bin/x86_64/gfClient gfClient.o ../lib/x86_64/jkOwnLib.a ../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lsocket -lnsl -lz -lstdc++ -lrt -lm -pthread -L/usr/lib/x86_64-linux-gnu -lpng12 -lm -lm
/usr/bin/ld: cannot find -lsocket
collect2: ld returned 1 exit status
make[1]: *** [/home/myshu/bin/x86_64/gfClient] Error 1
make[1]: Leaving directory `/analysis/software_han/blatSrc/gfClient'
make: *** [all] Error 2

can you help ?thank you!
myshu is offline   Reply With Quote
Old 11-11-2015, 07:58 PM   #3
Senior Member
Location: Montreal

Join Date: May 2013
Posts: 367

Any reason you can't just download the executable, instead of trying to build the executable from the source code?

Here is the link for the executables, available for several platforms.
blancha is offline   Reply With Quote

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