blat installation problem

[NicoBxl]

Hi,

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

Thanks,

N.

[myshu]

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!

[blancha]

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.

http://hgdownload.cse.ucsc.edu/admin/exe/