problem in installing BLAT

[Aritra Deb]

Hello,

I was trying to install BLAT using blatSrc34.zip in my workstation where ubuntu (Release 12.04 (precise) 64-bit) is installed. I was following the instructions from the page http://www.mutationtaster.org/NextGenerationSequencing.html and from the readme file given. But I found the following errors:
chainBlock.c:290:16: error: variable ‘bestLeaf’ set but not used [-Werror=unused-but-set-

variable]
cc1: all warnings being treated as errors
make[1]: *** [chainBlock.o] Error 1
make[1]: Leaving directory `/home/bose/BLAT/blatSrc/lib'
make: *** [all] Error 2

Please suggest me how I can install successfully. One more thing I was doing this as a standard user of linux, not as root user. Should I need to be root to do this? It will be helpful if you can give me a step by step instruction so that I can follow it. Please reply soon. Thanks.

Aritra Deb

[Aritra Deb]

Hello,

While searching in internet I got the page; https://lists.soe.ucsc.edu/pipermail/genome/2011-November/027576.html, and tried to follow the given solution and then I found that the previous errors are not occurring but the following errors occurred:
############################################################################
cd lib && make
make[1]: Entering directory `/home/bose/BLAT/blatSrc/lib'
ar rcus /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 phyloTree.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
ar: /jkweb.a: Permission denied
make[1]: *** [/jkweb.a] Error 1

make[1]: Leaving directory `/home/bose/BLAT/blatSrc/lib'
make: *** [all] Error 2

############################################################
Please suggest me a solution. Thanks.

Aritra Deb

[Hiram Clawson]

Good Morning Aritra:

You can find your problems described and work-around solutions in
the complete kent source tree README files in the src/product/
directory. You can view them here:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/product

Note the README.building.source information:

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source

It appears you do not have your shell environment variables set up correctly,
note the MACHTYPE variable in the README information.

--Hiram