BLAT error

[koustavpal]

make[1]: Entering directory `/home/koustav/Desktop/blatSrc/lib'
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o aliType.o -c aliType.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoColumn.o -c annoColumn.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoFilter.o -c annoFilter.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoFormatter.o -c annoFormatter.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoFormatTab.o -c annoFormatTab.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoGrator.o -c annoGrator.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoGratorQuery.o -c annoGratorQuery.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoOption.o -c annoOption.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoRow.o -c annoRow.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoStreamer.o -c annoStreamer.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o annoStreamVcf.o -c annoStreamVcf.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o apacheLog.o -c apacheLog.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o asParse.o -c asParse.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o axt.o -c axt.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o axtAffine.o -c axtAffine.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bamFile.o -c bamFile.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o base64.o -c base64.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o basicBed.o -c basicBed.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bbiRead.o -c bbiRead.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bbiWrite.o -c bbiWrite.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bigBed.o -c bigBed.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o binRange.o -c binRange.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bits.o -c bits.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o blastOut.o -c blastOut.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o blastParse.o -c blastParse.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o boxClump.o -c boxClump.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o boxLump.o -c boxLump.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bPlusTree.o -c bPlusTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bwgCreate.o -c bwgCreate.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bwgQuery.o -c bwgQuery.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o bwgValsOnChrom.o -c bwgValsOnChrom.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o cda.o -c cda.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chain.o -c chain.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainBlock.o -c chainBlock.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainConnect.o -c chainConnect.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainToAxt.o -c chainToAxt.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o chainToPsl.o -c chainToPsl.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o cheapcgi.o -c cheapcgi.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o cirTree.o -c cirTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o codebias.o -c codebias.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o colHash.o -c colHash.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o common.o -c common.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o correlate.o -c correlate.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o crTree.o -c crTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dgRange.o -c dgRange.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o diGraph.o -c diGraph.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dlist.o -c dlist.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaLoad.o -c dnaLoad.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaMarkov.o -c dnaMarkov.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaMotif.o -c dnaMotif.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnaseq.o -c dnaseq.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dnautil.o -c dnautil.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dsPrint.o -c dsPrint.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dtdParse.o -c dtdParse.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o dystring.o -c dystring.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o emblParse.o -c emblParse.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errCatch.o -c errCatch.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o errabort.o -c errabort.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fa.o -c fa.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffAli.o -c ffAli.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o ffScore.o -c ffScore.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o filePath.o -c filePath.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fixColor.o -c fixColor.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o flydna.o -c flydna.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fof.o -c fof.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier10.o -c font/mgCourier10.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier12.o -c font/mgCourier12.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier14.o -c font/mgCourier14.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier18.o -c font/mgCourier18.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier24.o -c font/mgCourier24.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier34.o -c font/mgCourier34.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgCourier8.o -c font/mgCourier8.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica10.o -c font/mgHelvetica10.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica12.o -c font/mgHelvetica12.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica14.o -c font/mgHelvetica14.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica18.o -c font/mgHelvetica18.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica24.o -c font/mgHelvetica24.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica34.o -c font/mgHelvetica34.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelvetica8.o -c font/mgHelvetica8.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold10.o -c font/mgHelveticaBold10.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold12.o -c font/mgHelveticaBold12.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold14.o -c font/mgHelveticaBold14.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold18.o -c font/mgHelveticaBold18.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold24.o -c font/mgHelveticaBold24.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold34.o -c font/mgHelveticaBold34.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgHelveticaBold8.o -c font/mgHelveticaBold8.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgSixhi6.o -c font/mgSixhi6.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgSail8.o -c font/mgSail8.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes10.o -c font/mgTimes10.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes12.o -c font/mgTimes12.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes14.o -c font/mgTimes14.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes18.o -c font/mgTimes18.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes24.o -c font/mgTimes24.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes34.o -c font/mgTimes34.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgTimes8.o -c font/mgTimes8.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o font/mgMenlo12.o -c font/mgMenlo12.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fuzzyShow.o -c fuzzyShow.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gapCalc.o -c gapCalc.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gdf.o -c gdf.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gemfont.o -c gemfont.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o genomeRangeTree.o -c genomeRangeTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfNet.o -c gfNet.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gff.o -c gff.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gff3.o -c gff3.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gfxPoly.o -c gfxPoly.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o gifLabel.o -c gifLabel.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hacTree.o -c hacTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hash.o -c hash.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o histogram.o -c histogram.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hmmPfamParse.o -c hmmPfamParse.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o hmmstats.o -c hmmstats.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o htmlPage.o -c htmlPage.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o htmshell.o -c htmshell.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o https.o -c https.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o intExp.o -c intExp.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o intValTree.o -c intValTree.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o internet.o -c internet.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o itsa.o -c itsa.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o iupac.o -c iupac.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o jointalign.o -c jointalign.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o jpegSize.o -c jpegSize.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o keys.o -c keys.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o knetUdc.o -c knetUdc.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o kxTok.o -c kxTok.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o linefile.o -c linefile.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o lineFileOnBigBed.o -c lineFileOnBigBed.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o localmem.o -c localmem.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o log.o -c log.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o maf.o -c maf.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mafFromAxt.o -c mafFromAxt.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mafScore.o -c mafScore.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o md5.o -c md5.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memalloc.o -c memalloc.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o memgfx.o -c memgfx.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o metaWig.o -c metaWig.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgCircle.o -c mgCircle.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mgPolygon.o -c mgPolygon.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o mime.o -c mime.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o net.o -c net.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nib.o -c nib.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nibTwo.o -c nibTwo.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o nt4.o -c nt4.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o numObscure.o -c numObscure.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o obscure.o -c obscure.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o oldGff.o -c oldGff.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o oligoTm.o -c oligoTm.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o options.o -c options.c
gcc -O -g -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o osunix.o -c osunix.c
In file included from osunix.c:10:0:
/usr/local/include/pwd.h:8:1: error: unknown type name ‘LIST’
osunix.c: In function ‘getUser’:
osunix.c:496:21: warning: initialization makes pointer from integer without a cast [enabled by default]
osunix.c:499:10: error: dereferencing pointer to incomplete type
make[1]: *** [osunix.o] Error 1
make[1]: Leaving directory `/home/koustav/Desktop/blatSrc/lib'
make: *** [all] Error 2



What I do not get is why is my makefile returning this error.....a solution to this problem would be helpful.....

[koustavpal]

char *getUser()
/* Get user name */
{
uid_t uid = geteuid();
struct passwd *pw = getpwuid(uid);
if (pw == NULL)
errnoAbort("getUser: can't get user name for uid %d", (int)uid);
return pw->pw_name;
}

so this is the part of osunix.c which is returning an error. any ideas anyone?

[koustavpal]

/* Copyright Vladimir Prus 2002. Distributed under the Boost */
/* Software License, Version 1.0. (See accompanying */
/* file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt) */

#ifndef PWD_H
#define PWD_H

LIST * pwd( void );
void pwd_done( void );

#endif


and this is the file pwd.h

[GenoMax]

What OS are you compiling this on?

Are you not able to use the pre-compiled binaries supplied by UCSC? http://hgdownload.cse.ucsc.edu/admin/exe/