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dentearl / mafJoin

mafJoin is a tool for combining pairs of MAF files that share a common sequence.
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Undefined reference while executing make #2

Open ramchalamkr opened 7 years ago

ramchalamkr commented 7 years ago

Hi I have been trying to set up mafjoin for evolverSimControl on a linux machine. While executing make kentDir="path to kent/src" , I am getting the below error:

make kentDir=$KENT/src cc -O3 -g -Wall -Werror --pedantic -funroll-loops -lm -DNDEBUG -I ../sonLib/lib -I ./src -I /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/inc -std=c99 -pedantic -o bin/mafJoin.tmp obj/mafJoin.o obj/jkmaf.o obj/genome.o obj/mafTree.o obj/malnComp.o obj/malnBlk.o obj/malnBlkCursor.o obj/malnBlkSet.o obj/malnSet.o obj/malnJoinBlks.o obj/malnJoinWithinSet.o obj/malnJoinSets.o obj/malnMergeComps.o obj/malnMultiParents.o obj/malnCompCompMap.o obj/malnAdjust.o /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/x86_64/jkweb.a -lssl -lcrypto -pthread ../sonLib/lib/sonLib.a -lm /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/x86_64/jkweb.a(linefile.o): In functionlineFileTabixAndIndexMayOpen': /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:240: undefined reference to hts_open' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:247: undefined reference totbx_index_load2' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:267: undefined reference to tbx_readrec' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:267: undefined reference tohts_itr_query' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/x86_64/jkweb.a(linefile.o): In function lineFileSetTabixRegion': /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:279: undefined reference totbx_name2id' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:282: undefined reference to tbx_name2id' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:285: undefined reference totbx_readrec' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:285: undefined reference to hts_itr_query' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:289: undefined reference tohts_itr_destroy' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/x86_64/jkweb.a(linefile.o): In function lineFileNext': /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:490: undefined reference tohts_get_bgzfp' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:490: undefined reference to hts_itr_next' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/x86_64/jkweb.a(linefile.o): In functionlineFileClose': /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:704: undefined reference to hts_itr_destroy' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:705: undefined reference totbx_destroy' /media/ramchalamkr/DriveG/McGill/ThesisProjects/MultipleSequenceAlignmentProblem/kent/src/lib/linefile.c:706: undefined reference to hts_close' collect2: error: ld returned 1 exit status Makefile:41: recipe for target 'bin/mafJoin' failed make: *** [bin/mafJoin] Error 1

I have installed kent/src/htslib, kent/src/lib, kent/src/hg, kent/src/utils/stringify. Is it compulsory to install all the utilities of kent/src for this to work? I added some extra flags (-lm, -pthread, -lcrypto, -lssl) in the makefile of mafJoin, which fixed undefined references to ceilf and some other references.
Thank you for your help in advance.

taoqxtaozi commented 11 months ago

Hi, I get the same problem. Did you find the solution?

Thanks!