Make error
Closed this issue · 4 comments
francicco commented
Hi,
I'm getting this error when trying to run the make:
cc -g -Wall -O3 -std=gnu99 -L../lib -L../../libBigWig -L../../htslib wiggletools.c -lwiggletools -l:libBigWig.a -lcurl -l:libhts.a -lgsl -lgslcblas -lz -lpthread -lm -o ../bin/wiggletools
../../htslib/libhts.a(cram_io.o): In function `lzma_mem_deflate':
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:709: undefined reference to `lzma_stream_buffer_bound'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:715: undefined reference to `lzma_easy_buffer_encode'
../../htslib/libhts.a(cram_io.o): In function `cram_compress_by_method':
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:1092: undefined reference to `BZ2_bzBuffToBuffCompress'
../../htslib/libhts.a(cram_io.o): In function `cram_uncompress_block':
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:1012: undefined reference to `BZ2_bzBuffToBuffDecompress'
../../htslib/libhts.a(cram_io.o): In function `lzma_mem_inflate':
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:731: undefined reference to `lzma_easy_decoder_memusage'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:731: undefined reference to `lzma_stream_decoder'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:749: undefined reference to `lzma_code'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:762: undefined reference to `lzma_code'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:773: undefined reference to `lzma_end'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:778: undefined reference to `lzma_end'
/mnt/storage/home/tk19812/scratch/software/htslib/cram/cram_io.c:773: undefined reference to `lzma_end'
collect2: error: ld returned 1 exit status
make[1]: *** [../bin/wiggletools] Error 1
make[1]: Leaving directory `/mnt/storage/scratch/tk19812/software/WiggleTools/src'
make: *** [Wiggletools] Error 2
Any help?
Thanks a lot
F
dzerbino commented
Hello @francicco ,
This appears to be a problem with the htslib dependencies, specifically liblzma which was not found.
Can you test whether the htslib compilation and installation worked well, e.g. whether the ../../htslib/tabix and ../../htslib/bgzip executables function properly?
Cheers,
Daniel
dahlo commented
@francicco I had the same issue, but managed to solve it by adding
-llzma -lbz2
to the LIBS variable in src/Makefile, line 6. Check my changes in https://github.com/dahlo/WiggleTools
dzerbino commented
Apologies for the slow response, commit merged in.