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Ensembl / WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
Apache License 2.0
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Make error #43

Closed francicco closed 4 years ago

francicco commented 5 years ago

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 5 years ago

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 5 years ago

@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 5 years ago

@dahlo: Thanks for that, could you please send us a PR?

dzerbino commented 4 years ago

Apologies for the slow response, commit merged in.