Cannot install Rhtslib on Mac OS 10.13
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@ryan-c-thompson-5618
Last seen 2.1 years ago
Scripps Research, La Jolla, CA

When I try to install Rhtslib on my Macbook running Mac OS 10.13.4 High Sierra, I get the following compilation error:

/bin/sh ./libtool  --tag=CC   --mode=link clang  -g -O2 -fPIC   -no-undefined -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o libhts.la -rpath /usr/
local/lib/R/3.4/site-library/Rhtslib/lib libhts_la-kfunc.lo libhts_la-knetfile.lo libhts_la-kstring.lo libhts_la-bgzf.lo libhts_la-faidx.lo libhts_la-hfile.lo libhts_la-hfile_net.
lo libhts_la-hts.lo libhts_la-regidx.lo libhts_la-sam.lo libhts_la-synced_bcf_reader.lo libhts_la-vcf_sweep.lo libhts_la-tbx.lo libhts_la-vcf.lo libhts_la-vcfutils.lo cram/libhts_
la-cram_codecs.lo cram/libhts_la-cram_decode.lo cram/libhts_la-cram_encode.lo cram/libhts_la-cram_index.lo cram/libhts_la-cram_io.lo cram/libhts_la-cram_samtools.lo cram/libhts_la
-cram_stats.lo cram/libhts_la-files.lo cram/libhts_la-mFILE.lo cram/libhts_la-md5.lo cram/libhts_la-open_trace_file.lo cram/libhts_la-pooled_alloc.lo cram/libhts_la-rANS_static.lo
 cram/libhts_la-sam_header.lo cram/libhts_la-string_alloc.lo cram/libhts_la-thread_pool.lo cram/libhts_la-vlen.lo cram/libhts_la-zfio.lo lib/libgnu.la -lm
libtool: link: clang -dynamiclib  -o .libs/libhts.0.dylib  .libs/libhts_la-kfunc.o .libs/libhts_la-knetfile.o .libs/libhts_la-kstring.o .libs/libhts_la-bgzf.o .libs/libhts_la-faid
x.o .libs/libhts_la-hfile.o .libs/libhts_la-hfile_net.o .libs/libhts_la-hts.o .libs/libhts_la-regidx.o .libs/libhts_la-sam.o .libs/libhts_la-synced_bcf_reader.o .libs/libhts_la-vc
f_sweep.o .libs/libhts_la-tbx.o .libs/libhts_la-vcf.o .libs/libhts_la-vcfutils.o cram/.libs/libhts_la-cram_codecs.o cram/.libs/libhts_la-cram_decode.o cram/.libs/libhts_la-cram_en
code.o cram/.libs/libhts_la-cram_index.o cram/.libs/libhts_la-cram_io.o cram/.libs/libhts_la-cram_samtools.o cram/.libs/libhts_la-cram_stats.o cram/.libs/libhts_la-files.o cram/.l
ibs/libhts_la-mFILE.o cram/.libs/libhts_la-md5.o cram/.libs/libhts_la-open_trace_file.o cram/.libs/libhts_la-pooled_alloc.o cram/.libs/libhts_la-rANS_static.o cram/.libs/libhts_la
-sam_header.o cram/.libs/libhts_la-string_alloc.o cram/.libs/libhts_la-thread_pool.o cram/.libs/libhts_la-vlen.o cram/.libs/libhts_la-zfio.o   -Wl,-force_load,lib/.libs/libgnu.a
-L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -lm  -O2   -install_name  /usr/local/lib/R/3.4/site-library/Rhtslib/lib/libhts.0.dylib -compatibility_v
ersion 1 -current_version 1.0 -Wl,-single_module
Undefined symbols for architecture x86_64:
  "_compressBound", referenced from:
      _bgzf_open in libhts_la-bgzf.o
      _bgzf_dopen in libhts_la-bgzf.o
      _bgzf_hopen in libhts_la-bgzf.o
  "_crc32", referenced from:
      _bgzf_compress in libhts_la-bgzf.o
      _cram_read_block in libhts_la-cram_io.o
      _cram_write_block in libhts_la-cram_io.o
      _cram_read_container in libhts_la-cram_io.o
      _cram_write_container in libhts_la-cram_io.o
  "_deflate", referenced from:
      _bgzf_flush in libhts_la-bgzf.o
      _bgzf_close in libhts_la-bgzf.o
      _bgzf_compress in libhts_la-bgzf.o
      _cram_compress_by_method in libhts_la-cram_io.o
  "_deflateEnd", referenced from:
      _bgzf_close in libhts_la-bgzf.o
      _bgzf_compress in libhts_la-bgzf.o
      _cram_compress_by_method in libhts_la-cram_io.o
  "_deflateInit2_", referenced from:
      _bgzf_write_init in libhts_la-bgzf.o
      _bgzf_compress in libhts_la-bgzf.o
      _cram_compress_by_method in libhts_la-cram_io.o
  "_gzclose", referenced from:
      _vcf_hdr_read in libhts_la-vcf.o
      _zfclose in libhts_la-zfio.o
  "_gzeof", referenced from:
      _zfeof in libhts_la-zfio.o
  "_gzgetc", referenced from:
      _zfpeek in libhts_la-zfio.o
  "_gzgets", referenced from:
      _zfgets in libhts_la-zfio.o
  "_gzopen", referenced from:
      _vcf_hdr_read in libhts_la-vcf.o
      _zfopen in libhts_la-zfio.o
  "_gzputs", referenced from:
      _zfputs in libhts_la-zfio.o
  "_gzread", referenced from:
      _vcf_hdr_read in libhts_la-vcf.o
  "_gzungetc", referenced from:
      _zfpeek in libhts_la-zfio.o
  "_inflate", referenced from:
      _bgzf_read_block in libhts_la-bgzf.o
      _inflate_gzip_block in libhts_la-bgzf.o
      _hts_detect_format in libhts_la-hts.o
      _zlib_mem_inflate in libhts_la-cram_io.o
     (maybe you meant: _zlib_mem_inflate)
  "_inflateEnd", referenced from:
      _bgzf_read_block in libhts_la-bgzf.o
      _bgzf_close in libhts_la-bgzf.o
      _hts_detect_format in libhts_la-hts.o
      _zlib_mem_inflate in libhts_la-cram_io.o
  "_inflateInit2_", referenced from:
      _bgzf_read_block in libhts_la-bgzf.o
      _hts_detect_format in libhts_la-hts.o
      _zlib_mem_inflate in libhts_la-cram_io.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [libhts.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [htslib/libhts.la] Error 2
ERROR: compilation failed for package ‘Rhtslib’

Unfortunately, there isn't any suggestion in the error message about how to resolve the error, and I can't find anyone else who has a similar error via Google searching. So can someone suggest how I might fix this error and get Rhtslib installed?

rhstlib installation compilation error • 772 views
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I don't have an answer, but all those missing symbols are usually defined in zlib.  I think Rhtslib depends on zlibbioc and it should download and link automatically, but maybe try making sure it's installed already.

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@ryan-c-thompson-5618
Last seen 2.1 years ago
Scripps Research, La Jolla, CA

Well, by chance, I happened to run brew upgrade today, and among other things, it upgraded R from 3.4.x to 3.5.0, and Rhstlib installed just fine on 3.5.0. So chalk this one up to just another ghost in the machine, I guess.

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FWIW zlibbioc provides zlib for windows; other platforms are expected to have (usually do) zlib available.

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