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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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sambamba: symbol lookup error #442

Closed mbk0asis closed 4 years ago

mbk0asis commented 4 years ago 
$ conda install sambamba      
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/bio0/anaconda2

  added / updated specs:
    - sambamba

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-4.8.3                |   py27h8c360ce_1         3.0 MB  conda-forge
    ldc-1.20.0                 |       h9a1ace1_1        36.9 MB  conda-forge
    python_abi-2.7             |         1_cp27mu           4 KB  conda-forge
    sambamba-0.7.1             |       h148d290_2         3.3 MB  bioconda
    ------------------------------------------------------------
                                           Total:        43.2 MB

The following NEW packages will be INSTALLED:

  ldc                conda-forge/linux-64::ldc-1.20.0-h9a1ace1_1
  python_abi         conda-forge/linux-64::python_abi-2.7-1_cp27mu
  sambamba           bioconda/linux-64::sambamba-0.7.1-h148d290_2

The following packages will be UPDATED:

  conda                                        4.8.2-py27_0 --> 4.8.3-py27h8c360ce_1

The following packages will be DOWNGRADED:

  htslib                                  1.10.2-h78d89cc_0 --> 1.9-h244ad75_9
  samtools                                  1.10-h9402c20_2 --> 1.9-h10a08f8_12

Proceed ([y]/n)? y

Downloading and Extracting Packages
python_abi-2.7       | 4 KB      | ####################################################################################################################################### | 100% 
ldc-1.20.0           | 36.9 MB   | ####################################################################################################################################### | 100% 
conda-4.8.3          | 3.0 MB    | ####################################################################################################################################### | 100% 
sambamba-0.7.1       | 3.3 MB    | ####################################################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

$ sambamba
sambamba: symbol lookup error: /usr/lib/x86_64-linux-gnu/libbiod.so.0: undefined symbol: _D3std11parallelism__T4TaskS_D3bio3std12experimental3hts11bgzf_writer16bgzfCompressFuncFAhiQdDFQhQjZvZSQCr8typecons__T5TupleTQBlTQBpTDFQBvQByZvZQBaTQCiTiTQCoTQzZQFj6__initZ

What might be the problem here?

Thank you!

pjotrp commented 4 years ago

It is a bioconda issue.