Issue with conda

[ptranvan]

Hi,

I am trying to install via conda install -c bioconda octopus

But I got this issue

octopus: error while loading shared libraries: libboost_thread.so.1.67.0: cannot open shared object file: No such file or directory

Basically all libboost* insalled are version 1.73 while octopus looks for 1.67.0

I did symbolic links but got this issue at the end:

octopus: symbol lookup error: octopus: undefined symbol: _ZN5boost6detail12set_tss_dataEPKvNS_10shared_ptrINS0_20tss_cleanup_functionEEEPvb

Is it something that has been reported before ?

[dancooke]

I think this is probably an issue for the Bioconda repo. Just a guess but have you tried updating Conda (conda update conda) and installing into a fresh environment (conda create -n octopus octopus)?

[ptranvan]

Yes I did conda update conda

Not I am trying to reinstall from scratch and still got (see libboost):

The following NEW packages will be INSTALLED:

  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
  curl               pkgs/main/linux-64::curl-7.71.1-hbc83047_1
  htslib             bioconda/linux-64::htslib-1.9-h4da6232_3
  icu                pkgs/main/linux-64::icu-58.2-he6710b0_3
  krb5               pkgs/main/linux-64::krb5-1.18.2-h173b8e3_0
  libboost           pkgs/main/linux-64::libboost-1.73.0-h3ff78a5_11
  libcurl            pkgs/main/linux-64::libcurl-7.71.1-h20c2e04_1
  libdeflate         bioconda/linux-64::libdeflate-1.2-h516909a_1
  libedit            pkgs/main/linux-64::libedit-3.1.20210216-h27cfd23_1
  libssh2            pkgs/main/linux-64::libssh2-1.9.0-h1ba5d50_1
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.3-h2531618_0
  octopus            bioconda/linux-64::octopus-0.5.2b-h14072f9_1
  pip                pkgs/main/linux-64::pip-21.0.1-py39h06a4308_0
  wheel              pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0
  zstd               pkgs/main/linux-64::zstd-1.4.5-h9ceee32_0

Is it working with you ?

[dancooke]

Somethings isn't right as your getting octopus v0.5.2b - this is over 2 years old! Try conda install -c bioconda octopus=0.7.4.

[ptranvan]

Sorry again, I tried but now I have an other issue.

conda install -c bioconda octopus=0.7.4
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.                                                                                                 failed                                                                                                                                                  

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
python=3.8 -> libgcc-ng[version='>=7.3.0']

Package openssl conflicts for:
octopus=0.7.4 -> htslib[version='>=1.12,<1.13.0a0'] -> openssl[version='>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a']
python=3.8 -> openssl[version='>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a']

Package libstdcxx-ng conflicts for:
python=3.8 -> libffi[version='>=3.2.1,<3.3a0'] -> libstdcxx-ng[version='>=7.2.0']
python=3.8 -> libstdcxx-ng[version='>=7.3.0']

At this stage I don't know if it's a problem with my cluster or the package ...

[dancooke]

Try installing into a fresh environment: conda create -n octopus octopus=0.7.4. If that fails then please report to the Bioconda repo.

[dancooke]

Closing as I don't believe this is something that can be fixed in this repo. Pleas re-open if I'm mistaken!