Unable to compile dependencies

[lcslyh]

Hello, I'm trying to install smrtsv2, and I can't build the dependencies. I get the following error:

PackagesNotFoundError: The following packages are not available from current channels:
- gcc=4.8.5

Then I installed GCC 4.8.5 and tried many times, but it still reports the same error, I don't know how to solve it. The following is the complete error message:

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    conda-forge/linux-64::ca-certificates-2019.11.28-hecc5488_0
  certifi            conda-forge/linux-64::certifi-2019.11.28-py36_0
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.2.0-hdf63c60_0
  ncurses            conda-forge/linux-64::ncurses-5.9-10
  openssl            conda-forge/linux-64::openssl-1.0.2t-h14c3975_0
  pip                conda-forge/linux-64::pip-19.3.1-py36_0
  python             conda-forge/linux-64::python-3.6.2-0
  readline           conda-forge/linux-64::readline-6.2-0
  setuptools         conda-forge/linux-64::setuptools-42.0.2-py36_0
  sqlite             conda-forge/linux-64::sqlite-3.13.0-1
  tk                 conda-forge/linux-64::tk-8.5.19-2
  wheel              conda-forge/linux-64::wheel-0.33.6-py36_0
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1006

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate tools
#
# To deactivate an active environment, use
#
#     $ conda deactivate

date > build/install_flags/env_tools_deploy
Warning: 'defaults' already in 'channels' list, moving to the top
Warning: 'bioconda' already in 'channels' list, moving to the top
Warning: 'conda-forge' already in 'channels' list, moving to the top
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - gcc=4.8.5

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

make[1]: *** [build/install_flags/env_tools_install] error 1
make[1]: Leaving directory `/opt/biosoft/smrtsv2/dep/conda'
make: *** [install_flags/dep_conda_build] error 2    

I am using Linux CentOS 6.9.

[lcslyh]

My GCC version:

[eldariont]

Hi,

I hope it's okay if I chip in on this but I experienced the very same problem last week and I almost gave up on trying to install SMRTSV2. Yesterday, I gave it a new try in a completely new directory and this time make completed successfully without any problems. I do not have any idea what made the difference.

gcc 4.8.5 was eventually found in channel anaconda (see here). So the question is why this package cannot be found in your case (and my case of last week).

Hoping that this helps somewhat. Best David

[lcslyh]

Hi,

I hope it's okay if I chip in on this but I experienced the very same problem last week and I almost gave up on trying to install SMRTSV2. Yesterday, I gave it a new try in a completely new directory and this time make completed successfully without any problems. I do not have any idea what made the difference.

gcc 4.8.5 was eventually found in channel anaconda (see here). So the question is why this package cannot be found in your case (and my case of last week).

Hoping that this helps somewhat. Best David

Thank you very much, David！I will try it.

[paudano]

I have already updated the dependency installation process to fix this, and I am currently testing. It's looking good, so I pushed the changes as v2.0.1 (fd4f2203b8c40416ac91c3ef095348f92a5a3f91).

I'll close this for now, but if it doesn't work, you can re-open this issue.