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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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Error with conda installation #11

Closed KristinaGagalova closed 4 years ago

KristinaGagalova commented 4 years ago

Hey Ka Ming, I am having this error when using conda for installation. I am using python 3.6

conda install -c bioconda rnabloom
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.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                        

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

Output in format: Requested package -> Available versions

Not sure what's going on Thank you in advance for the help!

kmnip commented 4 years ago

Hi Kristina,

Weird, I never encountered this issue before. The Python version shouldn't matter. Based on my bioconda recipe, openjdk and ntcard are the two packages that may cause conflicts. Can you please check their versions?

Otherwise, you may also create an environment specifically for rnabloom, e.g.

conda create -n assembly rnabloom

Hope that helps! Ka Ming

KristinaGagalova commented 4 years ago

Ok, I am actually using mamba and this is the error that it gives me:

mamba install -c bioconda rnabloom

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.5.1) supported by @QuantStack

        GitHub:  https://github.com/TheSnakePit/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) Done
bioconda/linux-64        [====================] (00m:00s) Done

Looking for: ['rnabloom']

Encountered problems while solving.
Problem: nothing provides llvm-openmp needed by ntcard-1.2.1-he513fc3_0

Any help ideas? or should I switch to conda?

KristinaGagalova commented 4 years ago

I solved the issue by adding conda-forge channel, in case anyone had similar issue

conda config --append channels conda-forge
kmnip commented 4 years ago

Glad to hear that you figured it out!