SpiecEasi on conda

[sghignone]

Hi! Has anyone managed to install SpiecEasi in a conda environment? Can you tell specification of your environment? thanks S.-

[zdk123]

Yes, there is a recipe on bioconda: https://anaconda.org/bioconda/r-spieceasi

[sghignone]

yes, I know the recipe exists, but I'm getting this..(I thought conda was able to solve those dependencies)

$ conda install -c bioconda r-spieceasi Retrieving notices: ...working... done 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 your system:

• feature:/linux-64::__glibc==2.31=0
• r-spieceasi -> r-rcpp -> __glibc[version='>=2.17,<3.0.a0']

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.

I'm getting this on a : Distributor ID: Ubuntu Description: Ubuntu 20.04.6 LTS Release: 20.04 Codename: focal

[zdk123]

I'm not sure why your system glibc doesn't satisfy that version requirement... The version strings look compatible at least. I'll see if I can reproduce this.

On Mon, Mar 20, 2023, 10:26 AM Stefano Ghignone @.***> wrote:

yes, I know the recipe exists, but I'm getting this..(I thought conda was able to solve those dependencies)

$ conda install -c bioconda r-spieceasi Retrieving notices: ...working... done 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 your system:

• feature:/linux-64::__glibc==2.31=0
• r-spieceasi -> r-rcpp -> __glibc[version='>=2.17,<3.0.a0']

Your installed version is: 2.31

Note that strict channel priority may have removed packages required for satisfiability.

— Reply to this email directly, view it on GitHub https://github.com/zdk123/SpiecEasi/issues/234#issuecomment-1476332708, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAUD2RBTQKETQ66AEZE2GSTW5BSIDANCNFSM6AAAAAAV6Q63SU . You are receiving this because you commented.Message ID: @.***>

[sghignone]

Zach, and those interested in the thread, this is how I successfully installed SpiecEasi in a conda R environment.

$ conda create -n R -c conda-forge r-base r-devtools r-essentials $ conda activate R $ R

library(devtools) install_github("zdk123/SpiecEasi") library(SpiecEasi)

So, it's better this way rather than using the conda recipe mentioned. Cheers, s.-

[zdk123]

Well sure, but I wouldn't necessarily call this a conda installation.