Dependency issues when installing

[sophiachen1]

Hi Bambu developer,

I have set up a new conda environment to install bambu through bioconductor, but it returns error that some dependency packages cannot be installed. I am using following command to set up the environment and install by bioconductor :

conda create -n bambu
conda activate bambu
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install r #R version 4.5.2 is installed

Then I install by:

R
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("bambu")

The Errors I got:
ERROR: dependencies ‘BSgenome’, ‘tidyr’, ‘GenomicAlignments’, ‘GenomicFeatures’, ‘Rsamtools’, ‘xgboost’, ‘RcppArmadillo’ are not available for package ‘bambu’

Do you have any ideas to troubleshoot?
Thank you!

[cying111]

Hi @sophiachen1 , this is related to a bug we are currently fixing. For now, you can use this branch: https://github.com/GoekeLab/bambu/tree/xgboost_bug_fix

Once the fix is pushed, we will update here and you can switch back to the Bioconductor version.

[sophiachen1]

Hi @cying111 ,
Thanks for your response. I tried the 3.2.4 version and installed through Docker. I also tested with the SG-NEx datasets following https://github.com/GoekeLab/sg-nex-data/blob/master/docs/SG-NEx_Bambu_tutorial.md. Thanks for making that tutorial! It can successfully save the output files except for some warnings. Probably I can use that version for now? I will closely watch your updates and switch to the new version after your release. Thank you so much!

[cying111]

Hi @sophiachen1 ,

The bambu Bioconductor site has been updated, so BiocManager::install("bambu") should work now.

Feel free to give it a try, and let us know if you run into any issues.

Thank you.

[sophiachen1]

Hi @cying111, I can install bambu 3.12.1 through bioconductor on R 4.4 now. Thank you so much for fixing the issue!