I previously wrote a blog post about using pixi’s tasks feature to fix missing dependency issues with Bioconductor packages (like GenomeInfoDbData, BSgenome.Hsapiens.UCSC.hg38, etc.) after installation. At the time, I only knew the problem existed but didn’t understand the root cause — I was just providing a less-than-ideal workaround.

But recently, with insights from AI responses, I finally figured out the real reason — it all comes down to the post-link script mechanism in the Conda ecosystem.

When using pixi to manage bioinformatics analysis environments, we often encounter issues where some Bioconductor R packages show missing dependencies after installation. The exact cause of this problem is currently unclear. After using pixi for a year, this issue still hasn’t been fixed (as of October 2025). This article introduces how to use pixi’s tasks feature to resolve such problems.