Fix compatibility with basilisk.utils >= 1.18#8
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NathanSkene wants to merge 1 commit intoRajLabMSSM:mainfrom
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Fix compatibility with basilisk.utils >= 1.18#8NathanSkene wants to merge 1 commit intoRajLabMSSM:mainfrom
NathanSkene wants to merge 1 commit intoRajLabMSSM:mainfrom
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The basilisk.utils package removed/renamed several functions in recent versions, breaking echoconda. This commit updates to the new API: API changes: - getCondaBinary(loc) + getCondaDir() → find() - installConda() → download() - activateEnvironment() → removed, now using reticulate fallback - deactivateEnvironment() → removed, no longer needed - isWindows() → moved from basilisk.utils to basilisk Files changed: - R/find_conda.R: Use basilisk.utils::find() - R/install_conda_basilisk.R: Use basilisk.utils::download() - R/activate_env_basilisk.R: Fall back to reticulate method - R/activate_env.R: Remove unused import - R/remove_env.R: Remove deactivateEnvironment call - R/basilisk.R: Use basilisk::isWindows() - NAMESPACE: Update imports Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
NathanSkene
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Jan 24, 2026
The upstream echoconda package (RajLabMSSM/echoconda) is broken with current Bioconductor versions due to removed functions in basilisk.utils. Temporarily pointing to neurogenomics fork with fix until upstream PR is merged: RajLabMSSM/echoconda#8 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Summary
The
basilisk.utilspackage removed/renamed several functions in recent versions (around Bioconductor 3.18+), causing echoconda to fail to install with:This PR updates echoconda to work with the new API.
API Changes
getCondaBinary(loc)+getCondaDir()find()installConda()download()activateEnvironment()deactivateEnvironment()isWindows()Files Changed
R/find_conda.R: Usebasilisk.utils::find()R/install_conda_basilisk.R: Usebasilisk.utils::download()R/activate_env_basilisk.R: Fall back to reticulate-based activationR/activate_env.R: Remove unused importR/remove_env.R: Remove deactivateEnvironment callR/basilisk.R: Usebasilisk::isWindows()NAMESPACE: Update importsTest Plan
Context
This fix is needed for downstream packages like PeakyFinders that depend on echoconda.