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GeorgGruenert authored
All 46 Dockerfile steps complete, 17/17 Python packages importable, 9/9 R Bioconductor packages loadable. Validated with: podman run --rm lopez:latest python3.7 -c 'import scanpy, anndata, louvain, leidenalg, h5py, rpy2, anndata2ri, tables, tiledb, ...' Root causes fixed (see docker/CHANGES.md for full details): System libraries: - Added libigraph-dev, libhdf5-dev, libblas-dev, liblapack-dev, libopenblas-dev to apt-get (missing in original) - Added cmake via apt-get (Debian 10 = 3.13.4) after python build to preserve layer cache; pip cmake>=3.17 wraps binary in Python entry- point that breaks MulticoreTSNE's subprocess cmake invocation R packages: - Set options(repos=...) in every RUN to fix BiocManager CRAN isolation - Pre-install RcppArmadillo 0.9.850.1.0, igraph 1.2.4.2, irlba 2.3.3 from CRAN archive (newer versions require cpp11/C++17, not in 2020) - CXX14 Makevars to fix RcppAnnoy/BiocNeighbors under GCC 8....f7f827a0