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bnprks / BPCells

Scaling Single Cell Analysis to Millions of Cells
https://bnprks.github.io/BPCells
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Installation error #136

Closed gevro closed 1 month ago

gevro commented 1 month ago

Latest version of R and BPCells on linux x64

** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘BPCells’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object ... R/library/00LOCK-BPCells/00new/BPCells/libs/BPCells.so': R/library/00LOCK-BPCells/00new/BPCells/libs/BPCells.so: undefined symbol: H5Treclaim Error: loading failed Execution halted ERROR: loading failed

immanuelazn commented 1 month ago

Hi gevro, Thanks for reaching out! The error you linked indicates that H5Treclaim is not available, which is part of HDF5. BPCells relies on having HDF5 installed. Could you confirm that you have HDF5 installed, and whether your version of HDF5 is up to date?

If not, to install, you can first run: sudo apt-get install libhdf5-dev to get the latest HDF5 . Then perhaps retry installing BPCells.

If it indeed installed, there is probably something wrong with the library search with finding libhdf5.so. If this is the case, could you try providing some additional debug info from running:

Sys.setenv(BPCELLS_DEBUG_INSTALL=TRUE)
remotes::install_github("bnprks/BPCells/r")

and providing the outputs here?

Best,

Immanuel

gevro commented 1 month ago

How do I install that in a conda environment?

immanuelazn commented 1 month ago

Hi gevro,

Thanks for the question! Being on a conda environment requires using conda to install hdf5 instead rather than your default linux installer, as it will likely use R specific to your conda environment. Try the following: conda install conda-forge::hdf5

Immanuel

gevro commented 1 month ago

Works now, thanks!