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Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
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Object '.replace_dir' not found #51

Closed BBBBunnyZ closed 9 months ago

BBBBunnyZ commented 1 year ago

I came up with this error when calling 'HDF5Array' in bsseq. Here is the source code from bsseq::read.bismark.

if (!dir.exists(dir)) { HDF5Array:::.create_dir(dir) } else { HDF5Array:::.replace_dir(dir, replace) } But when I run bsseq it shows this error:

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object '.replace_dir' not found

And it not just happened in '.replace_dir', but also happened in '.create_dir'. So I think maybe the problem is because the HDF5Array package was not successfully imported. But when I use library(HDF5Array), there is no error at all. So I'm wondering where the problem is. Thank you so much!

hpages commented 1 year ago

Please provide a reproducible example and your sessionInfo().

You're very likely mixing packages from different Bioconductor releases (e.g. an old bsseq with a recent HDF5Array), which is always a bad idea. This is why Bioconductor users should always install packages with BiocManager::install(), to avoid that problem. You should be able to fix your installation with BiocManager::install().

hpages commented 1 year ago

Were you able to sort this out @BBBBunnyZ ?