search

Bioconductor / HDF5Array

HDF5 backend for DelayedArray objects
https://bioconductor.org/packages/HDF5Array
9 stars 13 forks source link

Warning: no function found corresponding to methods exports from 'HDF5Array' for: 'write_sparse_block' #43

Closed DustinSokolowski closed 3 years ago

DustinSokolowski commented 3 years ago

Hey!

Thank you for your great package! I, along with many others, rely on your package for ours to function and it has made a world of difference.

I have been trying to update my package on CRAN for the last month or so and I've been unable to due to the following warning: "Warning: no function found corresponding to methods exports from 'HDF5Array' for: 'write_sparse_block'".

After googling that warning, I have noticed that about a half dozen other packages have been unable to update within the last week or so for the same reason.

I was wondering if you had any insight onto what this warning could mean? Perhaps you have removed that function and a package that I depend on that uses your package (e.g., Seurat) is relying on an older version?

Thanks so much! Dustin

hpages commented 3 years ago

Hi,

The write_sparse_block() method was removed from HDF5Array a while ago (in June 2020, see commit https://github.com/Bioconductor/HDF5Array/commit/9ebb3f8796f141d7a63565ea6b22076c3c5b3cb8) so it seems to me that your package is trying to import something that no longer exists in recent versions of HDF5Array.

The general recommendation is that, when you work on your package, and before you send it to CRAN, you need to make sure that you're using the current version of R (4.0) and Bioconductor (3.12), and that all your packages are up-to-date. You can check this with BiocManager::valid(). The current stable version of HDF5Array is 1.18.1. That's what you should have if you're using the current BioC release (BioC 3.12). Also make sure to run R CMD INSTALL <pkg_dir> + R CMD build <pkg_dir> + R CMD check --cran <pkg_src_tarball>: this should catch any problem.

Best, H.

DustinSokolowski commented 3 years ago

Hey!

Thank you for taking the time to explain what I should have probably already known so clearly. I don't have any more warnings and my package and I are better for it.

Thanks again! Dustin