[Bioc-devel] Package check error under BiocVersion 3.18
Hi, As you surmise, it looks like this is a conflict between Matrix and SeuratObject. It's reported in quite a few places e.g. https://github.com/satijalab/seurat/issues/7986 I don't think there's much you can do except wait for the Seurat maintainers to release an update to their package. Given that the issue is already closed as complete, hopefully that won't be too long. Then you'll need to wait a bit longer for the Bioconductor Build System to install that updated version - I'm not sure how often the BBS updates non-Bioconductor packages. Slightly frustrating, but this is the risk we take when using other packages. Generally speaking the effort saved in not reinventing all the cool stuff in Matrix & Seurat yourself is worth this hassle. Personally, I trust the Seurat developers will address this in a timely manner. Cheers, Mike On Sun, 12 Nov 2023 at 04:48, Jinjin Chen via Bioc-devel <
bioc-devel at r-project.org> wrote:
Hi, I got check error for my package after new release 3.18 of bioconductor on all 3 platforms (linux, windows and macOS). The build report shows the error like this: Error in validObject(.Object) : invalid class ?LogMap? object: superclass "mMatrix" not defined in the environment of the object's class But when I check the devel BiocVersion 3.19 report, it's OK under linux OS but failed with the same error under windows and macOS. I guess this is caused by the conflicts between Seurat and Matrix package? Could you please help me figure out how to fix this? Thanks! PhD student, Davis Laboratory Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research [WEHI Logo] Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville Victoria 3052 Australia www.wehi.edu.au<https://wehi.edu.au> Twitter<https://twitter.com/WEHI_research> | Facebook< https://www.facebook.com/WEHIresearch/> | Instagram< https://www.instagram.com/wehi_research> | Youtube< https://www.youtube.com/user/WEHImovies> | LinkedIn< https://www.linkedin.com/company/wehi_research> WEHI acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. Private and confidential The content of this e-mail and any attachments may be private and confidential, intended only for use of the individual or entity named. If you are not the intended recipient of this message you must not read, forward, print, copy, disclose, use or store in any way the information this e-mail or any attachment contains. If you are not the intended recipient, please notify the sender immediately and delete or destroy all copies of this e-mail and any attachment. [[alternative HTML version deleted]]
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