Re: [Bioc-devel] Package check error under BiocVersion 3.18

[Mike Smith]

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@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
>
>
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[Bioc-devel] Package check error under BiocVersion 3.18

[Jinjin Chen via Bioc-devel]

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

Twitter  |  
Facebook  |  
Instagram  |  
Youtube  |  
LinkedIn


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.

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