[Bioc-devel] CRAN downtime may effect package installation

2023-11-13 Thread Kern, Lori via Bioc-devel 


There is an announcement at  https://cran.r-project.org/

Dear users,
The CRAN Admin Team will perform system upgrades during the period Wednesday 
November 15 until Thursday November 16, 2023.
There will be intermittent outages in service during this time.
We thank you for your understanding and apologise for any inconvenience this 
may cause.
CRAN Admin Team


This may effect BiocManager and the ability to download/install packages.
We appreciate your patience and understanding during the CRAN update period.



On behalf of the Bioconductor ore Team


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Re: [Bioc-devel] Package check error despite commit

2023-11-13 Thread Kern, Lori via Bioc-devel 
Experiment Data packages are built twice a week on Tuesday and Thursday.  The 
schedule is found on the check home page
https://bioconductor.org/checkResults/

The changes were only pushed up on November 10 so they should be reflected in 
tomorrow's report.

Cheers,


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Dario 
Tommasini 
Sent: Friday, November 10, 2023 6:24 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Package check error despite commit

Hi,

I keep getting a check error for my data package multiWGCNAdata 1.0.0 even
though I committed changes in version 1.1.1. I never get a build report for
my new commit, despite the git push writing to the bioconductor repository.
The error was arising from not finding package BiocStyle in the vignette,
so I added BiocStyle to Suggests, which should clear that error up. Any
help on this would be appreciated!

Thanks,
Dario

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

2023-11-13 Thread 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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Re: [Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

2023-11-13 Thread Martin Grigorov 
Hi,

If you hover over the red LED you will see the following hint: NO, package
depends on 'miRBaseConverter' which is not available"

Regards,
Martin

On Mon, Nov 13, 2023 at 11:31 AM James Perkins  wrote:

> Hi,
>
> I am the maintainer of the Workflow package ExpHunterSuite.
>
> In the build report for the release branch, 3.18, my build and install
> status are green-OK.
>
> However, I have a red LED for Package Propagation. How can I tell what's
> gone wrong, and how could I fix it?
>
> https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/
>
> I've had a look through the documentation and the nearest I've found
> was: "propagation is still determined by the results of the nightly
> builds." - but I cannot find/workout the relevant section in the output
> of the nightly build report that is related to propagation status.
>
> The landing page of the package is not showing the documentation
> (vignette etc.), or letting me download the package source.
>
> https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html
>
> I suspect this is related, because the devel version of the package IS
> showing blue propagation status, and IS showing the
> documentation/package source etc.
>
> https://bioconductor.org/packages/3.19/workflows/html/ExpHunterSuite.html
>
> Cheers!
>
> Jim
>
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[Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

2023-11-13 Thread James Perkins 

Hi,

I am the maintainer of the Workflow package ExpHunterSuite.

In the build report for the release branch, 3.18, my build and install 
status are green-OK.


However, I have a red LED for Package Propagation. How can I tell what's 
gone wrong, and how could I fix it?


https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/

I've had a look through the documentation and the nearest I've found 
was: "propagation is still determined by the results of the nightly 
builds." - but I cannot find/workout the relevant section in the output 
of the nightly build report that is related to propagation status.


The landing page of the package is not showing the documentation 
(vignette etc.), or letting me download the package source.


https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html

I suspect this is related, because the devel version of the package IS 
showing blue propagation status, and IS showing the 
documentation/package source etc.


https://bioconductor.org/packages/3.19/workflows/html/ExpHunterSuite.html

Cheers!

Jim

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