[Bioc-devel] Workflow package build all OK but no vignette and red Package propagation status LED

[Hervé Pagès]

Hi Jim,

On 11/17/23 06:22, James Perkins wrote:
> Thanks I didn't know about the mouseover hint! It appears that this 
> package (miRBaseConverter) is failing the check on linux:
>
> https://bioconductor.org/checkResults/3.18/bioc-LATEST/miRBaseConverter/
>
> Leading to the red light ExpHunterSuite on the linux build only:
>
> https://bioconductor.org/checkResults/3.18/workflows-LATEST/ExpHunterSuite/ 
>
>
> However, what I'm not sure about - is this unavailable dependency the 
> reason why the landing page for ExpHunterSuite does not show the 
> vignette or source code?
>
> https://bioconductor.org/packages/3.18/workflows/html/ExpHunterSuite.html
>
Yes. The vignettes displayed on the package landing pages are generated 
from what's found in the _published_ source tarball. Since no source 
tarball for ExpHunterSuite ever made it to the BioC 3.18 repositories, 
the landing page that we produce is missing a few things (it's a 
degraded version of the standard landing page).

Note that miRBaseConverter has been failing on Linux for more than 6 
months, for not declaring BiocStyle in its Suggests field, and despite 
numerous reminders (emails sent by core team members in addition to the 
weekly automatic BBS notifications). Maybe you want to try and ping the 
miRBaseConverter maintainer by opening an issue at 
https://github.com/taoshengxu/miRBaseConverter ? Maybe you'll have more 
luck.

Otherwise, we will soon deprecate miRBaseConverter in BioC 3.19. 
Unfortunately this means that you'll need to modify the ExpHunterSuite 
workflow to no longer rely on it.

Best,

H.


> Or could it be another factor?
>
> Jim
>
> On 2023-11-13 12:08, Martin Grigorov wrote:
>> 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 <jimrperkins using uma.es>
>> 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
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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