[Bioc-devel] BioC 3.14: BSgenome.Mmusculus.UCSC.mm10.masked

[Hervé Pagès]

Hi Ulrich,

The updated BSgenome.Mmusculus.UCSC.mm10.masked (version 1.4.3) will 
become available via BiocManager::install() for BioC 3.14 users in about 
3 hours. It might be too late for the daily builds to pick it up today 
in which case podkat will still be in ERROR on tomorrow's report but it 
should turn green on Wednesday. Let us know if it doesn't.

Best,
H.


On 30/08/2021 09:56, Hervé Pagès wrote:
> Hi,
> 
> It's still on my list to reforge BSgenome.Mmusculus.UCSC.mm10.masked. I 
> reforged BSgenome.Mmusculus.UCSC.mm10 back in June after the UCSC folks 
> updated the mm10 genome and tracks (see 
> https://github.com/Bioconductor/GenomeInfoDb/issues/27). But 
> BSgenome.Mmusculus.UCSC.mm10.masked is still based on the old 
> BSgenome.Mmusculus.UCSC.mm10 and needs to be resynced with the new one.
> 
> I'll do this today. Sorry for the inconvenience.
> 
> H.
> 
> On 30/08/2021 06:58, Kern, Lori wrote:
>> We will look into the ERROR.  You do not have to alter your package at 
>> this time as the ERROR is on our end and we will look at correcting.
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ________________________________
>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of 
>> bodenhofer using bioinf.jku.at <bodenhofer using bioinf.jku.at>
>> Sent: Monday, August 30, 2021 9:12 AM
>> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
>> Subject: [Bioc-devel] BioC 3.14: BSgenome.Mmusculus.UCSC.mm10.masked
>>
>> Hi,
>>
>> The vignette of my package 'podkat' loads the
>> 'BSgenome.Mmusculus.UCSC.mm10.masked' package. Currently, my package 
>> fails
>> on all three BioC 3.14 servers because of this package. On nebbiolo2 and
>> riesling1, the package is not available, while the package is 
>> available, but
>> fails to load, on merida1
>> (http://bioconductor.org/checkResults/3.14/bioc-LATEST/podkat/merida1-builds 
>>
>> rc.html). Is the package no longer available in 3.14 or is there anything
>> else that goes wrong? Is there anything I can about it? (except 
>> removing it
>> from the 'podkat' vignette)
>>
>> Any help is gratefully appreciated, thank you,
>> Ulrich
>>
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> 

-- 
Hervé Pagès

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