[Bioc-devel] EWCE Bioconductor package

[Vincent Carey]

Please disregard my note.  As Lori has indicated formal review must proceed
before reinclusion.

On Thu, Feb 11, 2021 at 9:51 AM Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> EWCE may need to be reviewed for reinclusion.  I tried to check on R-devel
> with the repo you mentioned.  Do you
> have a current personal repo that passes check with Bioc 3.13/R-devel?
>
> Quitting from lines 220-223 (EWCE.Rmd)
> Error: processing vignette 'EWCE.Rmd' failed with diagnostics:
> Invalid attribute(s): percentage_gc_content
> Please use the function 'listAttributes' to get valid attribute names
> --- failed re-building ‘EWCE.Rmd’
>
> On Thu, Feb 11, 2021 at 9:41 AM Murphy, Alan E <a.murphy using imperial.ac.uk>
> wrote:
>
>> Hi all,
>>
>> My apologies in advance if this is not the correct mailing list for this
>> question, regarding development to the EWCE Bioconductor package.
>>
>> I work as part of Dr. Nathan Skene's group who submitted the package EWCE<
>> https://bioconductor.riken.jp/packages/3.5/bioc/html/EWCE.html#since> to
>> Bioconductor some years ago. The package fell out of maintenance and as
>> such was deprecated from Bioconductor 3.6. We are working to update and
>> hopefully, reinstate the package but are running into issues when pushing
>> any changes to Bioconductor. We have been following instructions here<
>> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/>
>> to try and sync our Github updates with the Bioconductor version but can't
>> seem to push the new, merged version to Bioconductor.
>>
>> To test the cause of the issue, we cloned the repo:
>>
>> git clone https://git.bioconductor.org/packages/EWCE
>>
>> And updated the version of the package in the DESCRIPTION file and tried
>> pushing the change, using Nathan's account which is associated with the
>> package. However, we still can't push to Bioconductor, getting the error:
>>
>>
>> -bash-4.2$ git push origin master
>> FATAL: W any packages/EWCE n.skene DENIED by fallthru
>> (or you mis-spelled the reponame)
>> fatal: Could not read from remote repository.Please make sure you have
>> the correct access rights
>> and the repository exists.
>>
>> It appears it does recognise Nathan's account but doesn't think he has
>> access rights to the repo. It is worth noting that EWCE is also not listed
>> on his account's webpage.
>>
>> We are wondering if this issue is caused by EWCE being deprecated and if
>> so, what are the necessary steps to reinstate it?
>>
>> Kind regards,
>> Alan.
>>
>> Alan Murphy
>> Bioinformatician
>> Neurogenomics lab
>> UK Dementia Research Institute
>> Imperial College London
>>
>>         [[alternative HTML version deleted]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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