[Bioc-devel] updated package but the Multiple platform for BioC 3.11 is still using the previous one

[Paola Rancoita]

Dear all,

I am the maintainer of the package mBPCR. I was asked to update the 
package due to the deprecation of another package that I was using in my 
code. I updated the package (the new version is mBPCR 1.41.1) and I 
pushed the changes on both GitHub and Bioconductor. The Bioconductor 
devel page of the package now correctly reports the information of the 
updated package 
http://bioconductor.org/packages/3.11/bioc/html/mBPCR.html. 
Nevertheless, the build report of yesterday still reports errors because 
it refers to the older version of the package 1.41.0 
(http://bioconductor.org/checkResults/devel/bioc-LATEST/mBPCR/), 
although I updated the code several hours before all checks ran.

I would like to know if it is simply an issue related to the 
synchronization (and thus today the system will check the correct 
version of the package) or I missed/did wrong some steps when I pushed 
the changes.

Thanks in advanced.

Best regards,

Paola




-------- Messaggio Inoltrato --------
Oggetto: 	Re: Bioconductor mBPCR
Data: 	Sat, 11 Jan 2020 15:31:28 +0100
Mittente: 	Paola Rancoita <rancoita.paola using gmail.com>
A: 	Shepherd, Lori <Lori.Shepherd using RoswellPark.org>



Dear Prof. Sheperd,

I would like to advise you that I changed the code (and updated the 
other files coherently) in order to avoid the usage of the package 
SNPchip. I updated both the versions of the package in GitHub and 
Bioconductor. I am only waiting for the results of the checks on the 
three platforms (on my computer the updated package passed all checks).

Best regards,

Paola


Il 14/12/2019 12:21, Shepherd, Lori ha scritto:
> Yes I can extend to January 12.� If you have any troubles please feel 
> free to ask on the bioc-devel using r-project.org Mailing list.
> There are useful git help guides for updating your package
> http://bioconductor.org/developers/how-to/git/
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------------------------------------------------------------------------
> *From:* Paola Rancoita <rancoita.paola using gmail.com>
> *Sent:* Friday, December 13, 2019 9:37:29 PM
> *To:* Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> *Cc:* marcus.hutter using anu.edu.au <marcus.hutter using anu.edu.au>
> *Subject:* Re: Bioconductor mBPCR
>
> Dear Prof. Sheperd,
>
> I am sorry not having answering you before. Somehow the previous 
> emails were filtered by my mail account and I did not realized it.
>
> I surely want to maintain my package, but I need some time to 
> understand how I can fix the issues. I will try to do it as soon as 
> possible but this is a very busy period for me.
>
> Moreover, I need to understand how the new procedure for updating the 
> code works since last time I used SVN.� Can you extend my deadline to 
> January 12th?
>
> Thank you in advanced.
>
> Best regards,
>
> Paola
>
>
> Il 13/12/2019 15:35, Shepherd, Lori ha scritto:
>> This is your second warning. �If the package is not fixed by the end 
>> of the month we will begin the deprecation process for your package.
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ------------------------------------------------------------------------
>> *From:* Shepherd, Lori
>> *Sent:* Monday, November 18, 2019 11:03 AM
>> *To:* rancoita.paola using gmail.com <mailto:rancoita.paola using gmail.com> 
>> <rancoita.paola using gmail.com> <mailto:rancoita.paola using gmail.com>; 
>> marcus.hutter using anu.edu.au <mailto:marcus.hutter using anu.edu.au> 
>> <marcus.hutter using anu.edu.au> <mailto:marcus.hutter using anu.edu.au>
>> *Subject:* Bioconductor mBPCR
>> Please be advised your package is failing on all three platforms in 
>> devel 3.11
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/mBPCR
>>
>> The package SNPchip has been user requested deprecated in 
>> Bioconductor 3.10. �You will have to alter your package to not 
>> utilize SNPchip to avoid your own package being deprecated. �We made 
>> you aware of this deprecation back in May and the SNPchip packages 
>> has had a deprecation since then as well.
>>
>> The other alternative is to take over maintainership of SNPchip 
>> package but you will need to reach out to the maintainer of the 
>> package to formalize this request.
>>
>> Cheers,
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>>
>> This email message may contain legally privileged and/or confidential 
>> information. If you are not the intended recipient(s), or the 
>> employee or agent responsible for the delivery of this message to the 
>> intended recipient(s), you are hereby notified that any disclosure, 
>> copying, distribution, or use of this email message is prohibited. If 
>> you have received this message in error, please notify the sender 
>> immediately by e-mail and delete this email message from your 
>> computer. Thank you. 
>
> This email message may contain legally privileged and/or confidential 
> information. If you are not the intended recipient(s), or the employee 
> or agent responsible for the delivery of this message to the intended 
> recipient(s), you are hereby notified that any disclosure, copying, 
> distribution, or use of this email message is prohibited. If you have 
> received this message in error, please notify the sender immediately 
> by e-mail and delete this email message from your computer. Thank you. 

	[[alternative HTML version deleted]]