[Bioc-devel] updated package but the Multiple platform for BioC 3.11 is still using the previous one
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Sun Jan 12 08:31:06 CET 2020
The build report says (left-hand side) that the build is based on the repo status as of 16:45 on Fri 10 Jan
Snapshot Date: 2020-01-10 16:45:16 -0500 (Fri, 10 Jan 2020)
URL: https://git.bioconductor.org/packages/mBPCR
Branch: master
Last Commit: 93a2ff2
Last Changed Date: 2019-10-29 13:35:04 -0500 (Tue, 29 Oct 2019)
And git log shows (printing from the 'Last Commit' shown above to the most recent commit)
mBPCR master$ git log --format="%h %cd" 93a2ff2^..HEAD
e5aae6f Sat Jan 11 07:59:19 2020 +0100
5d577db Sat Jan 11 07:57:36 2020 +0100
fd3b974 Sat Jan 11 07:53:06 2020 +0100
802d7ee Sat Jan 11 07:50:53 2020 +0100
2fe29a6 Sat Jan 11 07:50:17 2020 +0100
2d04f13 Sat Jan 11 07:48:28 2020 +0100
51176e1 Sat Jan 11 07:47:03 2020 +0100
44abd70 Sat Jan 11 07:46:17 2020 +0100
a730736 Sat Jan 11 07:45:21 2020 +0100
dd25165 Sat Jan 11 07:44:26 2020 +0100
9fb05f5 Sat Jan 11 07:42:37 2020 +0100
44aebc0 Sat Jan 11 07:39:33 2020 +0100
93a2ff2 Tue Oct 29 13:35:04 2019 -0400
So your commits missed the start of the build -- they will be picked up in the next builds, which are running now and will presumably post at about noon US Eastern time on Sunday. (I'm not sure what to specify to get the time offset to correctly match the build report...)
It is a mystery why on the landing page the 'Details' section lists
Version 1.41.1
...
Martin
On 1/12/20, 1:22 AM, "Bioc-devel on behalf of Paola Rancoita" <bioc-devel-bounces using r-project.org on behalf of rancoita.paola using gmail.com> wrote:
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
>>
>>
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