[Bioc-devel] updating released version of package

Thu Dec 10 19:19:39 CET 2020

There is information on this page:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/

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 Ted Natoli <ted.e.natoli using gmail.com>
Sent: Thursday, December 10, 2020 1:17 PM
To: jmacdon using u.washington.edu <jmacdon using u.washington.edu>
Cc: Bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] updating released version of package

Ah, I see. Ok thanks for that clarification. Do you know roughly how long
it might take to build?

On Thu, Dec 10, 2020 at 11:15 AM James W. MacDonald <jmacdon using uw.edu> wrote:

> You also have a commit from yesterday in master that isn't yet reflected
> on the build machine, again because it takes time for the build machine to
> build stuff. IIRC we are over 24 hours per build, but that may be old news
> (FAKE NEWS!).
>
> On Thu, Dec 10, 2020 at 11:09 AM James W. MacDonald <jmacdon using uw.edu>
> wrote:
>
>> It looks like you bumped it just yesterday:
>>
>> commit 5a9929aed33e40c11609f3d064b114d95d95e6cb
>> Author: Ted Natoli <ted.e.natoli using gmail.com>
>> Date:   Wed Dec 9 16:42:16 2020 -0500
>>
>>     fixing version bump
>>
>> commit accd8a5871fe38a8a1f63b32b4e79d2640e86792
>> Author: Ted Natoli <ted.e.natoli using gmail.com>
>> Date:   Wed Dec 9 16:32:47 2020 -0500
>>
>>     update RELEASE version number
>>
>> And it takes a while to propagate, so you are probably being too
>> impatient.
>>
>> Jim
>>
>> On Thu, Dec 10, 2020 at 10:59 AM Ted Natoli <ted.e.natoli using gmail.com>
>> wrote:
>>
>>> Hi James,
>>>
>>> Thanks for the response. The corresponding changes were committed to the
>>> master branch on November 23. The development build report seems to be
>>> using the correct code, or at least close to it, as the most recent commit
>>> it shows there is from December 8. I did push to both github and
>>> bioconductor repos and I did bump the version number too, which is
>>> reflected in the development build report but not release.
>>>
>>> Here are links to the build reports if it's helpful.
>>>
>>> devel: https://secure-web.cisco.com/1-1x1XOPmgvcYx-uk9wqvKLIcUzB7NcY56Pl8ujqdH2sTHkZOp4H9RJF5e6K5nU6Sqj3nEwtgA6xpUpSLSL7jiqF3JVwEJgmM4q79UaY1iBvLOfA9kU-gTk9_iwmL00kzN2yMCcY9orTK4fcvihoDj-ldKOYZFzQBRkqDdPzRAs4rQn-ZPfmEUkO3OAB8zDf-aVja6j87lZ86Jrrb9fzEWxB0K9jeD3DVLXoIyBIYgx_yjwAVl15_o9dwI2X1KOuHTS0sVqytOnv0RfJ8czSExzqpXpl82czloCYNOaCM9zkZpOoAmdKDcwLSutSxheHL/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.13%2Fbioc-LATEST%2FcmapR%2F
>>> release: https://secure-web.cisco.com/12_5xQ-XfxLpJNnk5VC8wKtBoVDDTo0Z8wxemZfI-18YLzB0Noy8MuPwvTY72U3wVYWjsKLzIN9A3mqVArwHY_ESztUpa3THjf9rZELyOTFXSuFOf4om6nypiil9jQPWQSIGiruvqNIwG1gL2xjyO7nRWSCTGVaULgKR1Ns64Y8JTvdlsSzH6ZZ24tAPmKNDEKx9l29inU1vq0_aQKKGX7F8C9RK8DCt4J44ZefPNPZLpHvaCA-_Ndt0wuoIgoLEIA2336TC85zU4sZRuV6PJeFTdnRg6R2Jdk8KOSJjVqKg9GN9xKqx9sOwCwx5-SzBo/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2FcmapR%2F
>>>
>>> Thanks again,
>>> Ted
>>>
>>> On Thu, Dec 10, 2020 at 10:41 AM James W. MacDonald <jmacdon using uw.edu>
>>> wrote:
>>>
>>>> Did you bump your version number? How long has it been since you
>>>> committed the changes? If you have a github repo, you remembered to push to
>>>> both the Bioconductor and GitHub repos?
>>>>
>>>> On Thu, Dec 10, 2020 at 10:19 AM Ted Natoli <ted.e.natoli using gmail.com>
>>>> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> I'm trying to update the released version of my package, cmapR,
>>>>> because one
>>>>> of the packages it depends on has been deprecated and hence install of
>>>>> cmapR now fails.
>>>>>
>>>>> I've followed the instructions here in order to get those changes over
>>>>> to
>>>>> the released version of the package:
>>>>>
>>>>> https://secure-web.cisco.com/1D5P1egX7dz5hm7CM0oANiK3VX-_MXhLCtIy8BsnJvMcVmQAonSNdwUsMDCsFqAhODKVOxwjOJErSovxX-JBMdBt1duxe5jNPQyGakv2UzVkZSysCvZVW9eDE3Ki7G8CaatM1godiuNSYPgglczPbeiooK1bQHITsl_9EpRiABQM5mLKJ3aAoiGsNpFlj4csvQ5_TlbGHH75lA87kcNZ89PdeJaSlRSGVsIjtmthogIWhYDRBXQkD3jpzUU1c2t3_aXkhpm6x6tA7M7BOJxOlBFy1nATTUw__TbC2tYXgKHdiT58URhaHLgZvn-o4K0iH/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F
>>>>>
>>>>> However, I don't see that the released version has been updated.
>>>>> Looking at
>>>>> the build reports, the latest commit reflected there is from before I
>>>>> made
>>>>> the code changes. How do I get these changes to propagate to the
>>>>> release
>>>>> branch?
>>>>>
>>>>> I'm sure I must be missing something very basic, but any help would be
>>>>> appreciated.
>>>>>
>>>>> Thanks in advance,
>>>>> Ted
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel using r-project.org mailing list
>>>>> https://secure-web.cisco.com/1Bbk5zhzZQCGLOzdeyngfDDg5gS-0079cppW1TDP0iqcVR8yfBvWE60I0sVi7khG_Gig4WNu5rFQ9XFyI_Gi7b93ZUuDH4BOzuIhtCtvuCsjbATYFikwJ_5Y0RGNlfomkBngiZyqfghdilLcPYXFDG79SGhl8OG-o_R_-PN0F5gAi_EGRSk3PXeF_TzeW-CHS8Bl-vjU0i89IoYpETBSiFcB8eVwfTpArlkaRW7KqNAQZKeMnRyd7UBJiX07FerFDyoqzEJ4DUEiBi-0h9ahH5SMqVmloom1fWj221XRQDw4VydJ_g7W30sk9Mj0TRINl/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>>>>>
>>>>
>>>>
>>>> --
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>
>>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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