[Bioc-devel] git push confusion

Tue Apr 24 20:03:20 CEST 2018

Wonderful, thank you.
It appears to be fixed now.

On Mon, Apr 23, 2018 at 8:25 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Karl,
>
> We don't have an easy way to know when exactly you pushed your changes
> to git.bioconductor.org but it seems that you did it only today so you
> need to wait about 24h to see this reflected on the build report.
>
> H.
>
> On 04/23/2018 09:26 AM, Turaga, Nitesh wrote:
>
>> You can check which version is being used by going to this link
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>> ctor.org_checkResults_devel_bioc-2DLATEST_rgsepd_malbec2-
>> 2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
>> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVK
>> xVhgfzC6Kw4xHSZwV_-Ng&s=STBZLhkw4xWhHtcRjR0pqgICNEPwujMXtkiAWkcKoe0&e=
>>
>> It seems that your package is using the commit from Oct 30th. We’ll take
>> a look at this, it seems to be an issue with the build system. Your
>> Bioconductor git server is up to date though, you can see if you commit
>> posted by taking a look at our log https://urldefense.proofpoint.
>> com/v2/url?u=http-3A__bioconductor.org_developers_gitlog_&d=
>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>> YiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_
>> -Ng&s=De6-RIOuVqDeKOJbsyThMPIz7ZNegINb7haUTl8XuFc&e= or subscribing to
>> our feed.
>>
>>
>> Best,
>>
>> Nitesh
>>
>>
>>
>> On Apr 23, 2018, at 12:19 PM, Karl Stamm <karl.stamm at gmail.com> wrote:
>>>
>>> I did all that. git push upstream master says "everything up to date"
>>> and step 7 says confirm the changes by browsing Github.
>>> Github.org has had the changes since Friday but the build servers did
>>> not have the changes when the build was attempted on Sunday.  Are they on a
>>> branch other than "master"? How can I tell what the build servers are using
>>> ?
>>>
>>> On Mon, Apr 23, 2018 at 11:14 AM, Turaga, Nitesh <
>>> Nitesh.Turaga at roswellpark.org> wrote:
>>> Please check out the documentation
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__biocondu
>>> ctor.org_developers_how-2Dto_git_push-2Dto-2Dgithub-2Dbioc_
>>> &d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYb
>>> W0WYiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZ
>>> wV_-Ng&s=6T2m63ST5D4aYpOTH1eh7nHJt6Ic5BrCT3AEg1uodWA&e=
>>>
>>> On Apr 23, 2018, at 12:13 PM, Karl Stamm <karl.stamm at gmail.com> wrote:
>>>>
>>>> How do I "push to both"? I dont understand the numerous git
>>>> terminology. On Friday I tried to push the bugfix but the build server
>>>> still errors.
>>>> git log
>>>> commit 17c35588bcb6d87a9520cfad6d7d52fa209c517f (HEAD -> master,
>>>> upstream/master, origin/master, origin/HEAD)
>>>>
>>>> So I guess the build servers are not "upstream/master" ??
>>>>
>>>> I have this setup as given in the bioconductor documentation
>>>> git remote -v
>>>> origin        git at github.com:kstammits/rgsepd.git (fetch)
>>>> origin        git at github.com:kstammits/rgsepd.git (push)
>>>> upstream      git at git.bioconductor.org:packages/rgsepd.git (fetch)
>>>> upstream      git at git.bioconductor.org:packages/rgsepd.git (push)
>>>>
>>>>
>>>> And when I do various push commands they say "everything up to date"
>>>> But I want to make sure the bioc servers get the update before the 3.7
>>>> lockdown. Is there any way to see what the are holding ?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, Apr 23, 2018 at 10:26 AM, Turaga, Nitesh <
>>>> Nitesh.Turaga at roswellpark.org> wrote:
>>>> Hi Karl,
>>>>
>>>> Bioconductor doesn’t automatically grab changes from your Github. A
>>>> large body of the work is maintained only on our Bioconductor git server.
>>>> The maintainer has to push to both Github and the Bioconductor server if
>>>> the changes have to propagate.
>>>>
>>>> RELEASE_3_6 is now frozen forever. We announced this on April 11th. You
>>>> cannot push to this anymore. You can still make your changes on your master
>>>> branch.
>>>>
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>> hz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013212.html&d=
>>>> DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W
>>>> YiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_
>>>> -Ng&s=P9oxAe7ZO_iYe2Q7bRf6AzXrSLZCjuKK928OwvRKE0A&e=
>>>>
>>>> Best,
>>>>
>>>> Nitesh
>>>>
>>>>
>>>>
>>>>
>>>> On Apr 23, 2018, at 11:21 AM, Karl Stamm <karl.stamm at gmail.com> wrote:
>>>>>
>>>>> I got a message this morning that malbec2 has build errors on my
>>>>> package.
>>>>> It's a bug I fixed a few days ago, but it looks like I didn't push
>>>>> changes
>>>>> to the right branches or something.  How do I get the bioc systems to
>>>>> take
>>>>> from the github updates?
>>>>> The help documents on the bioconductor website say to push to
>>>>> RELEASE_3_6
>>>>> but that doesn't seem to work. And the build server is running the
>>>>> previous
>>>>> code version, but calling it 3.7.
>>>>> I'm not sure they've gotten my changes, how can i see which versions
>>>>> the
>>>>> build servers have? Seems they do not automatically grab from github
>>>>> since
>>>>> the bug was fixed a few days ago there.
>>>>>
>>>>>        [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>>>>> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt
>>>>> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_U
>>>>> N1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-Ng&s=GJtx2ywtfga9KLph
>>>>> 4syU6WhkRTHnBBNhl1IkWjTBFwk&e=
>>>>>
>>>>
>>>>
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> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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>
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