[Bioc-devel] git push confusion

You can check which version is being used by going to this link

https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_rgsepd_malbec2-2Dbuildsrc.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-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_wJYbW0WYiZvSXAJJKaaPhzWA&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__bioconductor.org_developers_how-2Dto_git_push-2Dto-2Dgithub-2Dbioc_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_UN1AYHwq08NwBbWAg1aVKxVhgfzC6Kw4xHSZwV_-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.ethz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013212.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&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.

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