[Bioc-devel] git push confusion
Wonderful, thank you. It appears to be fixed now.
On Mon, Apr 23, 2018 at 8:25 PM, Herv? Pag?s <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.
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