Wonderful, thank you. It appears to be fixed now. On Mon, Apr 23, 2018 at 8:25 PM, Hervé Pagès <hpa...@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.st...@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.tur...@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.st...@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 g...@github.com:kstammits/rgsepd.git (fetch) >>>> origin g...@github.com:kstammits/rgsepd.git (push) >>>> upstream g...@git.bioconductor.org:packages/rgsepd.git (fetch) >>>> upstream g...@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.tur...@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.st...@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@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= >>>>> >>>> >>>> >>>> >>>> This email message may contain legally privileged and/or confidential >>>> information. If you are not the intended recipient(s), or the employee or >>>> agent responsible for the delivery of this message to the intended >>>> recipient(s), you are hereby notified that any disclosure, copying, >>>> distribution, or use of this email message is prohibited. If you have >>>> received this message in error, please notify the sender immediately by >>>> e-mail and delete this email message from your computer. Thank you. >>>> >>>> >>> >>> >>> This email message may contain legally privileged and/or confidential >>> information. If you are not the intended recipient(s), or the employee or >>> agent responsible for the delivery of this message to the intended >>> recipient(s), you are hereby notified that any disclosure, copying, >>> distribution, or use of this email message is prohibited. If you have >>> received this message in error, please notify the sender immediately by >>> e-mail and delete this email message from your computer. Thank you. >>> >>> >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-ma >> <https://maps.google.com/?q=immediately+by+e-ma&entry=gmail&source=g>il >> and delete this email message from your computer. Thank you. >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel