[Bioc-devel] updating released version of package

Ted Natoli ted@e@n@to|| @end|ng |rom gm@||@com
Thu Dec 10 19:28:08 CET 2020


Thanks Lori, I had not seen this page before.

Best,
Ted

On Thu, Dec 10, 2020 at 1:19 PM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> 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
> >
>
>         [[alternative HTML version deleted]]
>
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