Or: you could just rename your NPS repo -> BioTIP and recreate a very simple NPS repo that contains only a README.md file that says:
This repository has been moved to https://github.com/xyang2uchicago/BioTIP That kind of redirect should be OK from the grant submission perspective. H. On 8/22/19 04:51, Zhezhen Wang wrote: > I see, thanks Herve and Martin! > Zhezhen > >> On Aug 22, 2019, at 6:00 AM, Martin Morgan <mtmorgan.b...@gmail.com> wrote: >> >> The requirement that the repository and package name be the same is >> something imposed by Biocondcutor during the submission process (it's >> probably best practice, but that isn't why the requirement is there); once >> the package is accepted it gets cloned into Bioconductor (as BioTIP) the >> github repository used for submission could be deleted -- we will never look >> at the github repository again, the maintainer is responsible for pushing >> changes to the Bioconductor git repository. >> >> So one could create a temporary repository BioTIP and manage the complexity >> of two repositories during submission (basically two remotes 'origin' >> (github/user/NPS) and 'upstream' (github/user/BioTIP) on the local BioTIP >> repository, with any changes pushed to both. Once the package is accepted, >> change 'upstream' to g...@git.bioconductor.org:pacakges/BioTIP and delete >> github/user/BioTIP. Continue to push to upstream and remote, to keep the >> public github and canonical bioconductor repositories in sync. These steps >> are described at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_how-2Dto_git_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=dujEzslWeMIvlTaSOpEXKPSBhHSgfjJdT-5vXztzjNc&s=o36ekG8m2LTVHqFWfa1uu-vxfFxjblw1UE8I7Nm5fpc&e= >> >> Obviously not ideal, and really a workaround for limitations on the >> Bioconductor side of the fence, but it would not result in two permanent >> github repositories with the same content. >> >> Martin >> >> On 8/22/19, 12:27 AM, "Pages, Herve" <hpa...@fredhutch.org> wrote: >> >>> On 8/21/19 18:51, Zhezhen Wang wrote: >>> Thank you so much for that remainder. The thing is the NPS linkage is >>> already included in our grant submission, but then we found that there >>> already is a package called NPS so we decided to change it BioTIP. Is >>> making another copy and rename that to BioTIP the best way to solve my >>> situation? >> >> But then isn't it going to be somewhat painful to keep the 2 repos in >> sync? Sounds like using some kind of alias or redirect mechanism would >> be better but you would need to ask the Git or GitHub experts on how to >> do this. >> >> H. >> >>> >>> Zhezhen >>> ------------------------------------------------------------------------ >>> *From:* Pages, Herve <hpa...@fredhutch.org> >>> *Sent:* Wednesday, August 21, 2019 7:47 PM >>> *To:* Zhezhen Wang <zhez...@uchicago.edu>; Martin Morgan >>> <mtmorgan.b...@gmail.com>; Vincent Carey <st...@channing.harvard.edu> >>> *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org> >>> *Subject:* Re: [Bioc-devel] BiocCheck error >>> Note that the name of the package (BioTIP) differs from the name of the >>> GitHub repo (NPS). They will need to match if you intend to submit to >>> Bioconductor. Thanks! >>> >>> H. >>> >>> >>>> On 8/20/19 09:20, Zhezhen Wang wrote: >>>> I see, thank you Martin! >>>> Zhezhen >>>> ________________________________ >>>> From: Martin Morgan <mtmorgan.b...@gmail.com> >>>> Sent: Tuesday, August 20, 2019 11:15 AM >>>> To: Zhezhen Wang <zhez...@uchicago.edu>; Vincent Carey >>>> <st...@channing.harvard.edu> >>>> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> >>>> Subject: Re: [Bioc-devel] BiocCheck error >>>> >>>> I think this is from BiocCheck, needing access to CRAN / Bioconductor to >>>> look at package status. Likely there are issues accessing these sites >>>> (BiocManager::repositories()) from your computer. It seems not to be an >>>> issue that you as developer need to worry about, provided you are >>>> confident that you are using current packages. >>>> >>>> Martin >>>> >>>> On 8/20/19, 12:04 PM, "Bioc-devel on behalf of Zhezhen Wang" >>>> <bioc-devel-boun...@r-project.org on behalf of zhez...@uchicago.edu> wrote: >>>> >>>> The github repo is >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_xyang2uchicago_NPS&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw&s=XROazf2UylAST2t8NvzZfcr0Sv-Y4RL6G3WloKc-yVo&e= >>>> >>>> >>>> ________________________________ >>>> From: Vincent Carey <st...@channing.harvard.edu> >>>> Sent: Tuesday, August 20, 2019 10:52 AM >>>> To: Zhezhen Wang <zhez...@uchicago.edu> >>>> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> >>>> Subject: Re: [Bioc-devel] BiocCheck error >>>> >>>> If your package that generates the error is in a github repo, please >>>> give the details. >>>> If it is already in Bioconductor please give the name of the package >>>> and ensure we can >>>> get access to the code that is generating the error. In general it >>>> is very hard to help unless >>>> we can reproduce the error you report. >>>> >>>> On Tue, Aug 20, 2019 at 11:38 AM Zhezhen Wang >>>> <zhez...@uchicago.edu<mailto:zhez...@uchicago.edu>> wrote: >>>> Hi I am running BiocCheck on my new package and I get the following >>>> error message >>>> >>>> * Checking for deprecated package usage... Warning in >>>> readLines(file, skipNul = TRUE) : InternetOpenUrl failed: 'The server name >>>> or address could not be resolved' Error in readLines(file, skipNul = TRUE) >>>> : cannot open the connection >>>> >>>> May I know what this error message means and how I can correct it? >>>> >>>> Zhezhen >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw&s=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY&e= >>>> >>>> The information in this e-mail is intended only for the >>>> ...{{dropped:14}} >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw&s=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY&e= >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DsHb4fuqI94H_l8UosIRZgMvGezo2wlah7MV9lZVBuw&s=rUkBAd61x2nqJmy-a6Ntp-k3RP-XDMucc6r3jZipRFY&e= >>>> >>> >>> -- >>> 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 >> >> -- >> 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 >> -- 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
