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 http://bioconductor.org/developers/how-to/git/ > > 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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
