[Bioc-devel] BiocCheck error

Thu Aug 22 13:00:14 CEST 2019

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 git using 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" <hpages using 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 <hpages using fredhutch.org>
    > *Sent:* Wednesday, August 21, 2019 7:47 PM
    > *To:* Zhezhen Wang <zhezhen using uchicago.edu>; Martin Morgan 
    > <mtmorgan.bioc using gmail.com>; Vincent Carey <stvjc using channing.harvard.edu>
    > *Cc:* bioc-devel using r-project.org <bioc-devel using 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.bioc using gmail.com>
    >> Sent: Tuesday, August 20, 2019 11:15 AM
    >> To: Zhezhen Wang <zhezhen using uchicago.edu>; Vincent Carey <stvjc using channing.harvard.edu>
    >> Cc: bioc-devel using r-project.org <bioc-devel using 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-bounces using r-project.org on behalf of zhezhen using 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 <stvjc using channing.harvard.edu>
    >>      Sent: Tuesday, August 20, 2019 10:52 AM
    >>      To: Zhezhen Wang <zhezhen using uchicago.edu>
    >>      Cc: bioc-devel using r-project.org <bioc-devel using 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 <zhezhen using uchicago.edu<mailto:zhezhen using 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 using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
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    >> 
    >>      The information in this e-mail is intended only for the ...{{dropped:14}}
    >> 
    >>      _______________________________________________
    >>      Bioc-devel using 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 using r-project.org mailing list
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    >> 
    > 
    > -- 
    > 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: hpages using 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: hpages using fredhutch.org
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319