[Bioc-devel] Bioconductor package DegNorm

[Shepherd, Lori]

We do not see any changes in the version on Bioconductor  git.bioconductor.org.  You need to push the changes to that location not your github location and there needs to be a valid version bump for the changes to propagate.

Firstly,  please check your remotes
git remote -v

upstream should point to git.bioconductor.org
upstream  git using git.bioconductor.org:packages/DegNorm

The instructions you sent that you followed were for maintaining a Bioconductor-only repository for an existing package.  This would be if you did not have a github repository of your own or only wanted to use the git.bioconductor.org version.  If this is not the case please refer to

https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

These instructions would allow you to keep pointers to both a personal github  and the bioconductor official repository.

make sure there are no errors when you
git pull upstream master

and/or no errors when trying to push changes up:
git push upstream master


If there are and it says something about public keys:
Did you follow the instructions for initilizing your git credentials when the package was accepted
https://github.com/Bioconductor/Contributions/issues/1491#issuecomment-637138209

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Jiping Wang <jzwang using northwestern.edu>
Sent: Tuesday, September 22, 2020 8:48 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Bioconductor package DegNorm

Hi Lori,

   I have made changes to some of the R functions a few months ago, also I have changed version etc (recently
fixed a few bugs). But I noticed in the current Bioconductor version, such changed have never been included. Could you advise what happened? Or anything additional should I do? I believed I followed steps in the following.
Thanks.

jiping

https://secure-web.cisco.com/1C78sfLYvvhE9fnuPonlmLQohdaSv4_KuRnc8mKA4EZauqXZ2sarLLn6Nq2bwi5YanH8qClEyO0YZ6R7js8DLFny1IDlHiFhN6o0QuIxKYYeEb5Gn0od_wEtSKembRmYmefR-zKOWccVhCpfMCjluJRLSNz5DYwMG1fIr06DCG0yjsRFcj5wcNNMRTrN9pMAxsY18Bh-182Qe52J2vgS5HITGNAlqIr2VPj2TkidmkclTH5ByuO68nNfG4tH5WjqfjFa5I6hp6Ex7Pca_rKjjBKZdYjyEX86zW0qacVHr8OhHilbCFNMqciPumMPQqfyDvM-n7aOMexDEWhIIkJJCSQ/https%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fmaintain-bioc-only%2F

On 9/2/20, 12:29 PM, "Bioc-devel on behalf of Jiping Wang" <bioc-devel-bounces using r-project.org on behalf of jzwang using northwestern.edu> wrote:

    Hi Lori,

      I hope I have fixed all bugs. I have pushed all changed to github. Thanks for help.

    Best,
    jiping

    From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
    Date: Wednesday, September 2, 2020 at 9:40 AM
    To: jiping/wang User <jzwang using northwestern.edu>
    Subject: Bioconductor package DegNorm

    Hello Package Maintainer,

    The Bioconductor Team would like to notify you that your package is currently
    failing on the devel 3.12 version of Bioconductor, and has been for an extended
    period of time.  Please fix your package to R CMD build and R CMD check cleanly
    immediately to avoid deprecation of your package. While devel is a place to
    experiment with new features, we expect packages to build and check cleanly in a
    reasonable time period and not stay broken for any extended period of time. If
    you are having trouble or have any further questions please do not hesitate to
    reach out to the developers mailing list at bioc-devel using r-project.org

    We appreciate your attention to this matter. The package has been failing since 06/29/20

    Cheers

    https://secure-web.cisco.com/1Gu6p5E755WRiodhYC0LQ1Wj0EDIL2NGK6Iv20B_ZZkDNzRm670rMz9xHbEYGCVLuVUHHYj26wP8fuBf8BPjwfLfvOIY72aowjnoYc_IfFUcp8F7GccSbJ5S-0bnKw9SIV8q_1hQFzA_GRFtPFRPOddJSL0yAUWDu6B6uPYsvolsgei4cbq1myEH5fLoNrvrjeLrr9ByKsT3k69VStgs5IJLF7QLGgP8wk36a2SXGFzvNq-_1DaQzubh0P8u3jNPiGQkpSR3h_DR8Q8TBLpiEgrBVLOmqF-fEZOOPPCrsDeEJR0dokBTtwu6Go_JvKB1Po9My4GLqxMjNJgy1zYGsjA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FDegNorm__%3B%21%21Dq0X2DkFhyF93HkjWTBQKhk%21Fj9WnIAbw3NfGYpF-gcbNWKpL-EdvTmxq2BMLQVvyYgs3mA01UtyJ84W8D1TNLHHTmtBAA%24



    Lori Shepherd

    Bioconductor Core Team

    Roswell Park Comprehensive Cancer Center

    Department of Biostatistics & Bioinformatics

    Elm & Carlton Streets

    Buffalo, New York 14263

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