[Bioc-devel] [EXTERNAL]Re: A question about r package update

[Martin Morgan]

Packages are built nightly, so you must usually wait ~24 - 48 hours for your commits to be reflected in the build report. 

Sometimes issues prevent the build report from being processed, so on the build overview page such as

  http://bioconductor.org/checkResults/devel/bioc-LATEST/

compare

  - 'This page generated on...'
  - 'Approx snapshot date...'

and on individual package pages such as

  http://bioconductor.org/checkResults/devel/bioc-LATEST/epihet/

look for

  - 'Snapshot date...'
  - 'Last commit...' 

If your last commit (`git log --oneline`) was after the snapshot date, then changes you made will not be reflected in the build report.

Because of the delay in the nightly builds, it makes sense to do your best to ensure that commits are correct, ensuring that your R and Bioconductor packages are current for the version that you are committing to, and running

  R CMD build <pgk>
  R CMD check <pkg_....tar.gz>

locally before pushing changes.

Martin



On 10/16/20, 5:08 PM, "Bioc-devel on behalf of Xiaowen Chen" <bioc-devel-bounces using r-project.org on behalf of Xiaowen.Chen using jax.org> wrote:

    Hi Kern,
    I checked the epihet on the website “bioconductor.org/packages/devel/bioc/html/epihet.html”.
    I saw its version is 1.5.2
    Unfortunately, it is not the one I push this morning. It is not the latest one.
    Could you help me check what’s wrong here? I am so sorry about that.

    Best,
    Xiaowen
    From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
    Date: Friday, October 16, 2020 at 9:54 AM
    To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
    Subject: [EXTERNAL]Re: A question about r package update

    We apologize.  It was announced on the Bioconductor slack but we forgot to post on the bioc-devel mailing list. There was an issue with the builders and there was no report generated yesterday Thursday October 15.  The issue should be resolved and we expect a build report today.
    I do see 1.5.2 in our git repository so it should be reflected in the report today.
    We apologize for the confusion and the inconvenience


    Cheers,


    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 Xiaowen Chen <Xiaowen.Chen using jax.org>
    Sent: Friday, October 16, 2020 9:49 AM
    To: bioc-devel using r-project.org <bioc-devel using r-project.org>
    Subject: [Bioc-devel] A question about r package update

    Hi bioc-devel,
    I am sorry for email you so often, this morning I checked the check report website, it did not change.
    And I noticed that the data is “This page was generated on 2020-10-14 11:07:41 -0400 (Wed, 14 Oct 2020).”

    Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 1.5.1 shown in the website.
    Even it is not the one I pushed, now it have been two days.

    So this morning I push epihet again. The command is as following
    (base) [chenx using helix epihet]$ git remote add upstream git using git.bioconductor.org:packages/epihet.git
    (base) [chenx using helix epihet]$ git fetch --all
    Fetching origin
    Fetching upstream
    Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
    From git.bioconductor.org:packages/epihet
    * [new branch]      RELEASE_3_10 -> upstream/RELEASE_3_10
    * [new branch]      RELEASE_3_11 -> upstream/RELEASE_3_11
    * [new branch]      RELEASE_3_9 -> upstream/RELEASE_3_9
    * [new branch]      master     -> upstream/master
    (base) [chenx using helix epihet]$ git checkout master
    Already on 'master'
    (base) [chenx using helix epihet]$ git merge origin/master
    Already up-to-date.
    (base) [chenx using helix epihet]$ git merge upstream/master
    Already up-to-date.
    (base) [chenx using helix epihet]$ git push upstream master
    Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
    Everything up-to-date
    (base) [chenx using helix epihet]$ git push origin master
    Everything up-to-date


    Previously, when I typed “git merge upstream/master”, it returned something like this
    Merge made by recursive.
    DESCRIPTION |    2 +-
    NEWS        |    7 +++++--
    2 files changed, 6 insertions(+), 3 deletions(-)
    mode change 100755 => 100644 DESCRIPTION

    So I am curious whether epihet1.5.2 successfully push to upstream?
    Could you help me to check? Since tomorrow is weekend.
    Thank you pretty much.
    Best,
    Xiaowen
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