[Bioc-devel] Help me check if I push my package to git bioconductor

Kern, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Sep 28 15:14:00 CEST 2020

As explained before...

There is not a github location for packages on Bioconductor, only your personal github location. Bioconductor maintains a git server located at git.bioconductor.org NOT a copy of the repo in the Bioconductor/github.
So the location of the package on Bioconductor is the following server location:
git using git.bioconductor.org:packages/epihet.git
which is why you added this location as an upstream remote for git commands.

Addressing your concerns:


You need to look at this link (below) which points to the devel version of the package.


      You can check if your package is updated when you look at the build report



The landing page you reference will never be updated because it is pointing to the 3.9 landing page version.  instead of having 3.9  in the url,  you should use release or devel to have the current and upcoming landing page for the package.  Or the shorturl which defaults redirect to the release page if available and if devel if release is not available





 Yes in general the steps you listed were the steps to update the devel version of your package on Bioconductor in the future provided you set the remotes up as described in the link you included

Additional information:

General information on timing and when the landing pages will be updated can be found:


The builds happen once per day so depending on when you push changes it can take 12-36 hours to get through the builds and refresh the landing pages.

Bioconductor does not recognize changes in packages without a valid version bump.  The current version on the builder is 1.5.0.  To have changes propagate to users you need to bump the version to 1.5.1.

Hope this helps.

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: Monday, September 28, 2020 8:40 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Help me check if I push my package to git bioconductor

Hi there,
I have followed http://secure-web.cisco.com/1guEqRm3HekkGTNI_tlk4qFmrjoFY2cA4G2pfyNlgDvkA4iOfRznUPIIT8h_lvNfIITKfTTbQBu7AMMPgnVxhYspAdzV5dAIirjCNF_6utmP1IC8c3oGxfOIdt-S1T3orq7tpEC9754AnKUoGSbJpmItr1rAU1Vt0OAq1o7Jm2clwepAdgbIIGN3ysLIeM7RhvGSidCvpDQz3kKW6KgoyziU7zsiyebler-Xhc7wBU06tklX5rqpSrJD4p2rZqCjEJFrs681WJTNAWf3jJ8L3VMe520kYujY8B1uSbCQEtdxeWsS1TZ6js4oBUGSqK2vW/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F to push to both Bioconductor and GitHub repositories.

However, I went to the website https://secure-web.cisco.com/1PZj3ZKhxhjz4HRD9CNgwfUhWhd6_Xdyh3d58Z8KSh2VaINsbDs1-x7ilP-HLmnnGz28-4AY_nPsCmCspmocPy9J2Z04_cCed3PnHziZ35eImAsON8iNJdYExctzRtPzTT-E3L8T1EgEwA6sv0IzMkXV7OuP8jx-OK_I4_YaI_ip9DBROcXGePdmms4u6kXFQQ8Vp0BeiiM2rKFeDiJ4j1WmdHPRRlbK4C-6SQpBE-yG26qhotn1uiBjW_2RJ2r_q4ENW3ngeVtK5HPszigeqKV23GimLISsGXT_Clf_PDl2vVPrklhcWIJ0T9ZzShRb9/https%3A%2F%2Fgithub.com%2FBioconductor, I did not find my R package �epihet�,

  1.  Could you help me to check it?
  2.  When the epihet can be updated on the website https://secure-web.cisco.com/1sQLGyysVT2j0MuY9GQHQtufPRRVLg5RJINmfV12n7L3w9PX1-DkiS0SBFRA1jO9-TWI56-3-xBmhdcOS0Sj7Vs8CZzGRHW1_1L80mPYHo13uloFOWKKr6QvSTMMo9dawcC06b1SVdMfTR0qIcUslzUATCQei-G2LvnyfyTsgP4P8TYnDiTu5_HMqiKxuaUI-ofXHosQbSzvsZI6yBAqXwkN3p1mmK6HejxTbqLpdnib8S4gsAid7lliUvmb3SgXyNBuQT4IlFnQyiAltQRxHWOz9XeFarW3ax3o-e6KNtGES1M2lqMW9hefdt5wYIzWc/https%3A%2F%2Fbioconductor.riken.jp%2Fpackages%2F3.9%2Fbioc%2Fhtml%2Fepihet.html, since it is related with paper revision, the reviewer will check if I updated R document based on her/his comments
  3.  If I update my epihet later, how can I update Bioconductor?

Still performed the following command?

3.1  git fetch �all

3.2  git checkout master

3.3  git merge origin/master

3.4  git merge upstream/master

3.5  git push upstream master

3.6   git push origin master

Thank you! I will appreciate it.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

        [[alternative HTML version deleted]]

Bioc-devel using r-project.org mailing list

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list