Skip to content

[Bioc-devel] SurfR Enrichment_barplot git<->builder sync issues

5 messages · Shepherd, Lori, Aurora Maurizio

Aurora Maurizio
# 
Dear all,

I've noticed a discrepancy between the SurfR package functions on GitHub
(both the devel and RELEASE_3_20 branches) and those checked on the builder.

Specifically, the Enrichment_barplot function, which is causing errors on
several builders, has been updated recently. I rewrote the Example of this
function a few weeks ago (including also commenting it). Still, the updated
function on GitHub (linked here: GitHub RELEASE_3_20
<https://github.com/auroramaurizio/SurfR/blob/RELEASE_3_20/R/Enrichment_barplot.R>)
is quite different from the old version that is causing errors in the build
checks (see builder error
<https://bioconductor.org/checkResults/3.20/bioc-LATEST/SurfR/teran2-checksrc.html>
).

Could you please assist me in resolving this synchronization issue?

Thank you very much for your help.

Best regards,
Aurora
6 days later
Shepherd, Lori
# 
We do not sync github repositories automatically.

You will need to push your changes to git.bioconductor.org.  The repository on our git server is the only version Bioconductor knows/propagates.  A new version will not propagate without a valid version bump as well.

Please see
https://contributions.bioconductor.org/git-version-control.html



Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Aurora Maurizio
# 
Thank you Lori,
I see. All the functions in git.bioconductor.org:packages/SurfR.git look fine
and updated to me.
In the last month (before and after Bioc 3.20 release) looking at
the builder's reports it seemed that the package version associated with
the last bump was always consistent with my last edit, yet the tested
functions reported in the builder's report were not updated (e.g.
Enrichment_barplot in nebbiolo2*)*. I'll read carefully the manual and try
to figure it out.

Here my last commands:

# origin git at github.com:auroramaurizio/SurfR.git (fetch)

# origin git at github.com:auroramaurizio/SurfR.git (push)

# upstream git at git.bioconductor.org:packages/SurfR.git (fetch)

# upstream git at git.bioconductor.org:packages/SurfR.git (push)

git fetch --all
git merge origin/devel
git merge upstream/devel
git add vignettes/Intro_to_SurfR.Rmd
git add R/Enrichment_barplot.R
git add DESCRIPTION
git commit -m "bumped the package version v1.2.0"
git push origin devel
git push upstream devel

git checkout RELEASE_3_20
git merge upstream/RELEASE_3_20
git merge origin/RELEASE_3_20
git push upstream RELEASE_3_20
git push origin RELEASE_3_20

Best,
Aurora







Il giorno gio 7 nov 2024 alle ore 14:28 Kern, Lori <
Lori.Shepherd at roswellpark.org> ha scritto:

  
  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
      #
    

  


  

      
You mentioned it was the examples; I see you are using roxygen; did you run document and check in the new man files officially?





Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Aurora Maurizio
    

    

      
      #
    

  


  

      
Spotted!!
That was the issue, my bad, I did not update those files, thank you very
much Lori.

Aurora


Il giorno gio 7 nov 2024 alle ore 15:18 Kern, Lori <
Lori.Shepherd at roswellpark.org> ha scritto: