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

[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 using github.com:auroramaurizio/SurfR.git (fetch)

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

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

# upstream git using 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 using roswellpark.org> ha scritto:

> 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
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Aurora
> Maurizio <auroramaurizio1 using gmail.com>
> *Sent:* Friday, November 1, 2024 7:05 AM
> *To:* bioc-devel using r-project.org <bioc-devel using r-project.org>;
> Jennifer.Wokaty using sph.cuny.edu <Jennifer.Wokaty using sph.cuny.edu>
> *Subject:* [Bioc-devel] SurfR Enrichment_barplot git<->builder sync issues
>
> 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://secure-web.cisco.com/1cDlDmIhDitmf7EgCo7pvDt_4Xa0FvvcCrE3IOguFGVI54jktX5xJLx8oQYcNwbZevh91io-9EzRAFyOlBo5c9Xcmyvn32KWyn9uXzOHFaQrXJcAJBilGoT4wTuRBqRUZ2aQg8QXbhluxJ7WNGUYi4-2fXJmyPM_OKIVKd2sbZasLdqY3AH8XmDftXYKPYwVE-vhpzVePNgqpHwTUKL212TkaqWoAb3ejGzcaxZUZBY5pSXTID3e6yHdfO4Y_dPKP57V-8zF4FiKppzTOoZ_BjQiRYFLO8cq8TqAj0woW5xBEuNfK7-LUnKfiKxL5daSJSrS6scuHRCcakZovK5hRKA/https%3A%2F%2Fgithub.com%2Fauroramaurizio%2FSurfR%2Fblob%2FRELEASE_3_20%2FR%2FEnrichment_barplot.R
> >)
> is quite different from the old version that is causing errors in the build
> checks (see builder error
> <
> https://secure-web.cisco.com/1Ux_1GklNVCJzRM3BolzqjOFWciPZdo85Jr-yN58RY8kdUVyqdLPms7K1Rltm2awA___e7ymqw2T5t8Gp7qEzyXMu1d8yw23Y0n0Hc8PmVWwrSApIvM_ANaIRtYMheBae8O2vTx0MDklofe0WwgJxM0dQe-6_wzq7Y9y_xqXx7X4_Ig4BSXaQ9-0Y3cxAkNElxdtApxr4tKWwLb2XSjZ-dKj2zTNnL7FU8ByEyuvHorxWV5vxw-EuVZiD8uAsp49bb0PrMl2uy9V4yMn5dATDxXakMG_YMLCZ_qMWAopCs0CrYO_1FEL9-6n7dBZLcSRd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.20%2Fbioc-LATEST%2FSurfR%2Fteran2-checksrc.html
> >
> ).
>
> Could you please assist me in resolving this synchronization issue?
>
> Thank you very much for your help.
>
> Best regards,
> Aurora
>
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