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

Thu Nov 7 16:46:31 CET 2024

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 using roswellpark.org> ha scritto:

> 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
> ------------------------------
> *From:* Aurora Maurizio <auroramaurizio1 using gmail.com>
> *Sent:* Thursday, November 7, 2024 9:13 AM
> *To:* Kern, Lori <Lori.Shepherd using RoswellPark.org>
> *Cc:* 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:* Re: [Bioc-devel] SurfR Enrichment_barplot git<->builder sync
> issues
>
> 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
> <http://secure-web.cisco.com/1wl84pAh5urpB6uETdnWMqBJ8m1FBaEO-N1uJGcJYu-p1Sd3i-Gz0koRkjYWaiFnDJl2es7PSVDUHgEPW_F-2rlE-jwCFCZtBim-SVlNFHd_uGGW6QGZRtvso2i_Kb0c_UH5TDduHSoO1JWYN_KwwCwnRZOqLa9B4HZ3yLgzQHC1Fz8xOtGGl5WdW9JMuWFIp4PlMxQdoqt3MBbakLONtzIzqIdo05UunmbBppmqxqKhRXML6OJ4HSkP8V8rYKFMXMFAGQuvJo5ctXOuS76zwNcT_KxDwPDLanl1JrmOPaJL9Q3G0rYgq_bJlNDJZ3QU3/http%3A%2F%2Fgit.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
> <https://secure-web.cisco.com/1KyBTcrAGyzWkcgpnUSHAkH2pk_fexztmhS81UkpehRA6VZtt3WqUeCfekl0V0DEdKvB7jFZv0V_Fv80mF0olidovLArTmHIEpGnQIYG3_w1PqwUIbCEF5T8ddcjmMc2rH5zwphiKy2Dfa7-2tmMfaBhapdOfiDCumStVQxtq05JWZiO4VC4m5jJ0KX8gL4w96qWQZxYtyf0VUsSo7j6HEfCg7FzCOMPPSPsYnAssZjLFenY0NocwSDS-rB_U1Lh5uXa2xYJ2oiq8VabKqe4IvY5FnxWCkrjYm0Jote8Y7hU9t4tWIDpK7y-rCFn_KzR6/https%3A%2F%2Fcontributions.bioconductor.org%2Fgit-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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
>
> https://secure-web.cisco.com/1v2m-LAemqN38vBF8lhNIKOUWbAoe7YpYQUDuOU8R8ThgtRj0E62XjJ2__7v9kv3iTqI6cHnaVDc8AZjIizEkT_7d8AC3_juJUsfLM5wzRtSqAJbQi3dlmgh6EXUH-wU_QAU_MJ6QrmGvoZ4cWrKrGzysQu7tJYRvQf5PjqMI5VGFyC9sKNcc-pBD0CU7fio7TneIulKulEtULqOX_DvtCvXyTxSxZOo9Fe5TYBzyyCD69Z1XUmu_TlMdvwlOIS4SzyR_G0PIxAyEf9VGtj1fIO1XGlpZd7qLaqG8w2bxb5TOY5I4qGXsVOg4rdJ6OWR_/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
>
> 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.
>
>
> 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]]