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.sheph...@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 <auroramauriz...@gmail.com> > *Sent:* Thursday, November 7, 2024 9:13 AM > *To:* Kern, Lori <lori.sheph...@roswellpark.org> > *Cc:* bioc-devel@r-project.org <bioc-devel@r-project.org>; > jennifer.wok...@sph.cuny.edu <jennifer.wok...@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 g...@github.com:auroramaurizio/SurfR.git (fetch) > > # origin g...@github.com:auroramaurizio/SurfR.git (push) > > # upstream g...@git.bioconductor.org:packages/SurfR.git (fetch) > > # upstream g...@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.sheph...@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-boun...@r-project.org> on behalf of Aurora > Maurizio <auroramauriz...@gmail.com> > *Sent:* Friday, November 1, 2024 7:05 AM > *To:* bioc-devel@r-project.org <bioc-devel@r-project.org>; > jennifer.wok...@sph.cuny.edu <jennifer.wok...@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@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. 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