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<mailto: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<mailto:bioc-devel-boun...@r-project.org>> on behalf of Aurora Maurizio <auroramauriz...@gmail.com<mailto:auroramauriz...@gmail.com>> Sent: Friday, November 1, 2024 7:05 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>; jennifer.wok...@sph.cuny.edu<mailto:jennifer.wok...@sph.cuny.edu> <jennifer.wok...@sph.cuny.edu<mailto: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<mailto: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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