Re: [R-pkg-devel] EXTERNAL: CRAN packages dependency on bioconductor packages
Hi Marcel, I appreciate your suggestion and clarification. It is worth mentioning that �rmarkdown� is included in the Import filed, and I apologize for not stating it here. Interestingly, I was able to successfully upload StepReg version 1.5.0 to CRAN with BiocStyle listed in the Suggests field. However, I encountered this issue this time around. I attempted to address it by adding an empty `biocViews:` field in the DESCRIPTION, but unfortunately, it did not resolve the problem. It seems that there are some issues with CRAN check. Best, Junhui From: Ramos Perez, Marcel Date: Wednesday, May 15, 2024 at 17:50 To: Li, Junhui , r-package-devel@r-project.org Subject: Re: EXTERNAL: [R-pkg-devel] CRAN packages dependency on bioconductor packages Hi Junhui, There are about 25 packages in CRAN that use BiocStyle, including yours. It seems that MetaIntegrator is also facing the same error. I have not looked too deeply into the issue but it seems that you should also include "rmarkdown" in the Suggests field. AFAIK, there is no need to include an empty `biocViews:` field in the DESCRIPTION. CRAN knows about Bioconductor repositories via setRepositories(). Note. Users should use BiocManager to resolve Bioconductor dependencies (rather than setRepositories). Best regards, Marcel From: R-package-devel on behalf of Li, Junhui Sent: Tuesday, May 14, 2024 3:51 PM To: r-package-devel@r-project.org Subject: EXTERNAL: [R-pkg-devel] CRAN packages dependency on bioconductor packages Hi everyone, I recently developed an R package called 'StepReg' and used the Bioconductor R package 'BiocStyle' in my vignettes, as shown below: output: BiocStyle::html_document: toc_float: true BiocStyle::pdf_document: default In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included a new line 'biocViews:', as follows: VignetteBuilder: knitr biocViews: Suggests: knitr, testthat, BiocStyle, kableExtra You may find all those information here: https://github.com/JunhuiLi1017/StepReg/tree/dev There were no error messages when checking with 'R CMD check' and on https://win-builder.r-project.org/upload.aspx. However, an error message occurred when I attempted to upload it to CRAN: * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'StepReg.Rmd' using rmarkdown Error: processing vignette 'StepReg.Rmd' failed with diagnostics: there is no package called 'BiocStyle' --- failed re-building 'StepReg.Rmd' SUMMARY: processing the following file failed: 'StepReg.Rmd' Error: Vignette re-building failed. Execution halted For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), I successfully uploaded it to CRAN without including 'biocViews:' in the DESCRIPTION file two months ago. However, I'm encountering difficulties this time. Any insights or suggestions on resolving this issue would be greatly appreciated. Thanks, Junhui [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-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. [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages
Hi Llu�s, Thanks for your input. I believe it is ok to use a vignette output conditionally with knitr. However, what confuses me is that I was able to successfully upload StepReg version 1.5.0 to CRAN with BiocStyle listed in the Suggests field. It seems that there is some issues with CRAN check. Best, Junhui From: Llu�s Revilla Date: Tuesday, May 14, 2024 at 18:09 To: Li, Junhui Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages Hi Junhui, There is a separate log for checking if your package works without suggested packages: in the StepReg results The noSuggests title leads to: https://www.stats.ox.ac.uk/pub/bdr/noSuggests/StepReg.out Where you can see that it fails if a user don't have BiocStyle installed. I don't know if it is possible to use a vignette output conditionally with knitr: In any case it seems that it would be a requirement (Imports, or Depends). However, it is best to not use the Bioconductor style for a package in CRAN. You could use the *_vignette or *_document format directly (from rmarkdown if I recall correctly). You will remove a dependency and avoid this problem entirely. Best, Llu�s On Tue, 14 May 2024 at 22:48, Li, Junhui mailto:junhui.l...@umassmed.edu>> wrote: Hi everyone, I recently developed an R package called 'StepReg' and used the Bioconductor R package 'BiocStyle' in my vignettes, as shown below: output: BiocStyle::html_document: toc_float: true BiocStyle::pdf_document: default In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included a new line 'biocViews:', as follows: VignetteBuilder: knitr biocViews: Suggests: knitr, testthat, BiocStyle, kableExtra You may find all those information here: https://github.com/JunhuiLi1017/StepReg/tree/dev There were no error messages when checking with 'R CMD check' and on https://win-builder.r-project.org/upload.aspx. However, an error message occurred when I attempted to upload it to CRAN: * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'StepReg.Rmd' using rmarkdown Error: processing vignette 'StepReg.Rmd' failed with diagnostics: there is no package called 'BiocStyle' --- failed re-building 'StepReg.Rmd' SUMMARY: processing the following file failed: 'StepReg.Rmd' Error: Vignette re-building failed. Execution halted For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), I successfully uploaded it to CRAN without including 'biocViews:' in the DESCRIPTION file two months ago. However, I'm encountering difficulties this time. Any insights or suggestions on resolving this issue would be greatly appreciated. Thanks, Junhui [[alternative HTML version deleted]] __ R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] CRAN packages dependency on bioconductor packages
Hi everyone, I recently developed an R package called 'StepReg' and used the Bioconductor R package 'BiocStyle' in my vignettes, as shown below: output: BiocStyle::html_document: toc_float: true BiocStyle::pdf_document: default In my DESCRIPTION file, I added 'BiocStyle' to the Suggests field and included a new line 'biocViews:', as follows: VignetteBuilder: knitr biocViews: Suggests: knitr, testthat, BiocStyle, kableExtra You may find all those information here: https://github.com/JunhuiLi1017/StepReg/tree/dev There were no error messages when checking with 'R CMD check' and on https://win-builder.r-project.org/upload.aspx. However, an error message occurred when I attempted to upload it to CRAN: * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'StepReg.Rmd' using rmarkdown Error: processing vignette 'StepReg.Rmd' failed with diagnostics: there is no package called 'BiocStyle' --- failed re-building 'StepReg.Rmd' SUMMARY: processing the following file failed: 'StepReg.Rmd' Error: Vignette re-building failed. Execution halted For version 1.5.0 (https://cran.r-project.org/web/packages/StepReg/index.html), I successfully uploaded it to CRAN without including 'biocViews:' in the DESCRIPTION file two months ago. However, I'm encountering difficulties this time. Any insights or suggestions on resolving this issue would be greatly appreciated. Thanks, Junhui [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
