[Bioc-devel] Packages removing documentation
Dear Bioconductor community, One of the oldest requirements of Bioconductor is a vignette with some executed code. Recently I found some packages that do not have examples for some functions and vignettes with executed code in the current release while they did some versions ago. The vignette was replaced with a link to resources outside the Bioconductor repository. These resources might not be in sync with the released code of the package or might not work. Users, as I did, might get confused if code linked from the vignette does not work or is not found in the package. This is possible because submitted packages need to pass all checks specified by R CMD check and by BioCheck() in the BiocCheck package. However, once accepted, checks are no longer done with BiocCheck() and just with R CMD check. I think it would be desirable to keep the initial high quality of the packages after the peer review and with the BiocCheck. If authors need to move their code to a book they can use the book infrastructure set up by Bioconductor too. Perhaps Bioconductor checks on existing packages could use the same version of BiocCheck that was initially used or some specific tests to ensure that documentation is not dismissed. I would appreciate your thoughts on this. Best, Lluís ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] C++ compiler flags on Windows
On 01/08/2022 08:17, Martin Morgan wrote: ... I notice that on the package landing page https://bioconductor.org/packages/3.16/bioc/html/syntenet.html there is no Windows binary, suggesting that it has never built successfully. It could be that the intermittent results you observed was actually due to something else, like the Windows builder not reporting for that day. The single package builder results have expired, so I’m not sure why those builds were successful; the builders and single package builder are not identical. AFAIK the Single Package Builder no longer runs the Windows builds. So any Windows-related issue only gets detected once a contributed package is added to the daily builds. H. -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] C++ compiler flags on Windows
Dear Bioc developers, I recently had a package accepted that passed the build system during review. One week after acceptance, there were compilation problems on Windows. In the next build, the problems disappeared. Now, they're back again: http://bioconductor.org/checkResults/devel/bioc-LATEST/syntenet/palomino4-install.html These compilations problems - and the fact that they appear and disappear without any intervention from me - seem to be related to changing C++ compiler flags in the Bioconductor build system for Windows. Does anyone know if C++ compiler flags were changed recently on Windows in the Bioc build system? As I don't have a Makevars file in the /src directory of this package, does anyone know which flags I could include in a Makevars file to remove these Windows-specific warnings in compilation? I was wondering whether any of you had similar problems. Kind regards, Fabricio = Fabr�cio de Almeida Silva, MSc. PhD student in Bioinformatics (Ghent University, Belgium) UGent-VIB Center for Plant Systems Biology Personal website: https://almeidasilvaf.github.io [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
