Dear Lori, many thanks for your detailed explanations. I think that it makes sense from Bioconductor maintenance's point of view to require that the R version of a package should be the same of the R version in a Bioconductor release which includes the package, because it's the safest option. On the other hand, I still think that this requirement put some unnecessary limit on the scope of the R version which a package can be used with. For example, as the package creator I know that my package can work with R from 2.3.0 and upward, including the version 3.4 that the current Bioconductor used, then why should I have to restrict the R version to 3.4 and upward. I guess that it's the package creator's responsibility to determine which R version(s) their packages depend on? It seems to me that there is a R version problem between the package and the Biocondonctor only when the R versions that a package specifies does not include the R version of a Bioconductor release which the package is supposed to be included in.
I think that it probably makes no much difference in practice between what I think it should be and the current practice in Bioconductor, as one can easily upgrade the R to the latest version with no cost. But I hope you can see the difference in theory. Best regards, Yaoyong On Fri, Oct 20, 2017 at 1:02 PM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > We strongly recommend the version of R that is used on our builders when > building and checking your package. This is also to ensure that the > package dependencies are also in a version that is compatible with a new > package. We can't guarantee that a package will work with a previous > version of a dependency so the best practice is to use the current version > of R as we check against the most recent and current versions of packages > for the version of R and Bioconductor. This is also why we have biocValid > and biocLite to make sure packages are up-to-date and valid for a > particular version of R and Bioconductor. Package can change over time and > cause compatibility issues that are unforseen; R also can change from > version to version and cause unforseen problems. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------------------------------ > *From:* Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of > Yaoyong Li <liyaoyon...@gmail.com> > *Sent:* Friday, October 20, 2017 7:54:16 AM > *To:* bioc-devel@r-project.org > *Subject:* EXTERNAL: [Bioc-devel] R version dependence of a new package > > Hello, > > may I ask a question about the R version dependence? > > Currently I am trying to submit a package to Bioconductor repository. When > my package was built at bioconductor.org, I got a warning message > > "* WARNING: Update R version dependency from 2.3.0 to 3.4." > > So I changed the R dependency to 3.4 in my DESCRIPTION file, and > consequently the warning message disappeared. However, as one result of the > change, my package cannot be loaded and run in R whose version is earlier > than 3.4. On the other hand, my package actually doesn't need the R version > >= 3.4. For example, it works perfectly with R version 3.2.2 which was > installed in my computer. S my question is why the package builder at > bioconductor.org wanted my package to update the R version to 3.4. > > Best regards, > > Yaoyong > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
