[Bioc-devel] EXTERNAL: R version dependence of a new package
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.Shepherd at 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-bounces at r-project.org> on behalf of Yaoyong Li <liyaoyong85 at gmail.com> *Sent:* Friday, October 20, 2017 7:54:16 AM *To:* bioc-devel at 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
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