I lean to agree with Yaoyong, because I find it helpful to specify (or read):
Depends: R (>= 3.0.0) which sends a message that "the code is relying on features in R that was not available prior to R 3.0.0". Also, if that's the only dependency you have, then if it passed R CMD check on R 3.0.0 in the past, it will keep doing so in the future. On the other hand, if the package depends on other packages, which it's likely to do, then that "R (>= 3.0.0)" sends a message about what the lower bound is - it does not necessarily guarantee that it will work with R 3.0.0. I think that is a valid specification (for R and packages) because otherwise, what is the "(>= x.y.z)" specification meant to be used for otherwise? The alternative is to, as Stephanie proposes, to not specify "R (>= x.y.z)" or just "R", which is an unfortunate workaround. Somewhat related to this, couldn't there be a place-holder R package called 'Bioconductor' whose version corresponds to the Bioconductor release/devel version? Then a package could specify "Imports: Bioconductor (>= 3.6)" to clarify/specify that the package "depends on/is for" a particular version of the Bioconductor. The Bioconductor 3.6 package could in turn specify "R (>= 3.4.0)". BTW, unfortunately, R does not support specify a lower and an upper range, e.g. neither "R (>= 3.4.0 & < 3.5.0)" nor "R (>= 3.4.0), R (< 3.5.0)" is accepted which also means it's not possible to depend on "Bioconductor (== 3.6.*)". Henrik On Tue, Oct 24, 2017 at 10:27 AM, Stephanie M. Gogarten <sdmor...@uw.edu> wrote: > Dear Yaoyong, > > Can you remove the R version dependency from your DESCRIPTION file entirely? > That will eliminate the warning, but will also not suggest to users that > they need a newer version of R than is necessary. R 2.3.0 was released in > 2006, so it seems highly unlikely that anyone would be currently trying to > use an R version older than that. > > Lori's answer seems to be more about the R version you should be using to > test your package, which should indeed be current, but that is different > than the minimum R version required to run the package at all. I know > Bioconductor encourages users to stay up-to-date with R versions and does > not guarantee that older versions will work with all packages, but I think > there is still some utility in letting users know which packages depend on > recent versions of R, and which packages can be expected to work with older > versions. > > Stephanie > > > On 10/23/17 4:36 AM, Yaoyong Li wrote: >> >> 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 >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
