[Bioc-devel] EXTERNAL: R version dependence of a new package

Yaoyong Li liyaoyong85 at gmail.com
Mon Oct 23 13:36:59 CEST 2017

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,


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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