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

Stephanie M. Gogarten sdmorris at uw.edu
Tue Oct 24 19:27:17 CEST 2017

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.


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.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
>>          [[alternative HTML version deleted]]
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