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

[Henrik Bengtsson]

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 <sdmorris at 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.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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>>
>>         [[alternative HTML version deleted]]
>>
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