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

Wed Oct 25 21:16:54 CEST 2017

On 10/25/2017 11:18 AM, Henrik Bengtsson wrote:
> 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.*)".

My feeling is that people are very unlikely to do this. Or they'll
forget to bump that version requirement at each release. Also the
version of this place-holder package wouldn't follow the convention
that the middle number in its version is even in release and odd
in devel so would require special treatment when we bump versions
the days before the release.

Note that people can already do something similar by importing the
BiocInstaller package and requiring at least the current version.
Unfortunately the version number of BiocInstaller doesn't reflect
the BioC version it belongs too. That could be changed though e.g.
have the first 2 digits in x.y.z reflect the BioC version. But
again, that means it wouldn't follow the convention etc...

H.

>
> 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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>>>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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