Probably my rant yesterday was a bit confused.
BiocCheck tries to encourage better practice. If you've chosen to specify
version (maybe there are reasons for this, e.g., because in the past you have
distributed your package through non-Bioconductor channels), then specify it
correctly.
On the other hand, the Bioconductor release model doesn't require a version
specification and in practice maintainers do a poor job updating this
information. If the maintainer hasn't specified version, then no need to
suggest that they do so.
I guess it's analogous to many other tests where guidance is provided on
mis-use, rather than on non-use -- 'we notice that you didn't test for class,
but if you had a better approach is to use `is()` rather than `class() == `'.
Or perhaps suggesting straight-forward solutions rather than nuanced solutions
of uncertain merit 'instead of testing for class incorrectly with `class() ==
`, use method dispatch to avoid conditional code'.
Again, a best practice for github and other repositories outside Bioconductor
is likely to maintain distinct release branches. If one is choosing to specify
version, then each branch should closely specify relevant version.
Martin
On 1/15/19, 2:45 AM, "Alexey Sergushichev" <alserg...@gmail.com> wrote:
Martin,
> Having said that, I'll note that specifying R as a dependency, and a
version of R as a criterion for your package, is really a mis-nomer for a
Bioconductor package -- of course it uses R, and the version of R in use
determines the Bioconductor
version(s) that can be used! So a rational change is to remove R and its
version requirement from the DESCRIPTION file entirely, a strategy taken by I
think about 400 of our 1650+ packages.
Oh, it's actually an option not to include an R dependency at all. I find
it non-obvious, given the warning message that suggest to change the version
dependency to R-devel, not mentioning that omitting dependency will fix the
warning too. Should it be
put somewhere in BiocCheck message?
Also, given that, I find it even more strange to have such R requirement in
BiocCheck. You are either allowed very strict dependency: R >= R-devel or very
lenient (not specifying any), but nothing in the middle.
Best,
Alexey
On Tue, Jan 15, 2019 at 3:03 AM Martin Morgan <mtmorgan.b...@gmail.com>
wrote:
Maybe a little more helpfully, I think you should create a branch for
'before' Bioconductor, where you can specify R version dependency as you see
fit.
Indeed, at each release the version of your package at
git.bioconductor.org <http://git.bioconductor.org> will have a branch
created for that release, e.g., the RELEASE_3_8 branch, and you will want to
sync that branch with your github repository as outlined in step 10 of
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
<https://bioconductor.org/developers/how-to/git/sync-existing-repositories/> .
A conscientious developer would take the opportunity to increment the
version dependency of R in the master branch to the version of R in use in the
devel builds of Bioconductor.
Martin
On 1/14/19, 5:40 PM, "Bioc-devel on behalf of Lulu Chen"
<bioc-devel-boun...@r-project.org on behalf of
luluc...@vt.edu> wrote:
Dear all,
When submitting package to bioconductor, it is required to change R
version
in "Depends" to be >= the develop version (3.6) . As my package is also
available in GitHub, someone asks if it be possible to make it available
with the stable version of R (R3.5). In fact, my package can work well
with
R3.5 if I change "Depends" back to R(>=3.5) .
So I hope to support R3.5 for the moment before next release. Should I
create another repository? Can I use a branch to support R3.5?
Thanks,
Lulu
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