[Bioc-devel] R version check in BiocChech

It does not request users to make R-devel a _requirement_ of their

Here, I think the decision here boils down to how far back in terms of R

Personally, I haven't found it to be particularly difficult to update R,
or to run R-devel in parallel with R 3.4, even without root privileges.

I think many people underappreciate the benefits of moving to the latest
version of R.

Enforcing version consistency avoids heartache during release and
debugging.

I'll just throw in my two cents here.

I think many people underappreciate the benefits of moving to the latest
version of R. If you inspect the R-devel NEWS file, there's a couple of
nice fixes/features that a developer might want to take advantage of:

- sum() doesn't give NAs upon integer overflow anymore.
- New ...elt(n) and ...length() functions for dealing with ellipses.
- ALTREP support for 1:n sequences (wow!)
- zero length subassignment in a non-zero index fails correctly.

The previous 3.4.0 release also added support for more DLLs being loaded
at once, which was otherwise causing headaches in workflows. And 3.4.2
had a bug fix to LAPACK, which did result in a few user-level changes in
some packages like edgeR. So there are considerable differences between
the versions of R, especially if one is a package developer.

Enforcing version consistency avoids heartache during release and
debugging. There's a choice between users getting annoyed about having
to update R, and then updating R, and everything working as a result; or
everyone (developers/users) wasting some time figuring out whether a bug
in a package is due to the code in the package itself or the version of
R. The brief annoyance in the first option is better than the chronic
grief of the second option, especially given that the solution to the
problem in the second option would be to update R anyway.

Personally, I haven't found it to be particularly difficult to update R,
or to run R-devel in parallel with R 3.4, even without root privileges.

-Aaron

On 19/02/18 14:55, Kevin RUE wrote:

Hi Alexey,

I do agree with you that there is no harm in testing against other

version

of R. In a way, that is even good practice, considering that many HPC

users

do not always have access to the latest version of R, and that Travis is
making this fairly easy.

Now, with regard to your latest reply, I am wondering whether we're

having

confusion here between the "R?x.x" requirement, and the version(s) of R
that you use to develop/test your package (the version of R installed on
your own machine).

First, I think the "R?x.x" does not have an explicit rule.
To me, the point of this requirement is to declare the oldest version of

R

that the package has been tested/validated for. This does not necessarily
have to be the _next_ version of R (see the core Bioc package S4Vectors:
https://bioconductor.org/packages/release/bioc/html/S4Vectors.html, and

I

am sure there are older requirements in other packages).
Here, I think the decision here boils down to how far back in terms of R
versions the developer is willing to support the package. I suppose one
could state R?2.3 if they're confident about it.

On a separate note, going back to the Bioc guideline that I initially
highlighted ("Package authors should develop against the version of *R*

that

will be available to users when the *Bioconductor* devel branch becomes

the

*Bioconductor* release branch."), this rather refers to the

forward-looking

guideline that the cutting-edge version of any R package should be
compatible with the cutting edge version of R, and that developers should
be working with R-devel to ensure this.
In other words, this only refers to the version of R that the developer
should have installed on their own machine. It does not request users to
make R-devel a _requirement_ of their package.

I hope this addresses your question better, and I am curious to hear if
anyone else has an opinion or precisions to weigh in on this topic.

Best,
Kevin


On Mon, Feb 19, 2018 at 12:19 PM, Alexey Sergushichev <

alsergbox at gmail.com>

wrote:

Hello Kevin,

Well, bioc-devel packages are tested against bioc-devel (and R-3.5) in

any

case. What I'm saying is that aside from testing the package against
bioc-devel, I can as well test against bioc-release too on my own. If

the

package doesn't work with bioc-devel it shouldn't pass bioc-devel

checks,

if the package is properly developed and has a good test coverage. So I

see

no problem in allowing developers to test against other versions, on

top of

developing against bioc-devel. And as it's only possible to install the
package from github and not from Bioconductor, the developer alone is
responsible for the package to work properly.

I can't really see a scenario, where requiring R >= 3.5 helps to improve
the package quality.

A short-term workaround can be to create a git branch (e.g. "3.4").

That's the way I'm doing too, but supporting two branches different only
in R version looks ridiculous and unnecessary.

--
Alexey





On Mon, Feb 19, 2018 at 12:48 PM, Kevin RUE <kevinrue67 at gmail.com>

wrote:

Dear Alexey,

The reason is somewhat implicitly given at https://www.bioconductor.or
g/developers/how-to/useDevel/ :
"Package authors should develop against the version of *R* that will be
available to users when the *Bioconductor* devel branch becomes the
*Bioconductor* release branch."

In other words, developing against the _next_ version of R ensures that
all packages in development are tested in the environment where they

will

be released to the general community. In particular, that environment
includes the latest devel version of all Bioconductor packages, that

will

become their next release version.
If developers were allowed to develop and test their package in the
_current_ version of R, there is no guarantee that those packages would
still work when they are made available with the _next_ version of R

(e.g.

if one of their dependencies is about to introduce some breaking

changes).

That could cause all sorts of trouble in the first builds on the next
Bioconductor release, which is meant to be a place storing stable

working

code.

Overall, you will do yourself and your users a favor developing with

the

_next_ version of R, as this is a forward-looking strategy, as

explained

above. In contrast, the short-term benefit of developing with the

_current_

version of R is largely outweighed by the risk of wasting time looking

at

code that is about to be deprecated.

A short-term workaround can be to create a git branch (e.g. "3.4"),

where

the R version requirement is downgraded. Then, you can always keep
developing against R-devel on your master branch and back-port the more
recent commit to the "3.4" branch by typing "git rebase master 3.4" in

your

shell.
A recent example of this situation can be found in the discussion here

as

a branch to the original repository https://github.com/csoneson/iS
EE/pull/124 and here as a fork https://github.com/mdshw5
/iSEE/commit/6fb98192a635a6222491b66fb0474dc38f922495

I hope this helps.

Best wishes,
Kevin


On Mon, Feb 19, 2018 at 8:02 AM, Alexey Sergushichev <

alsergbox at gmail.com

wrote:

Dear Bioconducotr community,

I wonder, what is the reason behind requirement for dependency R >=

3.5

(currently) for new packages?

As a developer I really want an installation of my package to be as

easy

as
possible and want my package to be easily installed from github. So
currently, when I develop a package I put a R >= 3.4 in my DESCRIPTION
and
test it using Travis against bioc-release. Then, before submission
to Bioconductor, I have to change R >= 3.4 dependency to R >= 3.5, so
that
the package passes BiocCheck. However, most users don't have R-devel
installed, so they have R 3.4 in the best case, and for these users I
create another repository branch with R >= 3.4 dependency.

Overall, it is quite bothersome and it doesn't really make sense to

me to

to restrict potential users in this way. Am I the only one who have
issues
with this? Am I missing something? Or may be this check could be

removed?

Best,
Alexey Sergushichev

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