R devel - Apr 2016 - Suggested dependencies in context of R CMD check

Dear R team,

Are suggested dependencies mandatory in context of `R CMD check` when
using env var `_R_CHECK_FORCE_SUGGESTS_=FALSE`?

Suggested dependencies are nice because are optional.
But that feature often isn't valid when trying to run `R CMD check` on them.
I would like to use `export _R_CHECK_FORCE_SUGGESTS_=FALSE`, which
according to the comment in `tools/R/check.R`:
> The suggested packages are required for a complete check.
 Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

should be sufficient to run *check* process without installing suggested deps.
If it is not true, then how to differentiate the suggested packages
which are optional from those mandatory?
It would be helpful to have kind of `vignetteBuilder` DESCRIPTION
field called `testChecker`, so DESCRIPTION file could precisely manage
packages dependencies.
That way batch checking packages would be easier, as required dep
metadata would be at hand in description file. Batch checking pkgs
with all their suggests will simply result into testing whole CRAN.

In a single package it can be handled with `if (requireNamespace(.))
test_package(.)` for `testthat` and `knitr`, also with mocking up
`.Rout` files.

But I'm interested into canonical design of a suggested package and
`_R_CHECK_FORCE_SUGGESTS_` env var.
Is there any R core dev team recommendation/suggestion on that? and
don't you thing new field `testChecker` in DESCRIPTION could help for
batch checking pkgs? Installing all suggested packages of all reverse
dependencies doesn't scale.

Jan Gorecki

On Sat, Apr 2, 2016 at 5:33 AM, Jan G?recki <J.Gorecki at wit.edu.pl>
wrote:
> Dear R team,
>
> Are suggested dependencies mandatory in context of `R CMD check` when
> using env var `_R_CHECK_FORCE_SUGGESTS_=FALSE`?
>
> Suggested dependencies are nice because are optional.
> But that feature often isn't valid when trying to run `R CMD check` on
them.
> I would like to use `export _R_CHECK_FORCE_SUGGESTS_=FALSE`, which
> according to the comment in `tools/R/check.R`:
>
>> The suggested packages are required for a complete check.
>  Checking can be attempted without them by setting the environment
> variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
>
> should be sufficient to run *check* process without installing suggested
deps.
> If it is not true, then how to differentiate the suggested packages
> which are optional from those mandatory?
> It would be helpful to have kind of `vignetteBuilder` DESCRIPTION
> field called `testChecker`, so DESCRIPTION file could precisely manage
> packages dependencies.
> That way batch checking packages would be easier, as required dep
> metadata would be at hand in description file. Batch checking pkgs
> with all their suggests will simply result into testing whole CRAN.
>
> In a single package it can be handled with `if (requireNamespace(.))
> test_package(.)` for `testthat` and `knitr`, also with mocking up
> `.Rout` files.
>
> But I'm interested into canonical design of a suggested package and
> `_R_CHECK_FORCE_SUGGESTS_` env var.
> Is there any R core dev team recommendation/suggestion on that? and
> don't you thing new field `testChecker` in DESCRIPTION could help for
> batch checking pkgs? Installing all suggested packages of all reverse
> dependencies doesn't scale.
In principle, I believe a package should pass R CMD check if no
suggested packages are installed. However, since this is not currently
automatically checked, many packages will fail to cleanly pass R CMD
check if suggested packages are missing. In my experience, it's much
easier to simply install all dependencies of your reverse dependencies
(although this is obviously much easier when you're using a platform
with binary packages available from CRAN). I routinely do this for
hundreds to thousands of packages.

Hadley

-- 
http://hadley.nz

Jan and Hadley,

There's also the issue of tests, vignettes, or examples requiring Suggested
packages (one of the core applications of Suggests, in fact). These are all
checked by R CMD check, so to ensure any package which should pass check
would do so without suggested packages installed would require turning all
of those checks off, which takes quite a few of the teeth out of R CMD
check (and thus the assurances granted by knowing a package passes it).
AFAIK (without going off and checking right now) you /could/ force R CMD
check to do this now with a combination of options, though, if that's
really what you want (which would allow your package to pass when
_R_CHECK_FORCE_SUGGESTS_ is set to false).

~G

On Mon, Apr 4, 2016 at 7:25 AM, Hadley Wickham <h.wickham at gmail.com>
wrote:
> On Sat, Apr 2, 2016 at 5:33 AM, Jan G?recki <J.Gorecki at wit.edu.pl>
wrote:
> > Dear R team,
> >
> > Are suggested dependencies mandatory in context of `R CMD check` when
> > using env var `_R_CHECK_FORCE_SUGGESTS_=FALSE`?
> >
> > Suggested dependencies are nice because are optional.
> > But that feature often isn't valid when trying to run `R CMD
check` on
> them.
> > I would like to use `export _R_CHECK_FORCE_SUGGESTS_=FALSE`, which
> > according to the comment in `tools/R/check.R`:
> >
> >> The suggested packages are required for a complete check.
> >  Checking can be attempted without them by setting the environment
> > variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
> >
> > should be sufficient to run *check* process without installing
suggested
> deps.
> > If it is not true, then how to differentiate the suggested packages
> > which are optional from those mandatory?
> > It would be helpful to have kind of `vignetteBuilder` DESCRIPTION
> > field called `testChecker`, so DESCRIPTION file could precisely manage
> > packages dependencies.
> > That way batch checking packages would be easier, as required dep
> > metadata would be at hand in description file. Batch checking pkgs
> > with all their suggests will simply result into testing whole CRAN.
> >
> > In a single package it can be handled with `if (requireNamespace(.))
> > test_package(.)` for `testthat` and `knitr`, also with mocking up
> > `.Rout` files.
> >
> > But I'm interested into canonical design of a suggested package
and
> > `_R_CHECK_FORCE_SUGGESTS_` env var.
> > Is there any R core dev team recommendation/suggestion on that? and
> > don't you thing new field `testChecker` in DESCRIPTION could help
for
> > batch checking pkgs? Installing all suggested packages of all reverse
> > dependencies doesn't scale.
>
> In principle, I believe a package should pass R CMD check if no
> suggested packages are installed. However, since this is not currently
> automatically checked, many packages will fail to cleanly pass R CMD
> check if suggested packages are missing. In my experience, it's much
> easier to simply install all dependencies of your reverse dependencies
> (although this is obviously much easier when you're using a platform
> with binary packages available from CRAN). I routinely do this for
> hundreds to thousands of packages.
>
> Hadley
>
> --
> http://hadley.nz
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research

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On 4 April 2016 at 07:25, Hadley Wickham wrote:
| On Sat, Apr 2, 2016 at 5:33 AM, Jan G?recki <J.Gorecki at wit.edu.pl>
wrote:
| 
| In principle, I believe a package should pass R CMD check if no
| suggested packages are installed. However, since this is not currently

The relevant manual says

     The 'Suggests' field uses the same syntax as 'Depends' and
lists
  packages that are not necessarily needed.  This includes packages used
  only in examples, tests or vignettes (*note Writing package
  vignettes::), and packages loaded in the body of functions.  E.g.,
  suppose an example(1) from package *foo* uses a dataset from package
  *bar*.  Then it is not necessary to have *bar* use *foo* unless one
  wants to execute all the examples/tests/vignettes: it is useful to have
  *bar*, but not necessary.  Version requirements can be specified, and
  will be used by 'R CMD check'.

and later

   * All packages that are needed(2) to successfully run 'R CMD check'
     on the package must be listed in one of 'Depends' or
'Suggests' or
     'Imports'.  Packages used to run examples or tests conditionally
     (e.g. _via_ 'if(require(PKGNAME))') should be listed in
'Suggests'
     or 'Enhances'.  (This allows checkers to ensure that all the
     packages needed for a complete check are installed.)

| automatically checked, many packages will fail to cleanly pass R CMD
| check if suggested packages are missing.

I consider that to be a bug in those 'many packages'.  It essentially
takes
away the usefulness of having a Suggests: to provide a more fine-grained
dependency graph.

So I am with Jan here.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org