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

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

On 04/04/2016 1:35 PM, Dirk Eddelbuettel wrote:
> 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.
I think I agree with Jan, but not for the reason you state.

Suggests is useful even if "R CMD check" treats it as Depends, because
most users never need to run "R CMD check".  It allows them to use a 
subset of the functionality of a package without installing tons of 
dependencies.

I agree that packages that fail on examples when Suggested packages are 
missing are broken.  (Using if (require()) to skip particular examples 
isn't failing.)  It would be useful to be able to detect failure; I 
don't think that's easy now with "R CMD check".  That's
why you should
be able to run it with Suggested packages missing.

The ideal situation would be to be able to run all possible combinations 
of missing Suggested packages, but that's probably far too slow to be a 
default.

BTW, I'm not completely sure it needs to be possible to run vignettes 
without the Suggested packages they need.  Vignettes are allowed to 
depend on things that aren't available to all users, and adding all the 
require() tests could make them less clear.

Duncan Murdoch

On 04/04/2016 01:56 PM, Duncan Murdoch wrote:
> On 04/04/2016 1:35 PM, Dirk Eddelbuettel wrote:
>> 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.
>
> I think I agree with Jan, but not for the reason you state.
>
> Suggests is useful even if "R CMD check" treats it as Depends,
because
> most users never need to run "R CMD check".  It allows them to
use a
> subset of the functionality of a package without installing tons of
> dependencies.
>
> I agree that packages that fail on examples when Suggested packages are
> missing are broken.  (Using if (require()) to skip particular examples
> isn't failing.)  It would be useful to be able to detect failure; I
> don't think that's easy now with "R CMD check". 
That's why you should
> be able to run it with Suggested packages missing.
Perhaps I'm confused, it would not be the first time, but I have the 
impression that some/all? of you are arguing for a different philosophy 
around R CMD check and Suggests/Depends. But the current design is not 
broken, it is working the way it has been advertised for many years now. 
It provides a fine-grained dependency graph for end users, not 
developers and testers. Being able to suggest packages for use in 
testing, when they are not needed for regular use is a good thing. A 
package failing R CMD check when the suggested packages are not 
available is not a bug, it is a feature following the rules as they have 
been designed. If you want to check a package then you need to install 
things that are needed to check it. If R CMD check skipped testing 
because suggested packages were not available then you will have many 
packages not being tested properly, that is, lots of broken packages 
passing R CMD check. (I've done this to myself sometimes using 
if(require()).) There are situations where some testing needs to be 
skipped, for example, license requirements and special databases, but 
this needs to be done carefully, and my impression is that if(require()) 
provides most of what is necessary, sometimes along with environment 
variables. Perhaps this is not elegant, but it does work and is not 
difficult.
>
> The ideal situation would be to be able to run all possible combinations
> of missing Suggested packages, but that's probably far too slow to be a
> default.
But how do you decide pass/fail when you do this? I think it will only 
pass when all the suggested packages are available?

Paul Gilbert
>
> BTW, I'm not completely sure it needs to be possible to run vignettes
> without the Suggested packages they need.  Vignettes are allowed to
> depend on things that aren't available to all users, and adding all the
> require() tests could make them less clear.
>
> Duncan Murdoch
>
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