R devel - May 2021 - Testing R build when using --without-recommended-packages?

Sorry if this has been pointed out already, but some relevant text 
from 
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Suggested-packages

 > Note that someone wanting to run the examples/tests/vignettes may not 
have a suggested package available (and it may not even be possible to 
install it for that platform). The recommendation used to be to make 
their use conditional via if(require("pkgname")): this is OK if that 
conditioning is done in examples/tests/vignettes, although using 
if(requireNamespace("pkgname")) is preferred, if possible.

...

 > Some people have assumed that a ?recommended? package in ?Suggests? 
can safely be used unconditionally, but this is not so. (R can be 
installed without recommended packages, and which packages are 
?recommended? may change.)



On 5/4/21 5:10 PM, Gabriel Becker wrote:
> Hi Henrik,
> 
> A couple of things. Firstly, so far asI have ever heard, it's valid
that a
> package have hard dependencies in its tests for packages listed only in
> Suggests.  In fact, that is one of the stated purposes of Suggests. An
> argument could be made, I suppose, that the base packages should be under
> stricter guidelines, but stats isn't violating the letter or intention
of
> Suggests by doing this.
> 
> 
> Secondly, I don't have time to dig through the make
files/administration
> docs, but I do know that R CMD check has --no-stop-on-error, so you can
> either separately or as part of make check, use that option for stats (and
> elsewhere as needed?) and just know that the stats tests that depend on
> MASS are "false positive" (or, more accurately, missing value)
test
> results, rather than real positives, and go from there.
> 
> You could also "patch" the tests as part of your build process.
Somewhere I
> worked had to do that for parts of the internet tests that were unable to
> get through the firewall.
> 
> Best,
> ~G
> 
> 
> 
> On Tue, May 4, 2021 at 1:04 PM Henrik Bengtsson <henrik.bengtsson at
gmail.com>
> wrote:
> 
>> Two questions to R Core:
>>
>> 1. Is R designed so that 'recommended' packages are optional,
or
>> should that be considered uncharted territories?
>>
>> 2. Can such an R build/installation be validated using existing check
>> methods?
>>
>>
>> --
>>
>> Dirk, it's not clear to me whether you know for sure, or you draw
>> conclusions based your long experience and reading. I think it's
very
>> important that others don't find this thread later on and read your
>> comments as if they're the "truth" (unless they are).  I
haven't
>> re-read it from start to finish, but there are passages in 'R
>> Installation and Administration' suggesting you can build and
install
>> R without 'recommended' packages.  For example,
post-installation,
>> Section 'Testing an Installation' suggests you can run (after
making
>> sure `make install-tests`):
>>
>> cd tests
>> ../bin/R CMD make check
>>
>> but they fail the same way.  The passage continuous "... and other
>> useful targets are test-BasePackages and test-Recommended to run tests
>> of the standard and recommended packages (if installed)
respectively."
>> (*).  So, to me that hints at 'recommended' packages are
optional just
>> as they're "Priority: recommended".  Further down,
there's also a
>> mentioning of:
>>
>> $ R_LIBS_USER="" R --vanilla
>>> Sys.setenv(LC_COLLATE = "C", LC_TIME = "C",
LANGUAGE = "en")
>>> tools::testInstalledPackages(scope = "base")
>>
>> which also produces errors when 'recommended' packages are
missing,
>> e.g. "Failed with error:  'there is no package called
'nlme'".
>>
>> (*) BTW, '../bin/R CMD make test-BasePackages' gives
"make: *** No
>> rule to make target 'test-BasePackages'.  Stop."
>>
>> Thanks,
>>
>> /Henrik
>>
>> On Tue, May 4, 2021 at 12:22 PM Dirk Eddelbuettel <edd at
debian.org> wrote:
>>>
>>>
>>> On 4 May 2021 at 11:25, Henrik Bengtsson wrote:
>>> | FWIW,
>>> |
>>> | $ ./configure --help
>>> | ...
>>> |   --with-recommended-packages
>>> |                           use/install recommended R packages
[yes]
>>>
>>> Of course. But look at the verb in your Subject: no optionality _in
>> testing_ there.
>>>
>>> You obviously need to be able to build R itself to then build the
>> recommended
>>> packages you need for testing.
>>>
>>> Dirk
>>>
>>> --
>>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Hmm, that's fair enough Ben, I stand corrected.  I will say that this seems
to be a pretty "soft" recommendation, as these things go, given that
it
isn't tested for by R CMD check, including with the -as-cran extensions. In
principle, it seems like it could be, similar checks are made in package
code for inappropriate external-package-symbol usage/

Either way, though, I suppose I have a number of packages which have been
invisibly non-best-practices compliant for their entire lifetimes (or at
least, the portion of that where they had tests/vignettes...).

Best,
~G

On Tue, May 4, 2021 at 2:22 PM Ben Bolker <bbolker at gmail.com> wrote:
>
>    Sorry if this has been pointed out already, but some relevant text
> from
>
>
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Suggested-packages
>
>  > Note that someone wanting to run the examples/tests/vignettes may not
> have a suggested package available (and it may not even be possible to
> install it for that platform). The recommendation used to be to make
> their use conditional via if(require("pkgname")): this is OK if
that
> conditioning is done in examples/tests/vignettes, although using
> if(requireNamespace("pkgname")) is preferred, if possible.
>
> ...
>
>  > Some people have assumed that a ?recommended? package in ?Suggests?
> can safely be used unconditionally, but this is not so. (R can be
> installed without recommended packages, and which packages are
> ?recommended? may change.)
>
>
>
> On 5/4/21 5:10 PM, Gabriel Becker wrote:
> > Hi Henrik,
> >
> > A couple of things. Firstly, so far asI have ever heard, it's
valid that
> a
> > package have hard dependencies in its tests for packages listed only
in
> > Suggests.  In fact, that is one of the stated purposes of Suggests. An
> > argument could be made, I suppose, that the base packages should be
under
> > stricter guidelines, but stats isn't violating the letter or
intention of
> > Suggests by doing this.
> >
> >
> > Secondly, I don't have time to dig through the make
files/administration
> > docs, but I do know that R CMD check has --no-stop-on-error, so you
can
> > either separately or as part of make check, use that option for stats
> (and
> > elsewhere as needed?) and just know that the stats tests that depend
on
> > MASS are "false positive" (or, more accurately, missing
value) test
> > results, rather than real positives, and go from there.
> >
> > You could also "patch" the tests as part of your build
process.
> Somewhere I
> > worked had to do that for parts of the internet tests that were unable
to
> > get through the firewall.
> >
> > Best,
> > ~G
> >
> >
> >
> > On Tue, May 4, 2021 at 1:04 PM Henrik Bengtsson <
> henrik.bengtsson at gmail.com>
> > wrote:
> >
> >> Two questions to R Core:
> >>
> >> 1. Is R designed so that 'recommended' packages are
optional, or
> >> should that be considered uncharted territories?
> >>
> >> 2. Can such an R build/installation be validated using existing
check
> >> methods?
> >>
> >>
> >> --
> >>
> >> Dirk, it's not clear to me whether you know for sure, or you
draw
> >> conclusions based your long experience and reading. I think
it's very
> >> important that others don't find this thread later on and read
your
> >> comments as if they're the "truth" (unless they
are).  I haven't
> >> re-read it from start to finish, but there are passages in 'R
> >> Installation and Administration' suggesting you can build and
install
> >> R without 'recommended' packages.  For example,
post-installation,
> >> Section 'Testing an Installation' suggests you can run
(after making
> >> sure `make install-tests`):
> >>
> >> cd tests
> >> ../bin/R CMD make check
> >>
> >> but they fail the same way.  The passage continuous "... and
other
> >> useful targets are test-BasePackages and test-Recommended to run
tests
> >> of the standard and recommended packages (if installed)
respectively."
> >> (*).  So, to me that hints at 'recommended' packages are
optional just
> >> as they're "Priority: recommended".  Further down,
there's also a
> >> mentioning of:
> >>
> >> $ R_LIBS_USER="" R --vanilla
> >>> Sys.setenv(LC_COLLATE = "C", LC_TIME =
"C", LANGUAGE = "en")
> >>> tools::testInstalledPackages(scope = "base")
> >>
> >> which also produces errors when 'recommended' packages are
missing,
> >> e.g. "Failed with error:  'there is no package called
'nlme'".
> >>
> >> (*) BTW, '../bin/R CMD make test-BasePackages' gives
"make: *** No
> >> rule to make target 'test-BasePackages'.  Stop."
> >>
> >> Thanks,
> >>
> >> /Henrik
> >>
> >> On Tue, May 4, 2021 at 12:22 PM Dirk Eddelbuettel <edd at
debian.org>
> wrote:
> >>>
> >>>
> >>> On 4 May 2021 at 11:25, Henrik Bengtsson wrote:
> >>> | FWIW,
> >>> |
> >>> | $ ./configure --help
> >>> | ...
> >>> |   --with-recommended-packages
> >>> |                           use/install recommended R packages
[yes]
> >>>
> >>> Of course. But look at the verb in your Subject: no
optionality _in
> >> testing_ there.
> >>>
> >>> You obviously need to be able to build R itself to then build
the
> >> recommended
> >>> packages you need for testing.
> >>>
> >>> Dirk
> >>>
> >>> --
> >>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at
debian.org
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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