Testing R build when using --without-recommended-packages?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
15 messages Options
Reply | Threaded
Open this post in threaded view
|

Testing R build when using --without-recommended-packages?

Henrik Bengtsson-5
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Dirk Eddelbuettel
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Henrik Bengtsson-5
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Dirk Eddelbuettel
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Henrik Bengtsson-5
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Dirk Eddelbuettel
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Henrik Bengtsson-5
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Gabriel Becker-2
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

bbolker

   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 <[hidden email]>
> 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 <[hidden email]> 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 | [hidden email]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Dirk Eddelbuettel
In reply to this post by Gabriel Becker-2
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Gabriel Becker-2
In reply to this post by bbolker
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Martin Maechler
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Duncan Murdoch-2
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Dirk Eddelbuettel
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: Testing R build when using --without-recommended-packages?

Henrik Bengtsson-5
In reply to this post by Martin Maechler
CONTENTS DELETED
The author has deleted this message.