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.bengts...@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 <e...@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 | e...@debian.org
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