Gabriel,
It is the most basic CI use case. One wants to install only
dependencies only of the package, and run R CMD check on the package.
Unless you say that installing the package and then running R CMD
check on that package is considered good practice. Then yes,
functionality I am asking about is not needed. Somehow I never thought
that this could be considered a good practice just by the fact that
installation of the package could already impact environment in which
check is taking place.
Best,
Jan
On Fri, Oct 28, 2022 at 8:42 PM Gabriel Becker <gabembec...@gmail.com> wrote:
>
> Hi Jan,
>
> The reason, I suspect without speaking for R-core, is that by design you
> should not be specifying package dependencies as additional packages to
> install. install.packages already does this for you, as it did in the
> construct of a repository code that I provided previously in the thread. You
> should be *only* doing
>
> install.packages(<pkg in question>, repos = *)
>
> Then everything happens automatically via extremely well tested very mature
> code.
>
> I (still) don't understand why you'd need to pass install.packages the vector
> of dependencies yourself, as that is counter to install.packages' core design.
>
> Does that make sense?
>
> Best,
> ~G
>
> On Fri, Oct 28, 2022 at 12:18 PM Jan Gorecki <j.gore...@wit.edu.pl> wrote:
>>
>> Gabriel,
>>
>> I am trying to design generic solution that could be applied to
>> arbitrary package. Therefore I went with the latter solution you
>> proposed.
>> If we wouldn't have to exclude base packages, then its a 3 liner
>>
>> file.copy("DESCRIPTION", file.path(tdir<-tempdir(), "PACKAGES"));
>> db<-available.packages(paste0("file://", tdir));
>> utils::install.packages(tools::package_dependencies("pkgname", db,
>> which="most")[[1L]])
>>
>> As you noticed, we still have to filter out base packages. Otherwise
>> it won't be a robust utility that can be used in CI. Therefore we have
>> to add a call to tools:::.get_standard_package_names() which is an
>> internal function (as of now). Not only complicating the call but also
>> putting the functionality outside of safe use.
>>
>> Considering above, don't you agree that the following one liner could
>> nicely address the problem? The problem that hundreds/thousands of
>> packages are now addressing in their CI scripts by using a third party
>> packages.
>>
>> utils::install.packages(packages.dcf("DESCRIPTION", which="most"))
>>
>> It is hard to me to understand why R members don't consider this basic
>> functionality to be part of base R. Possibly they just don't need it
>> themselves. Yet isn't this sufficient that hundreds/thousands of
>> packages does need this functionality?
>>
>> Best regards,
>> Jan
>>
>> On Mon, Oct 17, 2022 at 8:39 AM Jan Gorecki <j.gore...@wit.edu.pl> wrote:
>> >
>> > Gabriel and Simon
>> >
>> > I completely agree with what you are saying.
>> > The thing is that obtaining recursive deps, all/most whatever, is already
>> > well supported in core R. What is missing is just this single
>> > functionality I am requesting.
>> >
>> > If you will look into the branch you can see there is mirror.packages
>> > function meant to mirror a slice of CRAN. It is doing exactly what you
>> > described: package_dependencies; to obtain recursive deps, then download
>> > all, etc.
>> > I would love to have this function provided by core R as well, but we need
>> > to start somewhere.
>> >
>> > There are other use cases as well.
>> > For example CI, where one wants to install all/most dependencies and then
>> > run R CMD check. Then we don't worry about recursive deps are they will be
>> > resolved automatically.
>> > I don't think it's reasonable to force users to use 3rd party packages to
>> > handle such a common and simple use case. Otherwise one has to hard code
>> > deps in CI script. Not robust at all.
>> >
>> > packages.dcf and repos.dcf makes all that way easier, and are solid base
>> > for building customized orchestration like mirroring slice of CRAN.
>> >
>> > Best regards
>> > Jan
>> >
>> > On Sun, Oct 16, 2022, 01:31 Simon Urbanek <simon.urba...@r-project.org>
>> > wrote:
>> >>
>> >> Jan,
>> >>
>> >> I think using a single DCF as input is not very practical and would not
>> >> be useful in the context you describe (creating self contained repos)
>> >> since they typically concern a list of packages, but essentially
>> >> splitting out the part of install.packages() which determines which files
>> >> will be pulled from where would be very useful as it would be trivial to
>> >> use it to create repository (what we always do in corporate environments)
>> >> instead of installing the packages. I suspect that install packages is
>> >> already too complex so instead of adding a flag to install.packages one
>> >> could move that functionality into a separate function - we all do that
>> >> constantly for the sites we manage, so it would be certainly something
>> >> worthwhile.
>> >>
>> >> Cheers,
>> >> Simon
>> >>
>> >>
>> >> > On Oct 15, 2022, at 7:14 PM, Jan Gorecki <j.gore...@wit.edu.pl> wrote:
>> >> >
>> >> > Hi Gabriel,
>> >> >
>> >> > It's very nice usage you provided here. Maybe instead of adding new
>> >> > function we could extend packages_depenedncies then? To accept file
>> >> > path to
>> >> > dsc file.
>> >> >
>> >> > What about repos.dcf? Maybe additional repositories could be an
>> >> > attribute
>> >> > attached to returned character vector.
>> >> >
>> >> > The use case is to, for a given package sources, obtain its
>> >> > dependencies,
>> >> > so one can use that for installing them/mirroring CRAN subset, or
>> >> > whatever.
>> >> > The later is especially important for a production environment where one
>> >> > wants to have fixed version of packages, and mirroring relevant subset
>> >> > of
>> >> > CRAN is the most simple, and IMO reliable, way to manage such
>> >> > environment.
>> >> >
>> >> > Regards
>> >> > Jan
>> >> >
>> >> > On Fri, Oct 14, 2022, 23:34 Gabriel Becker <gabembec...@gmail.com>
>> >> > wrote:
>> >> >
>> >> >> Hi Jan and Jan,
>> >> >>
>> >> >> Can you explain a little more what exactly you want the non-recursive,
>> >> >> non-version aware dependencies from an individual package for?
>> >> >>
>> >> >> Either way package_dependencies will do this for you* with a little
>> >> >> "aggressive convincing". It wants output from available.packages, but
>> >> >> who
>> >> >> really cares what it wants? It's a function and we are people :)
>> >> >>
>> >> >>> library(tools)
>> >> >>> db <- read.dcf("~/gabe/checkedout/rtables_clean/DESCRIPTION")
>> >> >>> package_dependencies("rtables", db, which = intersect(c("Depends",
>> >> >> "Suggests", "Imports", "LinkingTo"), colnames(db)))
>> >> >> $rtables
>> >> >> [1] "methods" "magrittr" "formatters" "dplyr" "tibble"
>> >> >> [6] "tidyr" "testthat" "xml2" "knitr" "rmarkdown"
>> >> >> [11] "flextable" "officer" "stats" "htmltools" "grid"
>> >> >>
>> >> >>
>> >> >> The only gotcha that I see immediately is that "LinkingTo" isn't always
>> >> >> there (whereas it is with real output from available.packages). If you
>> >> >> know your package doesn't have that (or that it does) at call time ,
>> >> >> this
>> >> >> becomes a one-liner:
>> >> >>
>> >> >> package_dependencies("rtables", db =
>> >> >> read.dcf("~/gabe/checkedout/rtables_clean/DESCRIPTION"), which =
>> >> >> c("Depends", "Suggests", "Imports"))
>> >> >> $rtables
>> >> >> [1] "methods" "magrittr" "formatters" "dplyr" "tibble"
>> >> >> [6] "tidyr" "testthat" "xml2" "knitr" "rmarkdown"
>> >> >> [11] "flextable" "officer" "stats" "htmltools" "grid"
>> >> >>
>> >> >> You can also trick it a slightly different way by giving it what it
>> >> >> actually wants
>> >> >>
>> >> >>> tdir <- tempdir()
>> >> >>> file.copy("~/gabe/checkedout/rtables_clean/DESCRIPTION",
>> >> >>> file.path(tdir,
>> >> >> "PACKAGES"))
>> >> >> [1] TRUE
>> >> >>> avl <- available.packages(paste0("file://", tdir))
>> >> >>> library(tools)
>> >> >>> package_dependencies("rtables", avl)
>> >> >> $rtables
>> >> >> [1] "methods" "magrittr" "formatters" "stats" "htmltools"
>> >> >> [6] "grid"
>> >> >>
>> >> >>> package_dependencies("rtables", avl, which = "all")
>> >> >> $rtables
>> >> >> [1] "methods" "magrittr" "formatters" "stats" "htmltools"
>> >> >> [6] "grid" "dplyr" "tibble" "tidyr" "testthat"
>> >> >> [11] "xml2" "knitr" "rmarkdown" "flextable" "officer"
>> >> >>
>> >> >> So the only real benefits I see that we'd be picking up here is
>> >> >> automatic
>> >> >> filtering by priority, and automatic extraction of the package name
>> >> >> from
>> >> >> the DESCRIPTION file. I'm not sure either of those warrant a new
>> >> >> exported
>> >> >> function that R-core has to maintain forever.
>> >> >>
>> >> >> Best,
>> >> >> ~G
>> >> >>
>> >> >> * I haven't tested this across all OSes, but I dont' know of any
>> >> >> reason it
>> >> >> wouldn't work generally.
>> >> >>
>> >> >> On Fri, Oct 14, 2022 at 2:33 PM Jan Gorecki <j.gore...@wit.edu.pl>
>> >> >> wrote:
>> >> >>
>> >> >>> Hello Jan,
>> >> >>>
>> >> >>> Thanks for confirming about many packages reinventing this missing
>> >> >>> functionality.
>> >> >>> packages.dcf was not meant handle versions. It just extracts names of
>> >> >>> dependencies... Yes, such a simple thing, yet missing in base R.
>> >> >>>
>> >> >>> Versions of packages can be controlled when setting up R pkgs repo.
>> >> >>> This
>> >> >>> is
>> >> >>> how I used to handle it. Making a CRAN subset mirror of fixed version
>> >> >>> pkgs.
>> >> >>> BTW. function for that is also included in mentioned branch. I am
>> >> >>> just not
>> >> >>> proposing it, to increase the chance of having at least this simple,
>> >> >>> missing, functionality merged.
>> >> >>>
>> >> >>> Best
>> >> >>> Jan
>> >> >>>
>> >> >>> On Fri, Oct 14, 2022, 15:14 Jan Netík <neti...@gmail.com> wrote:
>> >> >>>
>> >> >>>> Hello Jan,
>> >> >>>>
>> >> >>>> I have seen many packages that implemented dependencies "extraction"
>> >> >>>> on
>> >> >>>> their own for internal purposes and today I was doing exactly that
>> >> >>>> for
>> >> >>>> mine. It's not a big deal using read.dcf on DESCRIPTION. It was
>> >> >>> sufficient
>> >> >>>> for me, but I had to take care of some \n chars (the overall returned
>> >> >>> value
>> >> >>>> has some rough edges, in my opinion). However, the function from the
>> >> >>> branch
>> >> >>>> seems to not care about version requirements, which are crucial for
>> >> >>>> me.
>> >> >>>> Maybe that is something to reconsider before merging.
>> >> >>>>
>> >> >>>> Best,
>> >> >>>> Jan
>> >> >>>>
>> >> >>>> pá 14. 10. 2022 v 2:27 odesílatel Jan Gorecki <j.gore...@wit.edu.pl>
>> >> >>>> napsal:
>> >> >>>>
>> >> >>>>> Dear R devs,
>> >> >>>>>
>> >> >>>>> I would like to raise a request for a simple helper function.
>> >> >>>>> Utility function to extract package dependencies from DESCRIPTION
>> >> >>>>> file.
>> >> >>>>>
>> >> >>>>> I do think that tools package is better place, for such a
>> >> >>>>> fundamental
>> >> >>>>> functionality, than community packages.
>> >> >>>>>
>> >> >>>>> tools pkg seems perfect fit (having already great function
>> >> >>>>> write_PACKAGES).
>> >> >>>>>
>> >> >>>>> Functionality I am asking for is already in R svn repository since
>> >> >>> 2016,
>> >> >>>>> in
>> >> >>>>> a branch tools4pkgs. Function is called 'packages.dcf'.
>> >> >>>>> Another one 'repos.dcf' would be a good functional complementary to
>> >> >>>>> it.
>> >> >>>>>
>> >> >>>>> Those two simple helper functions really makes it easier for
>> >> >>> organizations
>> >> >>>>> to glue together usage of their own R packages repos and CRAN repo
>> >> >>>>> in a
>> >> >>>>> smooth way. That could possibly help to offload CRAN from new
>> >> >>> submissions.
>> >> >>>>>
>> >> >>>>> gh mirror link for easy preview:
>> >> >>>>>
>> >> >>>>>
>> >> >>> https://github.com/wch/r-source/blob/tools4pkgs/src/library/tools/R/packages.R#L419
>> >> >>>>>
>> >> >>>>> Regards
>> >> >>>>> Jan Gorecki
>> >> >>>>>
>> >> >>>>> [[alternative HTML version deleted]]
>> >> >>>>>
>> >> >>>>> ______________________________________________
>> >> >>>>> R-devel@r-project.org mailing list
>> >> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >> >>>>>
>> >> >>>>
>> >> >>>
>> >> >>> [[alternative HTML version deleted]]
>> >> >>>
>> >> >>> ______________________________________________
>> >> >>> R-devel@r-project.org mailing list
>> >> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >> >>>
>> >> >>
>> >> >
>> >> > [[alternative HTML version deleted]]
>> >> >
>> >> > ______________________________________________
>> >> > R-devel@r-project.org mailing list
>> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >> >
>> >>
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
