[Rd] tools:: extracting pkg dependencies from DCF
Jan Gorecki
j@goreck| @end|ng |rom w|t@edu@p|
Mon Oct 17 09:39:09 CEST 2022
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.urbanek using 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.gorecki using 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 <gabembecker using 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.gorecki using 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 <netikja using 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.gorecki using 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 using r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>>>
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
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> >>>
> >>
> >
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> >
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