[Rd] tools:: extracting pkg dependencies from DCF
Jan Gorecki
j@goreck| @end|ng |rom w|t@edu@p|
Tue Dec 19 19:29:40 CET 2023
Hello all,
Following up on this old thread as I have recently observed, rather a
bad practice (maintaining order of installation for R packages rather
than relying on R for that), for solving a problem that R branch
tools4pkgs (mentioned in this email) addresses very well.
More details can be found in
https://github.com/dewittpe/R-install-dependencies/issues/3
Therefore I extracted functionality from base R branch and put into
standalone package, named after R branch:
https://github.com/jangorecki/tools4pkgs
Sharing for whoever would reach this email thread in future.
Best Regards,
Jan Gorecki
On Sat, Oct 29, 2022 at 6:26 PM Jan Gorecki <j.gorecki using wit.edu.pl> wrote:
>
> Thank you Gabriel,
>
> Just for future readers. Below is a base R way to address this common
> problem, as instructed by you (+stopifnot to suppress print).
>
> Rscript -e 'stopifnot(file.copy("DESCRIPTION",
> file.path(tdir<-tempdir(), "PACKAGES")));
> db<-available.packages(paste0("file://", tdir));
> install.packages(setdiff(tools::package_dependencies(read.dcf("DESCRIPTION",
> fields="Package")[[1L]], db, which="most")[[1L]],
> installed.packages(priority="high")[,"Package"]))'
>
> 3 liner, 310 chars long command, far from ideal, but does work.
>
> Best,
> Jan
>
>
> On Fri, Oct 28, 2022 at 10:42 PM Gabriel Becker <gabembecker using gmail.com> wrote:
> >
> > Hi Jan,
> >
> >
> > On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki <j.gorecki using wit.edu.pl> wrote:
> >>
> >> 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.
> >
> >
> > Really what you're looking for though, is to install all the dependencies which aren't present right? Excluding base packages is just a particular way to do that under certain assumptions about the CI environment.
> >
> > So
> >
> >
> > needed_pkgs <- setdiff(package_dependencies(...), installed.packages()[,"Package"])
> > install.packages(needed_pkgs, repos = fancyrepos)
> >
> >
> > will do what you want without installing the package itself, if that is important. This will filter out base and recommended packages (which will be already installed in your CI container, since R is).
> >
> >
> > Now this does not take into account versioned dependencies, so it's not actually fully correct (whereas installing the package is), but it gets you where you're trying to go. And in a clean CI container without cached package installation for the deps, its equivalent.
> >
> >
> > Also, as an aside, if you need to get the base packages, you can do
> >
> > installed.packages(priority="base")[,"Package"]
> >
> > base compiler datasets graphics grDevices grid
> >
> > "base" "compiler" "datasets" "graphics" "grDevices" "grid"
> >
> > methods parallel splines stats stats4 tcltk
> >
> > "methods" "parallel" "splines" "stats" "stats4" "tcltk"
> >
> > tools utils
> >
> > "tools" "utils"
> >
> >
> > (to get base and recommended packages use 'high' instead of 'base')
> >
> > No need to be reaching down into unexported functions. So if you *really* only want to exclude base functions (which likely will give you some protection from versioned dep issues), you can change the code above to
> >
> > needed_pkgs <- setdiff(package_dependencies(...), installed.packages(priority = "high")[,"Package"])
> > install.packages(needed_pkgs, repos = fancyrepos)
> >
> > Best,
> > ~G
> >
> >>
> >> On Fri, Oct 28, 2022 at 8:42 PM Gabriel Becker <gabembecker using 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.gorecki using 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.gorecki using 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.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]]
> >> >> >> >>>
> >> >> >> >>> ______________________________________________
> >> >> >> >>> R-devel using r-project.org mailing list
> >> >> >> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >> >> >> >>>
> >> >> >> >>
> >> >> >> >
> >> >> >> > [[alternative HTML version deleted]]
> >> >> >> >
> >> >> >> > ______________________________________________
> >> >> >> > R-devel using r-project.org mailing list
> >> >> >> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >> >> >> >
> >> >> >>
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