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 <gabembec...@gmail.com> wrote: > > Hi Jan, > > > On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki <j.gore...@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 <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