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 at 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 at
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 at
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 at
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 Net?k <netikja at
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
> >>>>
> >>>> p? 14. 10. 2022 v 2:27 odes?latel Jan Gorecki
<j.gorecki at 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 at r-project.org mailing list
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>>>
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>>
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>
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