tools:: extracting pkg dependencies from DCF

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

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