[Rd] tools:: extracting pkg dependencies from DCF
Gabriel Becker
g@bembecker @end|ng |rom gm@||@com
Sat Oct 15 09:29:55 CEST 2022
On Fri, Oct 14, 2022 at 11:14 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.
>
Right. Thats why I asked though, because this only makes sense to do
recursively (i.e. collectively). Packages cannot meaningfully be treated in
isolation in R. If you capture/mirror the non-recursive dependencies only,
your package won't be (re-)installable.
What you actually want is either a frozen slice of CRAN, or a description
of either your full package library, or the full recursive subset of it
relevant to a particular package. (switchr was designed to do both of these
things easily, as an aside). Neither of which is achievable by looking at
an individual DESCRIPTION file.
Here's another fun trick if you don't want to just use switchr and let it
take care of it for you:
> .libPaths()
[1] "/Users/gabrielbecker/Rlib/syswide-4.1.2"
[2] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library"
> write_PACKAGES(.libPaths()[1], unpacked = TRUE, validate = FALSE)
> avl <- available.packages(paste0("file://", .libPaths()[1]))
> head(avl)
Package Version Priority
abind "abind" "1.4-5" NA
AnnotationDbi "AnnotationDbi" "1.56.2" NA
askpass "askpass" "1.1" NA
assertthat "assertthat" "0.2.1" NA
backports "backports" "1.4.1" NA
base64enc "base64enc" "0.1-3" NA
Depends
abind "R (>= 1.5.0)"
AnnotationDbi "R (>= 2.7.0), methods, utils, stats4, BiocGenerics
(>=\n0.29.2), Biobase (>= 1.17.0), IRanges"
askpass NA
assertthat NA
backports "R (>= 3.0.0)"
base64enc "R (>= 2.9.0)"
Imports
LinkingTo
abind "methods, utils" NA
AnnotationDbi "DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST" NA
askpass "sys (>= 2.1)" NA
assertthat "tools" NA
backports NA NA
base64enc NA NA
Suggests
abind NA
AnnotationDbi "hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db,
RUnit,\nTxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
reactome.db,\nAnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr"
askpass "testthat"
assertthat "testthat, covr"
backports NA
base64enc NA
Enhances License License_is_FOSS
abind NA "LGPL (>= 2)" NA
AnnotationDbi NA "Artistic-2.0" NA
askpass NA "MIT + file LICENSE" NA
assertthat NA "GPL-3" NA
backports NA "GPL-2 | GPL-3" NA
base64enc "png" "GPL-2 | GPL-3" NA
License_restricts_use OS_type Archs MD5sum
abind NA NA NA NA
AnnotationDbi NA NA NA NA
askpass NA NA "askpass.so.dSYM" NA
assertthat NA NA NA NA
backports NA NA "backports.so.dSYM" NA
base64enc NA NA "base64enc.so.dSYM" NA
NeedsCompilation File
abind "no" NA
AnnotationDbi "no" NA
askpass "yes" NA
assertthat "no" NA
backports "yes" NA
base64enc "yes" NA
Repository
abind "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
AnnotationDbi "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
askpass "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
assertthat "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
backports "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
base64enc "file:///Users/gabrielbecker/Rlib/syswide-4.1.2"
> package_dependencies("rtables", avl, recursive = TRUE)
$rtables
[1] "methods" "magrittr" "formatters" "stats" "htmltools"
[6] "grid" "utils" "digest" "grDevices" "base64enc"
[11] "rlang" "fastmap"
> package_dependencies("rtables", avl, which = "all", recursive = TRUE)
$rtables
[1] "methods"
[2] "magrittr"
[3] "formatters"
[4] "stats"
[5] "htmltools"
[6] "grid"
[7] "dplyr"
[8] "tibble"
<snip>
[653] "rjson"
[654] "rsolr"
[655] "rlecuyer"
[656] "filelock"
Now you should probably move the PACKAGES file somewhere else and not leave
it in your package library, but I trust this illustrated my point. Most of
the exported machinery is based on available.packages output, but that's
not really a meaningful blocker for this type of work. We can get
available.packages output if we need to. Remember the PACKAGES file is just
a bunch of DESCRIPTION files slightly trimmed and then appended one after
the other.
This also shows why recursive and which=all don't really go together. In
my opinion (and thus switchr's) the correct thing to do is do all for the
package in question and then only hard dependencies of those packages
recursively. That will let you build the package's vignettes (if you care
about such things), but won't pull in hundreds or thousands of reverse deps.
Best,
~G
> 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]]
More information about the R-devel
mailing list