Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 wrote:
> >
> > Hi Jan,
> >
> >
> > On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki 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"]
> >
> >basecompilerdatasetsgraphics grDevicesgrid
> >
> > "base" "compiler" "datasets" "graphics" "grDevices" "grid"
> >
> > methodsparallel 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
> >> 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(, 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
> >> > 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
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 wrote:
>
> Hi Jan,
>
>
> On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki 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"]
>
>basecompilerdatasetsgraphics grDevicesgrid
>
> "base" "compiler" "datasets" "graphics" "grDevices" "grid"
>
> methodsparallel 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 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(, 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 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
Re: [Rd] tools:: extracting pkg dependencies from DCF
Hi Jan,
On Fri, Oct 28, 2022 at 1:57 PM Jan Gorecki 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"]
basecompilerdatasetsgraphics grDevicesgrid
"base" "compiler" "datasets" "graphics" "grDevices" "grid"
methodsparallel 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
> 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(, 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
> 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
> 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
Re: [Rd] tools:: extracting pkg dependencies from DCF
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.
Unless you say that installing the package and then running R CMD
check on that package is considered good practice. Then yes,
functionality I am asking about is not needed. Somehow I never thought
that this could be considered a good practice just by the fact that
installation of the package could already impact environment in which
check is taking place.
Best,
Jan
On Fri, Oct 28, 2022 at 8:42 PM Gabriel Becker 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(, 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 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 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
>> > 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 wrote:
>> >> >
>> >> >
Re: [Rd] tools:: extracting pkg dependencies from DCF
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(, 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 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 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
> 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
> 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.
> >> >
> >> >
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 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 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 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"
Re: [Rd] 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
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 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
> 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]
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 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 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 wrote:
>>>
Hello Jan,
I have seen many packages that implemented dependencies
Re: [Rd] tools:: extracting pkg dependencies from DCF
On Fri, Oct 14, 2022 at 11:14 PM Jan Gorecki 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
assertthatNA
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
assertthatNA "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 NANA NA NA
AnnotationDbi NANA NA NA
askpass NANA "askpass.so.dSYM" NA
assertthatNANA NA NA
backports NANA "backports.so.dSYM" NA
base64enc NANA "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"
[653] "rjson"
[654] "rsolr"
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 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 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
>> > 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
>>
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 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
> > 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
> >>
> >
>
>
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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 > 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
Re: [Rd] tools:: extracting pkg dependencies from DCF
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 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
