Re: [Rd] Depending/Importing data only packages
Would "Suggests" not work in this situation? I don't understand why you would need Depends. In what sense do you rely on the data only package? Paul On 13-12-06 04:20 PM, Hadley Wickham wrote: Hi all, What should you do when you rely on a data only package. If you just "Depend" on it, you get the following from R CMD check: Package in Depends field not imported from: 'hflights' These packages needs to imported from for the case when this namespace is loaded but not attached. But there's nothing in the namespace to import, so adding it to imports doesn't seem like the right answer. Is that just a spurious note? Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
I don't know about this particular case, but in general it makes sense to rely on a data package. E.g. I am creating a package that does Bayesian inference for a particular problem, potentially relying on prior knowledge. I think it makes sense to put the data that is used to calculate the prior into another package, because it will be larger than the code, and it does not change that often. Gabor On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert wrote: > Would "Suggests" not work in this situation? I don't understand why you > would need Depends. In what sense do you rely on the data only package? > > Paul > > On 13-12-06 04:20 PM, Hadley Wickham wrote: >> >> Hi all, >> >> What should you do when you rely on a data only package. If you just >> "Depend" on it, you get the following from R CMD check: >> >> Package in Depends field not imported from: 'hflights' >>These packages needs to imported from for the case when >>this namespace is loaded but not attached. >> >> But there's nothing in the namespace to import, so adding it to >> imports doesn't seem like the right answer. Is that just a spurious >> note? >> >> Hadley >> > > __ > 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
Re: [Rd] Depending/Importing data only packages
> Would "Suggests" not work in this situation? I don't understand why you > would need Depends. In what sense do you rely on the data only package? Because I want someone who downloads the package to be able to run the examples without having to take additional action. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
On 13-12-07 12:19 PM, Gábor Csárdi wrote: I don't know about this particular case, but in general it makes sense to rely on a data package. E.g. I am creating a package that does Bayesian inference for a particular problem, potentially relying on prior knowledge. I think it makes sense to put the data that is used to calculate the prior into another package, because it will be larger than the code, and it does not change that often. Gabor On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert wrote: Would "Suggests" not work in this situation? I don't understand why you would need Depends. In what sense do you rely on the data only package? HW> Because I want someone who downloads the package to be able to run HW> the examples without having to take additional action. HW> HW> Hadley I went through this myself, including thinking it was a nuisance for users to need to attach other packages to run examples. In the end I decided it is not so bad to be explicit about what package the example data comes from, so illustrate it in the examples. Users may not always want this data, and other packages that build on yours probably do not want it. Even in the Bayesian inference case pointed out by Gábor, I am not convinced. It means the prior knowledge base cannot be exchanged for another one. The package would be more general if it allowed the possibility of attaching a different database of prior information. But this is clearly a more important case, since the code probably does not work without some database. (There are a few other situations where something like "RequireOneOf:" would be useful.) Paul Paul On 13-12-06 04:20 PM, Hadley Wickham wrote: Hi all, What should you do when you rely on a data only package. If you just "Depend" on it, you get the following from R CMD check: Package in Depends field not imported from: 'hflights' These packages needs to imported from for the case when this namespace is loaded but not attached. But there's nothing in the namespace to import, so adding it to imports doesn't seem like the right answer. Is that just a spurious note? Hadley __ 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
Re: [Rd] Depending/Importing data only packages
On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert wrote: > > > On 13-12-07 12:19 PM, Gábor Csárdi wrote: >> >> I don't know about this particular case, but in general it makes sense >> to rely on a data package. E.g. I am creating a package that does >> Bayesian inference for a particular problem, potentially relying on >> prior knowledge. I think it makes sense to put the data that is used >> to calculate the prior into another package, because it will be larger >> than the code, and it does not change that often. >> >> Gabor >> >> On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert >> wrote: >>> >>> Would "Suggests" not work in this situation? I don't understand why you >>> would need Depends. In what sense do you rely on the data only package? >>> > > HW> Because I want someone who downloads the package to be able to run > HW> the examples without having to take additional action. > HW> > HW> Hadley > > I went through this myself, including thinking it was a nuisance for users > to need to attach other packages to run examples. In the end I decided it is > not so bad to be explicit about what package the example data comes from, so > illustrate it in the examples. Users may not always want this data, and > other packages that build on yours probably do not want it. > > Even in the Bayesian inference case pointed out by Gábor, I am not > convinced. It means the prior knowledge base cannot be exchanged for another > one. The package would be more general if it allowed the possibility of > attaching a different database of prior information. But this is clearly a > more important case, since the code probably does not work without some > database. (There are a few other situations where something like > "RequireOneOf:" would be useful.) > Requiring users to load packages which could be loaded automatically seems to go against ease of use. Its just one more thing that they have to remember to do. It really should be possible to write a "batteries included" package while leveraging off of other packages. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert wrote: > > > On 13-12-07 12:19 PM, Gábor Csárdi wrote: >> >> I don't know about this particular case, but in general it makes sense >> to rely on a data package. E.g. I am creating a package that does >> Bayesian inference for a particular problem, potentially relying on >> prior knowledge. I think it makes sense to put the data that is used >> to calculate the prior into another package, because it will be larger >> than the code, and it does not change that often. >> >> Gabor >> >> >> On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert >> wrote: >>> >>> Would "Suggests" not work in this situation? I don't understand why you >>> would need Depends. In what sense do you rely on the data only package? >>> > > HW> Because I want someone who downloads the package to be able to run > HW> the examples without having to take additional action. > HW> > HW> Hadley > > I went through this myself, including thinking it was a nuisance for users > to need to attach other packages to run examples. In the end I decided it is > not so bad to be explicit about what package the example data comes from, so > illustrate it in the examples. Users may not always want this data, and > other packages that build on yours probably do not want it. > > Even in the Bayesian inference case pointed out by Gábor, I am not > convinced. It means the prior knowledge base cannot be exchanged for another > one. The package would be more general if it allowed the possibility of > attaching a different database of prior information. But this is clearly a > more important case, since the code probably does not work without some > database. (There are a few other situations where something like > "RequireOneOf:" would be useful.) First, as you say, you went through this yourself, which means that the "right" answer to the problem is not obvious. This is (mainly) a design decision, and if it is not obvious that depending on a data package is always bad design. Then why not let the package developer decide? Second, I very much think that using 'Suggests' is misleading in this case. The data package is clearly required. I, as a user, would expect that if I downloaded all requirements, then the package will work, which is not true any more. (Let's not go into what 'Suggests' actually means, and how totally confusing it is already.) 'RequireOneOf' would be indeed useful. Best, Gabor > Paul [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
On 7 December 2013 at 13:58, Gábor Csárdi wrote: | 'RequireOneOf' would be indeed useful. The DESCRIPTION file follows Debian Control File formats. Another aspect of these could be useful here: the '|' operator. Eg for ess (the Debian package) we have Depends: dpkg (>= 1.15.4) | install-info, emacs23 | emacs22 | emacs21 | emacsen saying that either a recent enough dpkg [package tool] or the install-info package are needed [to deal with .info files] and that one of the available emacs versions will do, with the first one being the default choice and the last one a virtual package providing a catch-all fallback. The R package does similar things to pick one of several blas and lapack packages: Depends: zip, unzip, libpaper-utils, xdg-utils, \ libblas3 | libblas.so.3 | libatlas3-base, [...] \ liblapack3 | liblapack.so.3 | libatlas3-base, [...] Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
On 13-12-06 4:20 PM, Hadley Wickham wrote:
Hi all,
What should you do when you rely on a data only package. If you just
"Depend" on it, you get the following from R CMD check:
Package in Depends field not imported from: 'hflights'
These packages needs to imported from for the case when
this namespace is loaded but not attached.
But there's nothing in the namespace to import, so adding it to
imports doesn't seem like the right answer. Is that just a spurious
note?
Hadley
I don't know whether the author of that note would consider it spurious
or not. A simple workaround for you (as the author of hflights) is to
put a function into the namespace. For example, get_hflights(), that
gets a copy of the data:
get_hflights <- function() {
data("hflights", package="hflights", envir=environment())
hflights
}
I don't know a simple workaround for someone who depends on a data-only
package that they did not author.
Duncan Murdoch
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Re: [Rd] Depending/Importing data only packages
> I don't know whether the author of that note would consider it spurious or
> not. A simple workaround for you (as the author of hflights) is to put a
> function into the namespace. For example, get_hflights(), that gets a copy
> of the data:
>
> get_hflights <- function() {
> data("hflights", package="hflights", envir=environment())
> hflights
> }
Another option is to put it in sysdata.rda and then export it - but
then (I think) you don't get the nice lazy loading. It would be nice
to have some official guidance on what is preferred.
Hadley
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Re: [Rd] Depending/Importing data only packages
On 13-12-07 01:47 PM, Gabor Grothendieck wrote: On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert wrote: On 13-12-07 12:19 PM, Gábor Csárdi wrote: I don't know about this particular case, but in general it makes sense to rely on a data package. E.g. I am creating a package that does Bayesian inference for a particular problem, potentially relying on prior knowledge. I think it makes sense to put the data that is used to calculate the prior into another package, because it will be larger than the code, and it does not change that often. Gabor On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert wrote: Would "Suggests" not work in this situation? I don't understand why you would need Depends. In what sense do you rely on the data only package? HW> Because I want someone who downloads the package to be able to run HW> the examples without having to take additional action. HW> HW> Hadley I went through this myself, including thinking it was a nuisance for users to need to attach other packages to run examples. In the end I decided it is not so bad to be explicit about what package the example data comes from, so illustrate it in the examples. Users may not always want this data, and other packages that build on yours probably do not want it. Even in the Bayesian inference case pointed out by Gábor, I am not convinced. It means the prior knowledge base cannot be exchanged for another one. The package would be more general if it allowed the possibility of attaching a different database of prior information. But this is clearly a more important case, since the code probably does not work without some database. (There are a few other situations where something like "RequireOneOf:" would be useful.) Requiring users to load packages which could be loaded automatically seems to go against ease of use. Its just one more thing that they have to remember to do. It really should be possible to write a "batteries included" package while leveraging off of other packages. Just to be clear, I distinguish the "batteries included" situation from the "spare batteries included" situation. I think it should be possible to automatically load everything that is really needed, that is why I think the Bayesian database is a more important case. But it strikes me as bad to attach everything that could ever possibly be wanted by a user. After all, it would be possible to automatically attach all packages. Some packages seemed to be headed in that direction before the new rules started to be enforced. There is certainly a trade-off here between ease of use, not needing the user to attach packages, and namespace conflicts, which will result in time and difficulty debugging. For packages that no one ever uses in other packages, there would be a tendency to lean toward ease of use. But as soon as anyone starts building on top of a package with another one, I think that avoiding potential conflicts will dominate. Paul __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
The Writing R Extensions manual says that Suggests is for packages which are required only for examples, which I believe matches Hadley's original question. In the Bayesian case, it seems like including one prior's worth of data in the package but having the infrastructure designed so that other data can be swapped in would allow all the examples to run without tying the analysis to a signle prior. Just my $0.02 ~G On Sat, Dec 7, 2013 at 2:08 PM, Paul Gilbert wrote: > > > On 13-12-07 01:47 PM, Gabor Grothendieck wrote: > >> On Sat, Dec 7, 2013 at 1:35 PM, Paul Gilbert >> wrote: >> >>> >>> >>> On 13-12-07 12:19 PM, Gábor Csárdi wrote: >>> I don't know about this particular case, but in general it makes sense to rely on a data package. E.g. I am creating a package that does Bayesian inference for a particular problem, potentially relying on prior knowledge. I think it makes sense to put the data that is used to calculate the prior into another package, because it will be larger than the code, and it does not change that often. Gabor On Sat, Dec 7, 2013 at 11:51 AM, Paul Gilbert wrote: > > Would "Suggests" not work in this situation? I don't understand why you > would need Depends. In what sense do you rely on the data only package? > > >>> HW> Because I want someone who downloads the package to be able to run >>> HW> the examples without having to take additional action. >>> HW> >>> HW> Hadley >>> >>> I went through this myself, including thinking it was a nuisance for >>> users >>> to need to attach other packages to run examples. In the end I decided >>> it is >>> not so bad to be explicit about what package the example data comes >>> from, so >>> illustrate it in the examples. Users may not always want this data, and >>> other packages that build on yours probably do not want it. >>> >>> Even in the Bayesian inference case pointed out by Gábor, I am not >>> convinced. It means the prior knowledge base cannot be exchanged for >>> another >>> one. The package would be more general if it allowed the possibility of >>> attaching a different database of prior information. But this is clearly >>> a >>> more important case, since the code probably does not work without some >>> database. (There are a few other situations where something like >>> "RequireOneOf:" would be useful.) >>> >>> >> Requiring users to load packages which could be loaded automatically >> seems to go against ease of use. Its just one more thing that they >> have to remember to do. >> >> It really should be possible to write a "batteries included" package >> while leveraging off of other packages. >> >> Just to be clear, I distinguish the "batteries included" situation from > the "spare batteries included" situation. I think it should be possible to > automatically load everything that is really needed, that is why I think > the Bayesian database is a more important case. But it strikes me as bad to > attach everything that could ever possibly be wanted by a user. After all, > it would be possible to automatically attach all packages. Some packages > seemed to be headed in that direction before the new rules started to be > enforced. > > There is certainly a trade-off here between ease of use, not needing the > user to attach packages, and namespace conflicts, which will result in time > and difficulty debugging. For packages that no one ever uses in other > packages, there would be a tendency to lean toward ease of use. But as soon > as anyone starts building on top of a package with another one, I think > that avoiding potential conflicts will dominate. > > Paul > > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
> Just to be clear, I distinguish the "batteries included" situation from the > "spare batteries included" situation. I think it should be possible to > automatically load everything that is really needed, that is why I think the > Bayesian database is a more important case. But it strikes me as bad to > attach everything that could ever possibly be wanted by a user. After all, > it would be possible to automatically attach all packages. Some packages > seemed to be headed in that direction before the new rules started to be > enforced. I agree, but for data only packages, attaching the namespace has no impact on other code because it's empty. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Depending/Importing data only packages
> The Writing R Extensions manual says that Suggests is for packages which
> are required only for examples, which I believe matches Hadley's original
> question.
Yes, but without this package they won't be able to run the majority
of examples, which I think delivers a poor experience to the user. It
also means I have to litter my examples with if(require("x")),
decreasing the signal to noise ratio in the examples.
But we're getting a bit far from my original question about the NOTE:
Package in Depends field not imported from: 'hflights'
These packages needs to imported from for the case when
this namespace is loaded but not attached.
Depending on (or linking to) a package is not just about making the
functions in the package available.
Hadley
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Re: [Rd] Depending/Importing data only packages
On 13-12-07 05:21 PM, Hadley Wickham wrote:
The Writing R Extensions manual says that Suggests is for packages which
are required only for examples, which I believe matches Hadley's original
question.
Yes, but without this package they won't be able to run the majority
of examples, which I think delivers a poor experience to the user. It
also means I have to litter my examples with if(require("x")),
I think you just need require("x") or library("x"). If it is in Suggests
then it is available whenever examples are tested, so you don't need the
if(). In my opinion, this increases the signal by indicating to the
reader where the data comes from.
decreasing the signal to noise ratio in the examples.
But we're getting a bit far from my original question about the NOTE:
Package in Depends field not imported from: 'hflights'
These packages needs to imported from for the case when
this namespace is loaded but not attached.
Depending on (or linking to) a package is not just about making the
functions in the package available.
Several of us used to think that, but the modern interpretation seems to
be just about making things in the package yours depends on available to
users of your package. "Exports:" might be a better term than
"Depends:", at least if Depends: was not trying to mean both Imports:
and Exports:".
Paul
Hadley
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