For the record, the only things switchr (my package) is doing internet wise should be hitting the bioconductor config file ( http://bioconductor.org/config.yaml) so that it knows the things it need to know about Bioc repos/versions/etc (at load time, actually, not install time, but since install does a test load, those are essentially the same).
I have fallback behavior for when the file can't be read, so there shouldn't be any actual build breakages/install breakages I don't think, but the check does happen. Advice on what to do for the above use case that is better practice is welcome. ~G On Mon, Sep 26, 2022 at 2:40 PM Simon Urbanek <simon.urba...@r-project.org> wrote: > > > > On 27/09/2022, at 10:21 AM, Iñaki Ucar <iu...@fedoraproject.org> wrote: > > > > On Mon, 26 Sept 2022 at 23:07, Simon Urbanek > > <simon.urba...@r-project.org> wrote: > >> > >> Iñaki, > >> > >> I'm not sure I understand - system dependencies are an entirely > different topic and I would argue a far more important one (very happy to > start a discussion about that), but that has nothing to do with declaring > downloads. I assumed your question was about large files in packages which > packages avoid to ship and download instead so declaring them would be > useful. > > > > Exactly. Maybe there's a misunderstanding, because I didn't talk about > system dependencies (alas there are packages that try to download things > that are declared as system dependencies, as Gabe noted). :) > > > > > Ok, understood. I would like to tackle those as well, but let's start that > conversation in a few weeks when I have a lot more time. > > > >> And for that, the obvious answer is they shouldn't do that - if a > package needs a file to run, it should include it. So an easy solution is > to disallow it. > > > > Then we completely agree. My proposal about declaring additional sources > was because, given that so many packages do this, I thought that I would > find a strong opposition to this. But if R Core / CRAN is ok with just > limiting net access at install time, then that's perfect to me. :) > > > > Yes we do agree :). I started looking at your list, and so far those seem > simply bugs or design deficiencies in the packages (and outright policy > violations). I think the only reason they exist is that it doesn't get > detected in CRAN incoming, it's certainly not intentional. > > Cheers, > Simon > > > > Iñaki > > > >> But so far all examples where just (ab)use of downloads for binary > dependencies which is an entirely different issue that needs a different > solution (in a naive way declaring such dependencies, but we know it's not > that simple - and download URLs don't help there). > >> > >> Cheers, > >> Simon > >> > >> > >>> On 27/09/2022, at 8:25 AM, Ucar <iu...@fedoraproject.org> wrote: > >>> > >>> On Sat, 24 Sept 2022 at 01:55, Simon Urbanek > >>> <simon.urba...@r-project.org> wrote: > >>>> > >>>> Iñaki, > >>>> > >>>> I fully agree, this a very common issue since vast majority of server > deployments I have encountered don't allow internet access. In practice > this means that such packages are effectively banned. > >>>> > >>>> I would argue that not even (1) or (2) are really an issue, because > in fact the CRAN policy doesn't impose any absolute limits on size, it only > states that the package should be "of minimum necessary size" which means > it shouldn't waste space. If there is no way to reduce the size without > impacting functionality, it's perfectly fine. > >>> > >>> "Packages should be of the minimum necessary size" is subject to > >>> interpretation. And in practice, there is an issue with e.g. packages > >>> that "bundle" big third-party libraries. There are also packages that > >>> require downloading precompiled code, JARs... at installation time. > >>> > >>>> That said, there are exceptions such as very large datasets (e.g., as > distributed by Bioconductor) which are orders of magnitude larger than what > is sustainable. I agree that it would be nice to have a mechanism for > specifying such sources. So yes, I like the idea, but I'd like to see more > real use cases to justify the effort. > >>> > >>> "More real use cases" like in "more use cases" or like in "the > >>> previous ones are not real ones"? :) > >>> > >>>> The issue with any online downloads, though, is that there is no > guarantee of availability - which is real issue for reproducibility. So one > could argue that if such external sources are required then they should be > on a well-defined, independent, permanent storage such as Zenodo. This > could be a matter of policy as opposed to the technical side above which > would be adding such support to R CMD INSTALL. > >>> > >>> Not necessarily. If the package declares the additional sources in the > >>> DESCRIPTION (probably with hashes), that's a big improvement over the > >>> current state of things, in which basically we don't know what the > >>> package tries download, then it may fail, and finally there's no > >>> guarantee that it's what the author intended in the first place. > >>> > >>> But on top of this, R could add a CMD to download those, and then some > >>> lookaside storage could be used on CRAN. This is e.g. how RPM > >>> packaging works: the spec declares all the sources, they are > >>> downloaded once, hashed and stored in a lookaside cache. Then package > >>> building doesn't need general Internet connectivity, just access to > >>> the cache. > >>> > >>> Iñaki > >>> > >>>> > >>>> Cheers, > >>>> Simon > >>>> > >>>> > >>>>> On Sep 24, 2022, at 3:22 AM, Iñaki Ucar <iu...@fedoraproject.org> > wrote: > >>>>> > >>>>> Hi all, > >>>>> > >>>>> I'd like to open this debate here, because IMO this is a big issue. > >>>>> Many packages do this for various reasons, some more legitimate than > >>>>> others, but I think that this shouldn't be allowed, because it > >>>>> basically means that installation fails in a machine without Internet > >>>>> access (which happens e.g. in Linux distro builders for security > >>>>> reasons). > >>>>> > >>>>> Now, what if connection is suppressed during package load? There are > >>>>> basically three use cases out there: > >>>>> > >>>>> (1) The package requires additional files for the installation (e.g. > >>>>> the source code of an external library) that cannot be bundled into > >>>>> the package due to CRAN restrictions (size). > >>>>> (2) The package requires additional files for using it (e.g., > >>>>> datasets, a JAR...) that cannot be bundled into the package due to > >>>>> CRAN restrictions (size). > >>>>> (3) Other spurious reasons (e.g. the maintainer decided that package > >>>>> load was a good place to check an online service availability, etc.). > >>>>> > >>>>> Again IMO, (3) shouldn't be allowed in any case; (2) should be a > >>>>> separate function that the user actively calls to download the files, > >>>>> and those files should be placed into the user dir, and (3) is the > >>>>> only legitimate use, but then other mechanism should be provided to > >>>>> avoid connections during package load. > >>>>> > >>>>> My proposal to support (3) would be to add a new field in the > >>>>> DESCRIPTION, "Additional_sources", which would be a comma separated > >>>>> list of additional resources to download during R CMD INSTALL. Those > >>>>> sources would be downloaded by R CMD INSTALL if not provided via an > >>>>> option (to support offline installations), and would be placed in a > >>>>> predefined place for the package to find and configure them (via an > >>>>> environment variable or in a predefined subdirectory). > >>>>> > >>>>> This proposal has several advantages. Apart from the obvious one > >>>>> (Internet access during package load can be limited without losing > >>>>> current functionalities), it gives more visibility to the resources > >>>>> that packages are using during the installation phase, and thus makes > >>>>> those installations more reproducible and more secure. > >>>>> > >>>>> Best, > >>>>> -- > >>>>> Iñaki Úcar > >>>>> > >>>>> ______________________________________________ > >>>>> R-devel@r-project.org mailing list > >>>>> https://stat.ethz.ch/mailman/listinfo/r-devel > >>>>> > >>>> > >>> > >>> > >>> -- > >>> Iñaki Úcar > >> > > > > > > -- > > Iñaki Úcar > > > > ______________________________________________ > 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
