[R-pkg-devel] Proper CRAN way - How to handle dependency of java jar file?
Rainer M Krug
R@|ner @end|ng |rom krug@@de
Mon Jul 13 13:14:01 CEST 2020
> On 13 Jul 2020, at 11:31, Paul SAVARY <paul.savary using univ-fcomte.fr> wrote:
>
> Thanks you too.
>
> That is also what I am doing. Note that I am downloading jar files into a directory created in rappdirs::user_data_dir() using the command download.file(url, ...).
Jup - exactly.
>
> If I do not specify 'mode='wb'' in download.file() on a Windows OS, downloaded jar file is corrupted and cannot be used because a text file is created in which \n are converted into \r\n, which does not make sens for a binary file.
Yes - the `mode = “wb”` bit me as well - developing on MacOS, testing on travis on GitHub with Linux and Mac,, and what did I get, a corrupt jar on windows.
Thanks,
Rainer
>
> I hope it can help
> Cheers
>
> Paul Savary - PhD Student
> UMR 6049 ThéMA (Besançon), UMR 6282 Biogéosciences (Dijon), ARP-Astrance (Paris)
> Phone number : +33.6.30.97.34.27
> Research topics: population genetics, landscape ecology, graph theory, spatial statistics
>
> ----- Mail original -----
> De: "Rainer M Krug" <Rainer using krugs.de>
> À: "Maëlle SALMON" <maelle.salmon using yahoo.se>
> Cc: "r-package-devel" <r-package-devel using r-project.org>
> Envoyé: Lundi 13 Juillet 2020 11:15:10
> Objet: Re: [R-pkg-devel] Proper CRAN way - How to handle dependency of java jar file?
>
> Thanks Maëlle - that is exactly what I am doing at the moment.
>
> Cheers,
>
> Rainer
>
>
>> On 13 Jul 2020, at 08:17, Maëlle SALMON <maelle.salmon using yahoo.se> wrote:
>>
>> Regarding where to save the jar file, you might be interested in "app dirs" (via tools::R_user_dir() in R from 4.0, the rappdirs package, the hoardr package) cf https://blog.r-hub.io/2020/03/12/user-preferences/#not-so-temporary-files3
>>
>> Maëlle.
>>
>> Den tisdag 23 juni 2020 14:56:30 CEST, Rainer M Krug <rainer using krugs.de> skrev:
>>
>>
>>
>>
>>
>> Thanks Duncan.
>>
>>> On 23 Jun 2020, at 14:35, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>>>
>>> Your assumption that .jar files are not allowed is wrong: a number of packages contain them: rscala, J4R, Rbgs, bartMachine, OpenStreetMap, ... There's a specific mention about how to include them in the CRAN policy document:
>>
>> That’s good to know.
>>
>>>
>>> "For Java .class and .jar files, the sources should be in a top-level java directory in the source package (or that directory should explain how they can be obtained)."
>>
>> So a tet file in the inst/jar directory giving the link to the GitHub repo would be fine in this case?
>>
>>>
>>> If you still decide not to include your .jar file (maybe it is too big, for example),
>>
>>
>> I guess it would be stretching it a bit, as the jar file is 8.2 MB, and plantuml has regular continuous updates, so I would prefer to keep it dynamic.
>>
>>
>>> then I think your option 1 is unusable for those people who can't write to the library location because of permission problems. (Admin privileges are often necessary to install packages in the main library.) Generally I think everyone can install packages somewhere, but users do really get confused when they have multiple library locations, possibly each containing a different version of a package.
>>
>> So the suggested option would be to have a function, which
>> 1) ask the user to create a directory in the home folder
>> 2) download the jar file into that directory or, when no permission is granted, into the tmpdir()
>>
>> Thanks, no major changes necessary for that,
>>
>> Rainer
>>
>>
>>>
>>> Duncan Murdoch
>>>
>>> On 23/06/2020 8:18 a.m., Rainer M Krug wrote:
>>>> Hi
>>>> I have a package called `plantuml` (https://github.com/rkrug/plantuml) which converts plantuml code to UML graphs. It uses for this the java program https://plantuml.com which is Open Source.
>>>> As it is not allowed to distribute a binary with an R package, I use the approach of a function which downloads the jar file into the directory `system.file("jar/plantuml.jar", package = "plantuml”)`.
>>>> This works nicely, and at the moment, the function is called automatically before the plantuml.jar is used.
>>>> Now I would like to submit the package to CRAN. I can’t find the guidelines anymore, so I am asking here:
>>>> What is the appropriate way of handling this?
>>>> I can think of a at least two ways of making it obvious to the user, that a binary is downloaded:
>>>> 1) if the file plantuml.jar is not present, ask the user to run the function `updatePlantumlJar()` which downloads the jar to the original location in the package directory
>>>> 2) tell the user to download the file manually and to put it somewhere, where the package will find it
>>>> I would prefer the first version, as the plantuml.jar would be in the package directory, where usually nobody but the package is doing stuff.
>>>> Any suggestions on how I could make this “CRAN conform”?
>>>> Thanks a lot,
>>>> Rainer
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>> Orcid ID: 0000-0002-7490-0066
>>>> Department of Evolutionary Biology and Environmental Studies
>>>> University of Zürich
>>>> Office Y34-J-74
>>>> Winterthurerstrasse 190
>>>> 8075 Zürich
>>>> Switzerland
>>>> Office: +41 (0)44 635 47 64
>>>> Cell: +41 (0)78 630 66 57
>>>> email: Rainer.Krug using uzh.ch
>>>> Rainer using krugs.de
>>>> Skype: RMkrug
>>>> PGP: 0x0F52F982
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>> Orcid ID: 0000-0002-7490-0066
>>>> Department of Evolutionary Biology and Environmental Studies
>>>> University of Zürich
>>>> Office Y34-J-74
>>>> Winterthurerstrasse 190
>>>> 8075 Zürich
>>>> Switzerland
>>>> Office: +41 (0)44 635 47 64
>>>> Cell: +41 (0)78 630 66 57
>>>> email: Rainer.Krug using uzh.ch
>>>> Rainer using krugs.de
>>>> Skype: RMkrug
>>>> PGP: 0x0F52F982
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>
>> Orcid ID: 0000-0002-7490-0066
>>
>> Department of Evolutionary Biology and Environmental Studies
>> University of Zürich
>> Office Y34-J-74
>> Winterthurerstrasse 190
>> 8075 Zürich
>> Switzerland
>>
>> Office: +41 (0)44 635 47 64
>> Cell: +41 (0)78 630 66 57
>> email: Rainer.Krug using uzh.ch
>> Rainer using krugs.de
>> Skype: RMkrug
>>
>> PGP: 0x0F52F982
>>
>>
>>
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>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>
> Orcid ID: 0000-0002-7490-0066
>
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 Zürich
> Switzerland
>
> Office: +41 (0)44 635 47 64
> Cell: +41 (0)78 630 66 57
> email: Rainer.Krug using uzh.ch
> Rainer using krugs.de
> Skype: RMkrug
>
> PGP: 0x0F52F982
>
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> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Orcid ID: 0000-0002-7490-0066
Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland
Office: +41 (0)44 635 47 64
Cell: +41 (0)78 630 66 57
email: Rainer.Krug using uzh.ch
Rainer using krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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