[R-pkg-devel] Proper CRAN way - How to handle dependency of java jar file?

On 13 Jul 2020, at 08:17, Ma?lle SALMON <maelle.salmon at 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

Ma?lle.

Den tisdag 23 juni 2020 14:56:30 CEST, Rainer M Krug <rainer at krugs.de> skrev: 





Thanks Duncan.

On 23 Jun 2020, at 14:35, Duncan Murdoch <murdoch.duncan at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland

Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at krugs.de
Skype:    RMkrug

PGP: 0x0F52F982




    [[alternative HTML version deleted]]

On 13 Jul 2020, at 08:17, Ma?lle SALMON <maelle.salmon at 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

Ma?lle.

Den tisdag 23 juni 2020 14:56:30 CEST, Rainer M Krug <rainer at krugs.de> skrev: 





Thanks Duncan.

On 23 Jun 2020, at 14:35, Duncan Murdoch <murdoch.duncan at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland

Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
        Rainer at krugs.de
Skype:    RMkrug

PGP: 0x0F52F982




    [[alternative HTML version deleted]]

On 13 Jul 2020, at 11:31, Paul SAVARY <paul.savary at 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, ...).

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.

I hope it can help
Cheers

Paul Savary - PhD Student
UMR 6049 Th?MA (Besan?on), UMR 6282 Biog?osciences (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 at krugs.de>
?: "Ma?lle SALMON" <maelle.salmon at yahoo.se>
Cc: "r-package-devel" <r-package-devel at r-project.org>
Envoy?: Lundi 13 Juillet 2020 11:15:10
Objet: Re: [R-pkg-devel]  Proper CRAN way - How to handle dependency of java jar file?

Thanks Ma?lle - that is exactly what I am doing at the moment.

Cheers,

Rainer

On 13 Jul 2020, at 08:17, Ma?lle SALMON <maelle.salmon at 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

Ma?lle.

Den tisdag 23 juni 2020 14:56:30 CEST, Rainer M Krug <rainer at krugs.de> skrev: 





Thanks Duncan.

On 23 Jun 2020, at 14:35, Duncan Murdoch <murdoch.duncan at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
       Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland
Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
       Rainer at 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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland

Office:    +41 (0)44 635 47 64
Cell:          +41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
       Rainer at krugs.de
Skype:    RMkrug

PGP: 0x0F52F982




   [[alternative HTML version deleted]]

--
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 Z?rich
Office Y34-J-74
Winterthurerstrasse 190
8075 Z?rich
Switzerland

Office:	+41 (0)44 635 47 64
Cell:       	+41 (0)78 630 66 57
email:      Rainer.Krug at uzh.ch
		Rainer at krugs.de
Skype:     RMkrug

PGP: 0x0F52F982




	[[alternative HTML version deleted]]