Re: [R-pkg-devel] CRAN submission error package newscatcheR_0.1.0

[Novica Nakov]

Hi,


Something with the ellipsis installation on the check machines seems
> broken, this is something for the CRAN team (which I am a member of) and
> will be fixed.
>

Should I wait for confirmation that the issue is fixed before resubmitting?

Thanks.
novica

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Re: [R-pkg-devel] CRAN submission error package newscatcheR_0.1.0

[Uwe Ligges]

No need to resubmit, we will trigger new checks.

Best,
Uwe Ligges

On 13.07.2020 10:57, Novica Nakov wrote:

Hi,


Something with the ellipsis installation on the check machines seems

broken, this is something for the CRAN team (which I am a member of) and
will be fixed.



Should I wait for confirmation that the issue is fixed before resubmitting?

Thanks.
novica

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

[Rainer M Krug]

Thanks Maëlle - that is exactly what I am doing at the moment.

Cheers,

Rainer


> On 13 Jul 2020, at 08:17, Maëlle SALMON  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  skrev: 
> 
> 
> 
> 
> 
> Thanks Duncan.
> 
>> On 23 Jun 2020, at 14:35, Duncan Murdoch  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: -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.k...@uzh.ch
>>> rai...@krugs.de
>>> Skype:RMkrug
>>> PGP: 0x0F52F982
>>> --
>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
>>> UCT), Dipl. Phys. (Germany)
>>> Orcid ID: -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.k...@uzh.ch
>>> rai...@krugs.de
>>> Skype:RMkrug
>>> PGP: 0x0F52F982
>>> __
>>> R-package-devel@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: -0002-7490-0066
> 
> Department of Evolutionary Biology and Environmental Studies
> University of Zürich
> Office Y34-J-74
> Winterthurerstrasse 190
> 8075 

[R-pkg-devel] Unable to post messages to this group

[Binit Kumar]

Hi Team,
I am unable to post messages to this group and keep getting "waiting for 
moderator" message from bounce email i.e. "R-package-devel 
".
Is there any criteria of sending the message to devel group?


Thanks & Regards,

Binit Kumar



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

[Paul SAVARY]

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 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" 
À: "Maëlle SALMON" 
Cc: "r-package-devel" 
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  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  skrev: 
> 
> 
> 
> 
> 
> Thanks Duncan.
> 
>> On 23 Jun 2020, at 14:35, Duncan Murdoch  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: -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.k...@uzh.ch
>>> rai...@krugs.de
>>> Skype:RMkrug
>>> PGP: 0x0F52F982
>>> --
>>> Rainer M. Krug, PhD (Conservation Ecology, S

[R-pkg-devel] mode='wb' in download.file()

[Berry Boessenkool]

On a related note:

I also need to set mode="wb" to download binary files on Windows in my rdwd 
package.
I'm considering calling download.file() with that mode as the default.
Is there any problem with that, potentially on other OS or for non-binary files?

Feel free to comment here to not crowd the mailing list:
https://github.com/brry/rdwd/issues/20

Thanks,
Berry




From: R-package-devel  on behalf of Paul 
SAVARY 
Sent: Monday, July 13, 2020 11:31
To: Rainer M Krug 
Cc: r-package-devel 
Subject: Re: [R-pkg-devel] Proper CRAN way - How to handle dependency of java 
jar file?

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, ...).


oaded 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

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

[Rainer M Krug]

> On 13 Jul 2020, at 11:31, Paul SAVARY  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" 
> À: "Maëlle SALMON" 
> Cc: "r-package-devel" 
> 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  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  
>> skrev: 
>> 
>> 
>> 
>> 
>> 
>> Thanks Duncan.
>> 
>>> On 23 Jun 2020, at 14:35, Duncan Murdoch  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: 00

Re: [R-pkg-devel] Unable to post messages to this group

[Sarah Goslee]

Clearly you can post messages to this group, since this message was received.

R-package-devel requires that the first time someone posts, their
message is approved by a human. After that first post, they may post
normally. It's not a problem, or anything you've done - this policy
applies to everyone, and cuts down enormously on spam since the
moderators only approve relevant posts. Since your post appeared here,
you've been cleared.

The policy is on the about page where you signed up:

https://stat.ethz.ch/mailman/listinfo/r-package-devel
You have to be a subscriber to the list in order to post any message.
Even then, your first messages are only posted after one manual
moderator approvement.

The moderation team are all volunteers, and sometimes they are busy or
away from the computer, especially on weekends.

Sarah


On Mon, Jul 13, 2020 at 5:28 AM Binit Kumar  wrote:
>
> Hi Team,
> I am unable to post messages to this group and keep getting "waiting for 
> moderator" message from bounce email i.e. "R-package-devel 
> ".
> Is there any criteria of sending the message to devel group?
>
>
> Thanks & Regards,
>
> Binit Kumar
>


--
Sarah Goslee (she/her)
http://www.numberwright.com

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[R-pkg-devel] Failing rhub::check_for_cran() because of data.table

[Chuck Powell]

Hi,

My first posting.  Apologies in advance if I misspeak or am asking a dumb
question.

I maintain a small package on CRAN
https://cran.r-project.org/web/packages/CGPfunctions/index.html

Source is on Github here https://github.com/ibecav/CGPfunctions/

Recently received note I needed to fix my package because of changes to
broom.  Corrections made and everything passes locally.

When I submit to rhub::check_for_cran() however it creates an error in the
development branch
*Build ID:* CGPfunctions_0.6.2.tar.gz-3e48a7f97fa04b64924552dc50b43fd2


with:

#> Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :

1181
#>
Calls: ... loadNamespace -> withRestarts -> withOneRestart ->
doWithOneRestart

1182
#>
Execution halted

1183
#>
there is no package called 'data.table'

1184
#>
ERROR: lazy loading failed for package 'CGPfunctions'

1185
#>
* removing 'C:/Users/USERDFJOuzrklm/R/CGPfunctions'



Looking at data.table on CRAN I see there is no windows binary
Windows binaries: r-devel: not available
,


I don't use any data.table functions, I don't import it, or suggest it or
enhance it it's being pulled in through some dependency in car and/or broom.

Am I okay to submit to CRAN?  Is there a setting I can change?
Obviously data.table exists despite what Rhub is reporting.

Thank you hopefully that is a clear enough description.

Chuck

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