Re: [R-pkg-devel] GitHub Actions - CI for pkg that depends on Java/rJava (Windows issue)

[Peter Meissner]

Hey,

Very interesting. I just made rJava work for Linux:

https://github.com/petermeissner/kafkaesque/blob/master/.github/workflows/tests.yml

Best, Peter




Blätte, Andreas  schrieb am Fr. 22. Jan. 2021
um 17:38:

> Dear colleagues,
>
> as recommended by rOpenSci (see
> https://ropensci.org/technotes/2020/11/19/moving-away-travis/) , I am
> moving to GitHub Actions for the CI for my R packages.
>
> My test case is the “bignlp” package I currently develop (
> https://github.com/https://github.com/PolMine/bignlpPolMine/bignlp). It
> is an interface to use the CoreNLP tools which are written in Java. (To
> explain: Unlike other existing packages that interface to CoreNLP, my
> intent is to make full use of Java multithreading.)
>
> Having used `usethis::use_github_action_check_full(),  CI works almost out
> of the box on the Ubuntu and macOS test environments. But I have a problem
> to ensure that rJava can find Java. The error I see (Windows, both
> architectures):
>
> Error: Error: R CMD check found ERRORs
> Execution halted
> .onLoad failed in loadNamespace() for 'rJava', details:
> call: inDL(x, as.logical(local), as.logical(now), ...)
> error: unable to load shared object
> 'D:/a/_temp/Library/rJava/libs/i386/rJava.dll':
> LoadLibrary failure: %1 is not a valid Win32 application.
>
> (For the full log, see: https://github.com/PolMine/bignlp/runs/1749892186)
>
> My first take was to add a step that would make sure that Java is present
> to .github/workflows/R-CMD-check.yaml:
>
>   - name: Install Java
> uses: actions/setup-java@v1
> with:
>   java-version: '8'
>   java-package: jdk
>
> But that only breaks things CI on Linux without having any change on
> Windows.
>
> I have consulted the manual ‘GitHub Actions with R’ (
> https://ropenscilabs.github.io/actions_sandbox/), but it does not address
> Java issues. I tried to find some R package on GitHub that would have rJava
> as a dependency and that uses GitHub Actions for CI – without success.
>
> This is why I’d like to query your experience: How I can make GitHub
> Actions work on Windows for the scenario of a package that depends on
> Java/rJava. Many thanks in advance!
>
> Kind regards
> Andreas (Blätte)
>
> --
> Prof. Dr. Andreas Blätte
> Professor of Public Policy and Regional Politics
> University of Duisburg-Essen
>
>
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>
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[R-pkg-devel] Publishing Java Wrappers The Right Way

[Peter Meissner]

Hey Everyone,

I have an R-package that wraps some Java code.
The dependencies needed are around 10MB.

Thus I split the package into 2 packages. One providing only the
dependencies:

https://github.com/petermeissner/kafkaesquejars

... and one providing the actual code:

https://github.com/petermeissner/kafkaesque


I submitted the first package to CRAN and it came back stating that:
"Package has FOSS license, installs .class/.jar but has no 'java' directory.
"

Of course there is no java directory because the package does not contain
any code, just dependencies
and those are placed in ./inst/java.

Now what to do? In response I added  ./java/sources.md file and listed all
dependencies as well as URLs where
the source code of those dependencies can be downloaded.

Is this correct? Do I miss something else?


I really would appreciate some guidance on doing this right.

Best, Peter

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Re: [R-pkg-devel] CRAN-Policies

[Peter Meissner]

Hey,

thanks for taking the time to reply - I will start working on my changes
requests then.

Best, Peter




Am Do., 23. Apr. 2020 um 20:51 Uhr schrieb Duncan Murdoch <
murdoch.dun...@gmail.com>:

> On 23/04/2020 2:34 p.m., Peter Meissner wrote:
> > Hello Everyone,
> >
> > some weeks back I already wrote to CRAN but got no response. So, I post
> my
> > question here seeking for advice.
> >
> > I am trying to publish a package to CRAN. I got rejected once with some
> > minor change requests. I implemented them and submitted again. This time
> I
> > got a whole array of change requests.
> >
> > The problem is, I am confused since none of the requests is mentioned
> > anywhere in CRAN policies. So, are those mere suggestions? Are these
> common
> > policy now? Has everyone to implement them? How should I proceed?
>
> I'd say that the changes being requested are all things stated in the
> Writing R Extensions manual, so this falls under the blanket statement
> in the policy that "CRAN hosts packages of publication quality and is
> not a development platform."
>
> > (In general, I have no problem with complying with CRAN policies, but I
> am
> > not sure if these are actually common requirements now or not.)
>
> I'd guess the requests will vary depending on who the reviewer is and
> what their mood is, but if you ignore their requests, you're not going
> to put them in a better mood.
>
> Duncan Murdoch
>
> >
> > Copy of the change requests:
> >
> > * quote >>>> **
> > Please add \value to all .Rd files for exported functions and explain
> > the functions results in the documentation.
> > f.i.: time_stamp.Rd
> > If a function does not return a value, please document that too, e.g.
> > \value{None}.
> >
> > The \description tag in the .Rd files should be one or two sentences on
> > how the function works and what it's good for. Don't just repeat the
> > function name.
> > F.i.: stats_modus_multi.Rd
> >
> > An .Rd file title should:
> > - be capitalized
> > - not end in a period
> > - be at most 65 characters long
> > - exist and stand alone (there must be exactly one title)
> > Please adjust to these standards and again don't simply repeat the name.
> >
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-functions
> > F.i.: stats_modus_multi.Rd
> >
> > Please fix and resubmit, and document what was changed in the submission
> > comments.
> > * <<<< quote **
> >
> >
> > Best, Peter
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>

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[R-pkg-devel] CRAN-Policies

[Peter Meissner]

Hello Everyone,

some weeks back I already wrote to CRAN but got no response. So, I post my
question here seeking for advice.

I am trying to publish a package to CRAN. I got rejected once with some
minor change requests. I implemented them and submitted again. This time I
got a whole array of change requests.

The problem is, I am confused since none of the requests is mentioned
anywhere in CRAN policies. So, are those mere suggestions? Are these common
policy now? Has everyone to implement them? How should I proceed?

(In general, I have no problem with complying with CRAN policies, but I am
not sure if these are actually common requirements now or not.)

Copy of the change requests:

* quote  **
Please add \value to all .Rd files for exported functions and explain
the functions results in the documentation.
f.i.: time_stamp.Rd
If a function does not return a value, please document that too, e.g.
\value{None}.

The \description tag in the .Rd files should be one or two sentences on
how the function works and what it's good for. Don't just repeat the
function name.
F.i.: stats_modus_multi.Rd

An .Rd file title should:
- be capitalized
- not end in a period
- be at most 65 characters long
- exist and stand alone (there must be exactly one title)
Please adjust to these standards and again don't simply repeat the name.
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Documenting-functions
F.i.: stats_modus_multi.Rd

Please fix and resubmit, and document what was changed in the submission
comments.
*  quote **


Best, Peter

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Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

[Peter Meissner]

Hey,

Maybe webmockr (or something alike) can help:
https://cran.r-project.org/web/packages/webmockr/index.html

Best, Peter

Rainer M Krug  schrieb am Mi., 5. Sep. 2018, 15:38:

> OK - thanks. I will than disable the checks for CRAN.
>
> Thanks,
>
> Rainer
>
>
> > On 5 Sep 2018, at 15:37, Uwe Ligges 
> wrote:
> >
> > You should not run on CRAN. Note that the checks are done almost daily
> oin several platforms, hence the API key is used for about 10 check runs a
> day.
> >
> > Best,
> > Uwe Ligges
> >
> >
> >
> > On 05.09.2018 09:28, Rainer Krug wrote:
> >> Hi
> >> I have a package at GitHub (https://github.com/rkrug/ROriginStamp)
> which I am pre[paring for CRAN.
> >> It creates a trusted timestamp using the API fro OriginStamp (
> https://originstamp.org/home) which requires an API key. Now this API
> should not be made public, as to much traffic through one API key will lead
> to it’s blocking.
> >> I have stored the key encrypted in the travis.yml, and the package
> passes all tests.
> >> But if I send it to CRAN, it would fail the tests, as the api key is
> not in the package itself.
> >> I could disable all tests for CRAN which need the API key, but I think
> it would be better tu run the tests there as well (as an additional check
> to travis).
> >> My question:
> >> Is there a way of storing the API key encrypted, so that only the CRAN
> test servers can decrypt it, or is there another way can steal with this?
> >> Thanks,
> >> Rainer
> >> --
> >> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
> >> University of Zürich
> >> Cell:   +41 (0)78 630 66 57
> >> email:  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)
>
> University of Zürich
>
> Cell:   +41 (0)78 630 66 57
> email:  rai...@krugs.de
> Skype:  RMkrug
>
> PGP: 0x0F52F982
>
>
>
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> R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] new package? - Sports data from transfermarkt.com using rvest

[Peter Meissner]

Hey,

I am not a laywer but their terms are quite explicitly prohibiting
redistribution of their data without written consent.

Now you might build a package that does not collect, store and
redistributes the data but only allows to access the data provided there
'live' via some convenience functions. But I don't really know if that
argument actually is valid in any legal sense.

To be on the safe side, you probably should contact them.

Best, Peter


Am 24.01.2018 12:13 nachm. schrieb "Thierry Onkelinx" <
thierry.onkel...@inbo.be>:

> Dear Daniel,
>
> First of all you need to make sure that the licence of
> transfermarkt.com allows the usage that you have intended. If that is
> not clear from their website, then you should contact them rather than
> us.
>
> CRAN has several packages to assists in downloading data from online
> sources. But the source has to allow that kind of usage.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
> 
> ///
> To call in the statistician after the experiment is done may be no
> more than asking him to perform a post-mortem examination: he may be
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does
> not ensure that a reasonable answer can be extracted from a given body
> of data. ~ John Tukey
> 
> ///
>
>
>
>
> 2018-01-23 16:27 GMT+01:00 Kehl Dániel :
> > Dear List members,
> >
> > maybe this is not the right place to ask, if that is the case, please
> forward me to the right place.
> > I developed some functions to download and transform football/soccer
> related data from transfermarkt.com.
> > There are plans to create my first package based on these functions and
> of course develop them and add more later. As far as I know there is no API
> to that page, so I am using the rvest package.
> > My question is: is this an OK thing to do? Should I contact
> transfermarkt.com? My german is not perfect (just like my english), this
> is what I've found on thier webpage. Does that mean one can not create a
> package related to that page? Or can't crawl at all? Or just not allowed to
> sell the data? If it is allowed, can one post the package on CRAN at the
> end?
> >
> > Please if any of you have experience in that or just show me where to
> ask, do not hesitate!
> >
> > LEGAL NOTICE
> > © Transfermarkt GmbH & Co. KG 2000-2018
> >
> > All rights reserved.
> >
> > Der Inhalt dieser Website ist urheberrechtlich geschützt. Nachdruck,
> Aufnahme in Online-Dienste, Internet und Vervielfältigung auf Datenträger
> wie CD-ROM, DVD-ROM usw. dürfen, auch auszugsweise, nur nach vorheriger
> schriftlicher Zustimmung durch Transfermarkt erfolgen. Eine kommerzielle
> Weitervermarktung des Inhalts ist untersagt.
> >
> > Transfermarkt haftet nicht für unverlangt eingesandte Inhalte,
> Manuskripte und Fotos. Für Inhalte externer Links und fremde Inhalte
> übernimmt Transfermarkt keine Verantwortung.
> >
> > Thank you for all your insights and/or comments,
> >
> > best regards
> > Daniel
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Dr. KEHL Dániel
> >
> > adjunktus
> >
> >
> >
> >
> >
> > PÉCSI TUDOMÁNYEGYETEM KÖZGAZDASÁGTUDOMÁNYI KAR
> >
> > Közgazdaságtan és Ökonometria Intézet
> >
> > H-7622 Pécs, Rákóczi út 80. | www.ktk.pte.hu
> >
> > +36 72 501 599/ 23144 | ke...@ktk.pte.hu
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > __
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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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