Re: [R-pkg-devel] Using ggplot2 within another package
Hi Kevin,
I was faced to the same problem and I used 'aes_string()' instead of 'aes()'.
You can then just write the name of the columns containing the data to plot as
character strings.
Example:
myPlot <- function(myData, ...) {
# get ready
ggplot(myData, aes_string(x = "myX", y = "myY")) +
# add my decorations
theme_bw()
}
It is probably already the case for your function but you need to include #'
@import ggplot2 in your function preamble (if I am not wrong).
Kind regards
Paul
- Mail original -
De: "Kevin R. Coombes"
À: "r-package-devel"
Envoyé: Jeudi 22 Avril 2021 22:28:55
Objet: [R-pkg-devel] Using ggplot2 within another package
Hi,
I'm trying to help clean up an R package for someone else to submit to
CRAN. He has used ggplot2 to implement a plotting function for the kinds
of things that his packages generates. His plotting routine basically
looks like (after changing names to protect the innocent):
myPlot <- fucntion(myData, ...) {
# get ready
ggplot(myData, aes(x = myX, y = myY)) +
# add my decorations
theme_bw()
}
Of course, "R CMD check --as-cran" complains that there is no global
binding for "myX" or "myY" since they are columns defined in the
data.frame "myData".
What is the best way to work around this issue?
Of course, dinosaurs like myself might be tempted to suggest just using
plain old "plot", so I don't need to see those suggestions.
Do I just ignore the usual ggplot conventions and write "myData$myX"
inside "aes" in order to appease the CRAN checker? Or is there some
tidy-er way to solve this problem?
Thanks,
Kevin
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[R-pkg-devel] Error vignette rebuilding and package imports when re-submitting package
Hello, I'm having trouble re-submitting a package (graph4lg). - With r-patched_osx, vignette rebuilding fails with the following message : checking re-building of vignette outputs ... [12s/16s] WARNING Error(s) in re-building vignettes: ... --- re-building ‘vignette_graph4lg.Rmd’ using rmarkdown dyld: lazy symbol binding failed: Symbol not found: chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: chkstk_darwin Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib Error: processing vignette 'vignette_graph4lg.Rmd' failed with diagnostics: pandoc document conversion failed with error 6 --- failed re-building ‘vignette_graph4lg.Rmd’ SUMMARY: processing the following file failed: ‘vignette_graph4lg.Rmd’ Error: Vignette re-building failed. Execution halted - Besides, although I removed some unused packages from the imports in DESCRIPTION file, I still obtain this message : checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’ All declared Imports should be used. Except Rdpack which is needed to build the vignette, I removed these packages. Finally, although I submit version 0.4.0, I receive checking errors relative to version 0.3.0. I thank you in advance for your feedbacks. Regards Paul Savary [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Warning R-hub Windows Server 2008 : qpdf needed
Hello, I'm having trouble checking a package (graph4lg). With devtools::check_rhub(), I obtain a warning message on Windows Server 2008 *checking data fro ASCII and uncompressed saves ... OK WARNING 'qpdf' is needed for checks on size reduction of PDFs I checked that qpdf is intalled. It is, because I have Rtools. Rtools is in my environment path That's the first time I obtain this message, although I checked my package several times on Rhub. I do not obtain similar messages with other checking platforms. I thank you in advance Regards Paul Savary [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] (SOLVED) Warning R-hub Windows Server 2008 : qpdf needed
Hi, Here is the build log showing this warning message: https://builder.r-hub.io/status/graph4lg_0.5.0.tar.gz-31e8935d0c724c4b9d6986f31eeff357 I have just tried again and this warning message does not show up anymore. I thank you Gabor for your help. (new build log: https://builder.r-hub.io/status/graph4lg_0.5.0.tar.gz-6e69d658b38242d0a81efaae5d942be9) Best regards Paul - Mail original - De: "Gábor Csárdi" À: "Paul SAVARY" Cc: "r-package-devel" Envoyé: Mercredi 22 Avril 2020 18:54:32 Objet: Re: [R-pkg-devel] Warning R-hub Windows Server 2008 : qpdf needed Hi, which R version was this? Can you point to a build log? qpdf is definitely installed on R-hub's Windows machines, and it is even on the PATH. Maybe the new toolchain did not find it, I have copied it to a better place now, please try again. Best, Gabor On Wed, Apr 22, 2020 at 5:44 PM Paul SAVARY wrote: > > Hello, > > I'm having trouble checking a package (graph4lg). > > With devtools::check_rhub(), I obtain a warning message on Windows Server 2008 > > *checking data fro ASCII and uncompressed saves ... OK > WARNING > 'qpdf' is needed for checks on size reduction of PDFs > > I checked that qpdf is intalled. It is, because I have Rtools. > Rtools is in my environment path > > That's the first time I obtain this message, although I checked my package > several times on Rhub. > I do not obtain similar messages with other checking platforms. > > I thank you in advance > Regards > Paul Savary > > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Making possible the use of external java codes by downloading it
Hello everyone, I would like to include external java codes (.jar files) to a package in order to speed up some computations. However, this would increase the package size above 5 Mb and this code would not be working for users without java installation. Instead, I could include a default parameter in the function calling another R package making the same computation but more slowly. It would be best for users without java on their computer. Besides, I could allow users to download the external java code from a stable url, and include in the R function all the arguments to launch this java code (wrapper for the java code). When downloaded, the jar file should be copied directly into the extdata directory in the user computer if possible. Does it seem feasible to you? Many thanks Regards Paul __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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, ...).
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,
&g
