[R-pkg-devel] URLencode at DESCRIPTION file and citation()

[Amanda Rehbein]

Dear Maëlle and Jeff,

Thank you so much!

Best,
Amanda

Em ter., 3 de nov. de 2020 às 10:10, Jeff Newmiller <
jdnewmil using dcn.davis.ca.us> escreveu:

> Section 2.1 of the Writing R Extensions manual points out that percent
> symbols must (practically) always be escaped in Rd files. This includes
> within URLs.
>
> On November 3, 2020 2:08:05 AM PST, "Maëlle SALMON via R-package-devel" <
> r-package-devel using r-project.org> wrote:
> >Hello,
> >
> >1) I found (via GitHub search for DOIs in DESCRIPTION
> >files
> https://github.com/search?q=org%3Acran+%3Cdoi+user%3Acran+filename%3ADESCRIPTION&type=Code&ref=advsearch&l=&l=
> )
> >a package with an URL-encoded DOI see
> >
> https://github.com/cran/clust.bin.pair/blob/e464ac7e5d094bffd25b7c4cbba67820b60f1cc1/DESCRIPTION
> >and the resulting CRAN page
> >https://cran.r-project.org/web/packages/clust.bin.pair/index.html So I
> >think you are right to use URL encoding.
> >
> >I can reproduce the problem you get with the roxygen2-generated
> >package-level manual page. The problem is that when going from Rd to
> >HTML, the parts after "%" are ignored indeed. I'm not sure at what
> >level this should be fixed. I opened an issue in roxygen2
> >https://github.com/r-lib/roxygen2/issues/1164 I hope others will have
> >more useful answers. :-)
> >
> >2) For that aspect I looked into a CITATION file I knew
> >https://github.com/ropensci/bomrang/blob/master/inst/CITATION
> >
> >For finding the version it uses meta$Version. So your CITATION could
> >e.g. become
> >
> >citHeader("To cite raytracing in publications use at least the first,
> >if not both:")
> >
> >year <- sub("-.*", "", meta$Date)
> >note <- sprintf("R package version %s", meta$Version)
> >
> >citEntry(entry = "manual",
> >   title          = "raytracing: An R package for identification and
> >tracking the atmospheric Rossby waves",
> >   author         = personList(c(person("Amanda", "Rehbein"),
> >                    person("Tercio", "Ambrizzi"),
> >                    person("Sergio", "Ibarra-Espinosa"),
> >                    person("Livia M. M.", "Dutra"))),
> >   year           = year,
> >   url            = "https://github.com/salvatirehbein/raytracing",
> >   note          = note,
> >   textVersion  =
> >   paste0("Rehbein, A., Ambrizzi, T., Ibarra-Espinosa, S., Dutra, L. M.
> >M.: Rossby Wave Ray Tracing v", meta$Version, ".
> >https://github.com/salvatirehbein/raytracing, ", year,".")
> >)
> >
> >citation(auto = meta)
> >
> >citFooter("Thanks")
> >
> >Maëlle.
> >
> >
> >Den söndag 1 november 2020 21:29:54 CET, Amanda Rehbein
> ><amanda.rehbein using usp.br> skrev:
> >
> >
> >
> >
> >
> >Dear R-Devs,
> >
> >I was wondering if someone could please help me to with two errors when
> >submitting a package to CRAN.
> >
> >1) At the DESCRIPTION file I added some DOI's with curled brackets "<>"
> >inside the "<>" (e.g.
> ><doi:10.1175/1520-0469(1981)038<1179:TSLROA>2.0.CO;2>).
> >I tried URLencode() the string in R and copy/paste the output into
> >the DESCRIPTION file, like this:
> ><doi:10.1175/1520-0469(1981)038%3C1179:TSLROA%3E2.0.CO;2>. But when I
> >load,
> >build, check, etc, and ?raytracing the DOI does not appear correctly.
> >Everything after the first "%" disappeared and obviously, the DOI
> >doesn't
> >work anymore.
> >
> >
> >2) I have a CITATION file at the sub-directory ins. Its content is like
> >this:
> >
> >citHeader("To cite raytracing in publications use one of below:")
> >
> >citEntry(entry = "manual",
> >  title          = "Atmospheric Rossby waves identification and
> >tracking
> >with a raytracing numerical model",
> >  author        = personList(c(person("Amanda", "Rehbein"),
> >                    person("Tercio", "Ambrizzi"),
> >                    person("Sergio", "Ibarra-Espinosa"),
> >                    person("Livia M. M.", "Dutra"))),
> >  year          = "2020",
> >  url            = "https://github.com/salvatirehbein/raytracing",
> >
> >  textVersion  =
> >  paste0("Rehbein, A., Ambrizzi, T., Ibarra-Espinosa, S., Dutra, L. M.
> >M.:
> >Atmospheric Rossby waves identification and tracking with a raytracing
> >numerical model ", packageVersion("raytracing"), ".
> >https://github.com/salvatirehbein/raytracing, 2020.")
> >)
> >
> >It passes all checks and gives a-okay citation when I type
> >citation("raytracing"). However, it fails in the CRAN tests with the
> >following error message.
> >
> >Reading CITATION file fails with
> >    there is no package called 'raytracing'
> >  when package is not installed.
> >
> >I will be very thankful for any help with this! Best,
> >Amanda
> >
> >    [[alternative HTML version deleted]]
> >
> >______________________________________________
> >R-package-devel using r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> >______________________________________________
> >R-package-devel using r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> --
> Sent from my phone. Please excuse my brevity.
>


-- 
*Amanda Rehbein*
MSc Atmospheric Sciences
Department of Atmospheric Sciences,
University of São Paulo
Group of Climate Studies (GrEC) | http://www.grec.iag.usp.br
Rua do Matão, 1226 - Cidade Universitária, São Paulo - SP - Brazil -
05508-090
Skype: amanda_rehbein1 | Phone: +55 11 3091-2852

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