[R-pkg-devel] Package submission failed with two warnings

Fri May 15 23:57:09 CEST 2020

The reason is that CRAN does not have an R-devel binary for
data.table, and because of this install.packages() decides not to
install it. Here is a workaround:
https://github.com/r-hub/rhub/issues/367#issuecomment-621757715

Gabor

On Fri, May 15, 2020 at 10:50 PM Max Turgeon <Max.Turgeon using umanitoba.ca> wrote:
>
> Hi Farshad,
>
>
> The error you get when compiling your vignette gives us a hint:
>
> Error: processing vignette 'Rpvt.Rmd' failed with diagnostics:
> package or namespace load failed for 'ggpubr' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
>  there is no package called 'data.table'
>
> There is a long chain of dependencies here: if I write A -> B to say that package A lists package B as an Import (and therefore package B is loaded when package A is attached), we have
>
>
> ggpubr -> rstatix -> car -> rio -> data.table.
>
>
> I think the issue is that, since you list ggpubr in "Suggests", there's never a check that all its dependencies (and their dependencies etc) are installed, and therefore data.table was not installed before checking your package. (But I'm not sure exactly why ggpubr is installed but not all the dependencies.)
>
>
> A solution would be to make your whole vignette fail "gracefully" when ggpubr isn't attached properly. Which is good practice anyway.
>
>
> Max Turgeon
> Assistant Professor
> Department of Statistics
> Department of Computer Science
> University of Manitoba
> maxturgeon.ca<http://maxturgeon.ca>
>
>
> ________________________________
> From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of FARSHAD TABASINEJAD <farshad.tabasinejad using susaenergy.com>
> Sent: May 15, 2020 4:11:36 PM
> To: Duncan Murdoch; r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Package submission failed with two warnings
>
> ********************************************************
> Caution: This message was sent from outside the University of Manitoba.
> ********************************************************
>
> Hi Duncan,
>
> I changed the version, recreated the package, and then tested it with the rhub::check_for_cran(). The function failed to create a summary for all the platform results together, however individual results are available in the following links.
>
>
> https://builder.r-hub.io/status/Rpvt_0.1.1.tar.gz-5e89b16f7bfb420ebe310a57eb8357b3
> https://artifacts.r-hub.io/Rpvt_0.1.1.tar.gz-5e89b16f7bfb420ebe310a57eb8357b3/
> https://artifacts.r-hub.io/Rpvt_0.1.1.tar.gz-2ee682316e0f4bc7b09faf7a9e46b670/
> https://builder.r-hub.io/status/original/Rpvt_0.1.1.tar.gz-08fc2dbd591f4d80b2e0049a7c8db8b8
>
> you can also find the source code in the following link:
> https://github.com/susaenergy/Rpvt
>
> Thank you for the help!
>
> Farshad
>
>
> From: Duncan Murdoch
> Sent: Friday, May 15, 2020 9:28 AM
> To: FARSHAD TABASINEJAD; r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Package submission failed with two warnings
>
> For your first warning, see the CRAN policy:  "Updates to
> previously-published packages must have an increased version. Increasing
> the version number at each submission reduces confusion so is preferred
> even when a previous submission was not accepted."
>
> For the second, it's hard to say what's happening.  Is your package
> online somewhere so we could try it on different machines?
>
> Duncan Murdoch
>
> On 15/05/2020 12:46 a.m., FARSHAD TABASINEJAD wrote:
> > Dear R-package-devel experts,
> >
> > This is the first time I’m writing to this platform about a package I recently submitted to CRAN (my first package).
> > While the package is already available on CRAN, I still must fix a few warnings and one error as reported on the CRAN package check results page:
> > https://cran.r-project.org/web/checks/check_results_Rpvt.html
> >
> > I recently resubmitted a modified version of the package to CRAN, however, it didn’t pass the automatic incoming checks.
> >
> > Windows:  https://win-builder.r-project.org/incoming_pretest/Rpvt_0.1.0_20200512_051950/Windows/00check.log
> > Status: 1 WARNING
> >
> > Debian:  https://win-builder.r-project.org/incoming_pretest/Rpvt_0.1.0_20200512_051950/Debian/00check.log
> > Status: 2 WARNINGs
> >
> >
> > 1) The first warning that appears on both Windows and Debian results is “Insufficient package version (submitted: 0.1.0, existing: 0.1.0)”.
> >
> > Since the package is conditionally available on CRAN, do I need to modify the package version to 0.1.1 to get rid of this warning?
> > Is there any way to fix this problem with the current version of the package(0.1.0)?
> >
> > 2) The second problem appears on the Debian test results:
> >
> >      * checking re-building of vignette outputs ... [8s/8s] WARNING
> >
> >      Error(s) in re-building vignettes:
> >      ...
> >      --- re-building ‘Rpvt.Rmd’ using rmarkdown
> >
> >      pandoc-citeproc: Error in $: Incompatible API versions: encoded with [1,20] but attempted to decode with [1,17,5,4].
> >
> >      CallStack (from HasCallStack):
> >      error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4 5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON
> >
> >      Error running filter /usr/bin/pandoc-citeproc:
> >
> >      Filter returned error status 1
> >      Error: processing vignette 'Rpvt.Rmd' failed with diagnostics:
> >      pandoc document conversion failed with error 83 ---
> >      failed re-building ‘Rpvt.Rmd’
> >
> >      SUMMARY: processing the following file failed:
> >      ‘Rpvt.Rmd’
> >
> >      Error: Vignette re-building failed.
> >      Execution halted
> >
> > I’ve created this package on a Windows operating system with no problem in creating the ‘Rpvt.Rmd’ file as is the case with the CRAN tests on x86_64-w64-mingw32 (64-bit).
> > Why does it fail to create the “Rpvt.Rmd” file on x86_64-pc-linux-gnu (Debian)? Is this something related to the citation style of the library.bib file that I’ve used in my vignettes folder? It is the “apa-6th-edition.csl” file downloaded from https://raw.githubusercontent.com/citation-style-language/styles/master/apa-6th-edition.csl
> >
> > Thank you in advance!
> >
> > Regards,
> > Farshad
> >
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>
>
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