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.turg...@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-boun...@r-project.org> on behalf of > FARSHAD TABASINEJAD <farshad.tabasine...@susaenergy.com> > Sent: May 15, 2020 4:11:36 PM > To: Duncan Murdoch; r-package-devel@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@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > [[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
