Re: [R-pkg-devel] Package submission failed with two warnings
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 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 on behalf of > FARSHAD TABASINEJAD > 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 ve
Re: [R-pkg-devel] Package submission failed with two warnings
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 on behalf of FARSHAD TABASINEJAD 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 d
Re: [R-pkg-devel] Package submission failed with two warnings
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
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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package submission failed with two warnings
On Fri, 15 May 2020 at 10:34, 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)? >From https://cran.r-project.org/web/packages/policies.html: "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." > > 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 > >From https://cran.r-project.org/submit.html "Package authors should make all reasonable efforts to provide cross-platform portable code. Packages will not normally be accepted that do not run on at least two of the major R platforms. Cases for Windows-only packages will be considered, but CRAN may not be the most appropriate place to host them."" You might want to use win-builder (https://win-builder.r-project.org/) to test your package on other platforms. All the best, Mauricio = Department of Civil Engineering Faculty of Engineering and Sciences Universidad de La Frontera, Temuco, Chile http://hzambran.github.io/ = mailto : mauricio.zambr...@ufrontera.cl work-phone : +56 45 259 2812 = "Life goes by so fast, that if you don't stop and look around, you might miss it" (from the film Ferris Bueller's Day Off) = Linux user #454569 -- Linux Mint user -- La información contenida en este correo electrónico y cualquier anexo o respuesta relacionada, puede contener datos e información confidencial y no puede ser usada o difundida por personas distintas a su(s) destinatario(s). Si usted no es el destinatario de esta comunicación, le informamos que cualquier divulgación, distribución o copia de esta información constituye un delito conforme a la ley chilena. Si lo ha recibido por error, por favor borre el mensaje y todos sus anexos y notifique al remitente. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Package submission failed with two warnings
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
