Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine
I just re-submitted now. Thank you.
Best regards,
Christophe
On Mon, Mar 4, 2024 at 4:57 PM Uwe Ligges
wrote:
>
> OK, can you pls submit that one to CRAN again?
>
> Best,
> Uwe Ligges
>
> On 04.03.2024 16:53, Christophe Dervieux wrote:
> > Hi,
> >
> > yes I have defined in DESCRIPTION
> >
> > VignetteBuilder:
> > quarto
> >
> > and running `tools:::loadVignetteBuilder` on the package source
> > directory reads it correctly.
> >
> > > tools:::loadVignetteBuilder(".")
> > [1] "quarto" "utils"
> >
> > Best regards,
> >
> > Christophe
> >
> >
> > On Mon, Mar 4, 2024 at 4:40 PM Uwe Ligges
> > wrote:
> >>
> >> So you have defined
> >>
> >>
> >> VignetteBuilder: quarto
> >>
> >> ??
> >>
> >> Best,
> >> Uwe
> >>
> >> On 26.02.2024 21:28, Jeroen Ooms wrote:
> >>> On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux
> >>> wrote:
>
> Hi,
>
> I am trying to release a new version of the quarto R package. This new
> version is adding support for a new vignette engine that will use quarto
> CLI (https://quarto.org) when available. The vignettes inside the package
> itself are '.qmd' files built with quarto.
>
> While developing the feature, I noticed that R CMD check will query for
> vignette engines information, and it will find engine in already
> installed
> package (with `tools:::vignetteEngine`). So a package adding a new
> engine,
> and using this engine for its vignette only works when the package is
> installed before check.
> >>>
> >>>
> >>> This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191
> >>>
> >>> Based on what I can see from the public cran incoming files [1,2], I
> >>> suspect the Debian check is loading the CRAN version of quarto (1.3),
> >>> rather than the one being checked (1.4), to test vignettes. As a
> >>> result it does not recognize the new qmd type vignettes introduced in
> >>> this version.
> >>>
> >>> If this is indeed the case, the problem will resolve itself once the
> >>> submission is approved.
> >>>
> >>>[1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz
> >>>[2]
> >>> https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/
> >>>
> >>> __
> >>> 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] CRAN checks for release of a package with new vignette engine
OK, can you pls submit that one to CRAN again?
Best,
Uwe Ligges
On 04.03.2024 16:53, Christophe Dervieux wrote:
Hi,
yes I have defined in DESCRIPTION
VignetteBuilder:
quarto
and running `tools:::loadVignetteBuilder` on the package source
directory reads it correctly.
> tools:::loadVignetteBuilder(".")
[1] "quarto" "utils"
Best regards,
Christophe
On Mon, Mar 4, 2024 at 4:40 PM Uwe Ligges
wrote:
So you have defined
VignetteBuilder: quarto
??
Best,
Uwe
On 26.02.2024 21:28, Jeroen Ooms wrote:
On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux wrote:
Hi,
I am trying to release a new version of the quarto R package. This new
version is adding support for a new vignette engine that will use quarto
CLI (https://quarto.org) when available. The vignettes inside the package
itself are '.qmd' files built with quarto.
While developing the feature, I noticed that R CMD check will query for
vignette engines information, and it will find engine in already installed
package (with `tools:::vignetteEngine`). So a package adding a new engine,
and using this engine for its vignette only works when the package is
installed before check.
This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191
Based on what I can see from the public cran incoming files [1,2], I
suspect the Debian check is loading the CRAN version of quarto (1.3),
rather than the one being checked (1.4), to test vignettes. As a
result it does not recognize the new qmd type vignettes introduced in
this version.
If this is indeed the case, the problem will resolve itself once the
submission is approved.
[1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz
[2]
https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/
__
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] CRAN checks for release of a package with new vignette engine
Hi,
yes I have defined in DESCRIPTION
VignetteBuilder:
quarto
and running `tools:::loadVignetteBuilder` on the package source
directory reads it correctly.
> tools:::loadVignetteBuilder(".")
[1] "quarto" "utils"
Best regards,
Christophe
On Mon, Mar 4, 2024 at 4:40 PM Uwe Ligges
wrote:
>
> So you have defined
>
>
>VignetteBuilder: quarto
>
> ??
>
> Best,
> Uwe
>
> On 26.02.2024 21:28, Jeroen Ooms wrote:
> > On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux wrote:
> >>
> >> Hi,
> >>
> >> I am trying to release a new version of the quarto R package. This new
> >> version is adding support for a new vignette engine that will use quarto
> >> CLI (https://quarto.org) when available. The vignettes inside the package
> >> itself are '.qmd' files built with quarto.
> >>
> >> While developing the feature, I noticed that R CMD check will query for
> >> vignette engines information, and it will find engine in already installed
> >> package (with `tools:::vignetteEngine`). So a package adding a new engine,
> >> and using this engine for its vignette only works when the package is
> >> installed before check.
> >
> >
> > This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191
> >
> > Based on what I can see from the public cran incoming files [1,2], I
> > suspect the Debian check is loading the CRAN version of quarto (1.3),
> > rather than the one being checked (1.4), to test vignettes. As a
> > result it does not recognize the new qmd type vignettes introduced in
> > this version.
> >
> > If this is indeed the case, the problem will resolve itself once the
> > submission is approved.
> >
> > [1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz
> > [2]
> > https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/
> >
> > __
> > 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] CRAN checks for release of a package with new vignette engine
So you have defined VignetteBuilder: quarto ?? Best, Uwe On 26.02.2024 21:28, Jeroen Ooms wrote: On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux wrote: Hi, I am trying to release a new version of the quarto R package. This new version is adding support for a new vignette engine that will use quarto CLI (https://quarto.org) when available. The vignettes inside the package itself are '.qmd' files built with quarto. While developing the feature, I noticed that R CMD check will query for vignette engines information, and it will find engine in already installed package (with `tools:::vignetteEngine`). So a package adding a new engine, and using this engine for its vignette only works when the package is installed before check. This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191 Based on what I can see from the public cran incoming files [1,2], I suspect the Debian check is loading the CRAN version of quarto (1.3), rather than the one being checked (1.4), to test vignettes. As a result it does not recognize the new qmd type vignettes introduced in this version. If this is indeed the case, the problem will resolve itself once the submission is approved. [1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz [2] https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/ __ 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] CRAN checks for release of a package with new vignette engine
Thank you. I wasn't aware of this bug report [1] but definitely what I encountered while working on the feature, and for CI testing. My understanding is similar to Jeroen, and I believe it will solve itself once the new version is made available. Is the following step to reply to the CRAN teams after automated checks to explain the situation ? Christophe [1] https://bugs.r-project.org/show_bug.cgi?id=18191 On Mon, Feb 26, 2024 at 9:28 PM Jeroen Ooms wrote: > > On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux wrote: > > > > Hi, > > > > I am trying to release a new version of the quarto R package. This new > > version is adding support for a new vignette engine that will use quarto > > CLI (https://quarto.org) when available. The vignettes inside the package > > itself are '.qmd' files built with quarto. > > > > While developing the feature, I noticed that R CMD check will query for > > vignette engines information, and it will find engine in already installed > > package (with `tools:::vignetteEngine`). So a package adding a new engine, > > and using this engine for its vignette only works when the package is > > installed before check. > > > This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191 > > Based on what I can see from the public cran incoming files [1,2], I > suspect the Debian check is loading the CRAN version of quarto (1.3), > rather than the one being checked (1.4), to test vignettes. As a > result it does not recognize the new qmd type vignettes introduced in > this version. > > If this is indeed the case, the problem will resolve itself once the > submission is approved. > > [1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz > [2] > https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine
On Mon, Feb 26, 2024 at 5:50 PM Christophe Dervieux wrote: > > Hi, > > I am trying to release a new version of the quarto R package. This new > version is adding support for a new vignette engine that will use quarto > CLI (https://quarto.org) when available. The vignettes inside the package > itself are '.qmd' files built with quarto. > > While developing the feature, I noticed that R CMD check will query for > vignette engines information, and it will find engine in already installed > package (with `tools:::vignetteEngine`). So a package adding a new engine, > and using this engine for its vignette only works when the package is > installed before check. This looks similar to https://bugs.r-project.org/show_bug.cgi?id=18191 Based on what I can see from the public cran incoming files [1,2], I suspect the Debian check is loading the CRAN version of quarto (1.3), rather than the one being checked (1.4), to test vignettes. As a result it does not recognize the new qmd type vignettes introduced in this version. If this is indeed the case, the problem will resolve itself once the submission is approved. [1] https://cran.r-project.org/incoming/archive/quarto_1.4.tar.gz [2] https://win-builder.r-project.org/incoming_pretest/quarto_1.4_20240221_175256/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine
Thank you for your reply. I understand from the reply that the package is installed first from the built .tar.gz uploaded before R CMD check is ran on the bundle. I made my assumption based on experience on CI environment where I needed to explicitly install the package before running checks in order for the vignette engine to be found. Install did not fail. Here is the install log for `r-devel-linux-x86_64-debian-gcc` platform * installing *source* package ‘quarto’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (quarto) And the check log for the `r-devel-linux-x86_64-debian-gcc` platform * using log directory ‘/srv/hornik/tmp/CRAN/quarto.Rcheck’ * using R Under development (unstable) (2024-02-21 r85960) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘quarto/DESCRIPTION’ ... OK * this is package ‘quarto’ version ‘1.4’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Christophe Dervieux ’ New maintainer: Christophe Dervieux Old maintainer(s): JJ Allaire * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘quarto’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [3s/3s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [1s/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/10s] OK Running ‘testthat.R’ [16s/10s] * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE As I shared, the log on Windows r-devel environment does not have the same NOTE * using log directory 'd:/RCompile/CRANincoming/R-devel/quarto.Rcheck' * using R Under development (unstable) (2024-02-20 r85959 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'quarto/DESCRIPTION' ... OK * this is package 'quarto' version '1.4' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Christophe Dervieux ' New maintainer: Christophe Dervieux Old maintainer(s): JJ Allaire * checking package namespace informat
Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine
Could you show us the install and check logs for the problematic platform? I don't think you'd get to the message you quote unless the install succeeded, so I think your diagnosis of the problem isn't right. But maybe I'm wrong about that, and the install failed, perhaps because the Quarto tools were not available. Duncan Murdoch On 26/02/2024 10:34 a.m., Christophe Dervieux wrote: Hi, I am trying to release a new version of the quarto R package. This new version is adding support for a new vignette engine that will use quarto CLI (https://quarto.org) when available. The vignettes inside the package itself are '.qmd' files built with quarto. While developing the feature, I noticed that R CMD check will query for vignette engines information, and it will find engine in already installed package (with `tools:::vignetteEngine`). So a package adding a new engine, and using this engine for its vignette only works when the package is installed before check. Automated checks works ok on `r-devel-windows-x86_64`, but fails on `r-devel-linux-x86_64-debian-gcc` because of this note Check: package vignettes, Result: NOTE Package has 'vignettes' subdirectory but apparently no vignettes. Perhaps the 'VignetteBuilder' information is missing from the DESCRIPTION file? I believe this happens because the package is not installed, so when R CMD Check is doing the vignette checking, it won't find the quarto vignette engine. I am trying to understand what I could do for this package release, considering checks are ok on windows r-devel, and only having the NOTE on debian environment. Should I consider this a false positive for this specific case ? Is there any consideration to take for adding a new engine ? Thank you Christophe Dervieux [[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
