Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-03-04 Thread Christophe Dervieux
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

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-03-04 Thread Uwe Ligges

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/

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-03-04 Thread Christophe Dervieux
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

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-03-04 Thread Uwe Ligges

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/

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-02-27 Thread Christophe Dervieux
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/

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-02-26 Thread Jeroen Ooms
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/

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Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-02-26 Thread Christophe Dervieux
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 

Re: [R-pkg-devel] CRAN checks for release of a package with new vignette engine

2024-02-26 Thread Duncan Murdoch

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]]

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