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

[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 <cderv using posit.co>’
New maintainer:
  Christophe Dervieux <cderv using posit.co>
Old maintainer(s):
  JJ Allaire <jj using rstudio.com>
* 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 <cderv using posit.co>'
New maintainer:
  Christophe Dervieux <cderv using posit.co>
Old maintainer(s):
  JJ Allaire <jj using rstudio.com>
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'quarto' can be installed ... OK
* checking installed package size ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [22s] OK
  Running 'testthat.R' [22s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s] OK
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... OK
* DONE

So if my assumption about new version of package not being installed
is wrong, what could explain the difference between the two
environments, and the new engine not being found only on one platform
?

If anyone has some hints about this, I'll take them to verify and fix
this. Thank you

Christophe


On Mon, Feb 26, 2024 at 6:20 PM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> 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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>