Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
Ah, brilliant. Thanks. On Sun, Jun 14, 2020 at 11:28:17AM -0400, Duncan Murdoch wrote: > On 14/06/2020 10:59 a.m., Joshua N Pritikin wrote: > > On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote: > > > knitr::opts_chunk$set(eval = !is_CRAN) > > > > This works except for in-text `r 1+1` code fragments. Is there an option > > to make these evaluate to "[MISSING]" or similar? > > To suppress evaluation of those, you can use this: > > knitr::knit_hooks$set(evaluate.inline = function(x, envir) x) __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
On 14/06/2020 10:59 a.m., Joshua N Pritikin wrote: On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote: Since you're using Rmarkdown, you can use a variable for the eval chunk option, e.g. put this in your setup chunk: knitr::opts_chunk$set(eval = !is_CRAN) This works except for in-text `r 1+1` code fragments. Is there an option to make these evaluate to "[MISSING]" or similar? To suppress evaluation of those, you can use this: knitr::knit_hooks$set(evaluate.inline = function(x, envir) x) This will show the code in place of evaluating it and showing its value. Replace the function value with "[MISSING]" if you don't want to see the code. Duncan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote: > Since you're using Rmarkdown, you can use a variable for the eval > chunk option, e.g. put this in your setup chunk: > > knitr::opts_chunk$set(eval = !is_CRAN) This works except for in-text `r 1+1` code fragments. Is there an option to make these evaluate to "[MISSING]" or similar? __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
Ah, thank you!
Sorry for the duplicate posts.
On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote:
> On 13/06/2020 1:29 p.m., Joshua N Pritikin wrote:
> >
> > I'm trying to include vignettes that take much too long for CRAN check.
> >
> > At the beginning of the Rmarkdown vignette, I use
> >
> >is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
> >if (is_CRAN) q()
> >
> > And then I use
> >
> >export NOT_CRAN=true
> >
> > when I build locally. But CRAN check still complains,
>
> You shouldn't call q() from a vignette. Since you're using Rmarkdown, you
> can use a variable for the eval chunk option, e.g. put this in your setup
> chunk:
>
> knitr::opts_chunk$set(eval = !is_CRAN)
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
On 13/06/2020 1:29 p.m., Joshua N Pritikin wrote:
I'm trying to include vignettes that take much too long for CRAN check.
At the beginning of the Rmarkdown vignette, I use
is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
if (is_CRAN) q()
And then I use
export NOT_CRAN=true
when I build locally. But CRAN check still complains,
You shouldn't call q() from a vignette. Since you're using Rmarkdown,
you can use a variable for the eval chunk option, e.g. put this in your
setup chunk:
knitr::opts_chunk$set(eval = !is_CRAN)
Duncan Murdoch
On Mon, Jun 08, 2020 at 04:24:43PM +0200, lig...@statistik.tu-dortmund.de wrote:
Flavor: r-devel-linux-x86_64-debian-gcc
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
...
--- re-building 'GeneEnvironmentInteraction.Rmd' using rmarkdown
--- re-building 'OneFactorModel.Rmd' using rmarkdown
--- re-building 'PostGWASprocessing.Rmd' using rmarkdown
--- re-building 'ResidualsModel.Rmd' using rmarkdown
--- re-building 'StandardGWAS.Rmd' using rmarkdown
--- re-building 'TwoFactorModel.Rmd' using rmarkdown
--- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
--- re-building 'growth.Rmd' using rmarkdown
Error: Vignette re-building failed.
Execution halted
What's the correct way to avoid CRAN complaints?
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
On Sun, 14 Jun 2020 at 14:32, Joshua N Pritikin wrote:
>
>
> I'm trying to include vignettes that take much too long for CRAN check.
>
> At the beginning of the Rmarkdown vignette, I use
>
> is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
> if (is_CRAN) q()
>
> And then I use
>
> export NOT_CRAN=true
>
> when I build locally. But CRAN check still complains,
Because you're just exiting and nothing is generated. Instead, you
should mark all chunks as eval=FALSE. You could use something as
follows in the initial chunk:
if (is_CRAN) knitr::opts_chunk$set(eval = FALSE)
--
Iñaki Úcar
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
I'm trying to include vignettes that take much too long for CRAN check.
At the beginning of the Rmarkdown vignette, I use
is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
if (is_CRAN) q()
And then I use
export NOT_CRAN=true
when I build locally. But CRAN check still complains,
On Mon, Jun 08, 2020 at 04:24:43PM +0200, lig...@statistik.tu-dortmund.de wrote:
> Flavor: r-devel-linux-x86_64-debian-gcc
> Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> ...
> --- re-building 'GeneEnvironmentInteraction.Rmd' using rmarkdown
> --- re-building 'OneFactorModel.Rmd' using rmarkdown
> --- re-building 'PostGWASprocessing.Rmd' using rmarkdown
> --- re-building 'ResidualsModel.Rmd' using rmarkdown
> --- re-building 'StandardGWAS.Rmd' using rmarkdown
> --- re-building 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Biotech One, Suite 1-133
Richmond, VA 23219
http://exuberant-island.surge.sh
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
I'm trying to include vignettes that take much too long for CRAN check.
At the beginning of the Rmarkdown vignette, I use
is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
if (is_CRAN) q()
And then I use
export NOT_CRAN=true
when I build locally. But CRAN check still complains,
On Mon, Jun 08, 2020 at 04:24:43PM +0200, lig...@statistik.tu-dortmund.de wrote:
> Flavor: r-devel-linux-x86_64-debian-gcc
> Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> ...
> --- re-building 'GeneEnvironmentInteraction.Rmd' using rmarkdown
> --- re-building 'OneFactorModel.Rmd' using rmarkdown
> --- re-building 'PostGWASprocessing.Rmd' using rmarkdown
> --- re-building 'ResidualsModel.Rmd' using rmarkdown
> --- re-building 'StandardGWAS.Rmd' using rmarkdown
> --- re-building 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Biotech One, Suite 1-133
Richmond, VA 23219
http://exuberant-island.surge.sh
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3
I'm trying to include vignettes that take much too long for CRAN check.
At the beginning of the Rmarkdown vignette, I use
is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
if (is_CRAN) q()
And then I use
export NOT_CRAN=true
when I build locally. But CRAN check still complains,
On Mon, Jun 08, 2020 at 04:24:43PM +0200, lig...@statistik.tu-dortmund.de wrote:
> Flavor: r-devel-linux-x86_64-debian-gcc
> Check: re-building of vignette outputs, Result: WARNING
> Error(s) in re-building vignettes:
> ...
> --- re-building 'GeneEnvironmentInteraction.Rmd' using rmarkdown
> --- re-building 'OneFactorModel.Rmd' using rmarkdown
> --- re-building 'PostGWASprocessing.Rmd' using rmarkdown
> --- re-building 'ResidualsModel.Rmd' using rmarkdown
> --- re-building 'StandardGWAS.Rmd' using rmarkdown
> --- re-building 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Biotech One, Suite 1-133
Richmond, VA 23219
http://exuberant-island.surge.sh
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
