Re: [R-pkg-devel] Problem with "additional repository".
Certainly there was more in the output that caused rejection as the
stuff you describe below seems to be fine.
I do not know which package this refers to, so cannot easily look.
Best,
Uwe
On 16.10.2023 11:25, Duncan Murdoch wrote:
Whoops, I just read the next line. Sorry!
On 15/10/2023 9:34 p.m., Rolf Turner wrote:
I have submitted a new package to CRAN, and this package has been
knocked back on the basis of a NOTE:
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ionChannelData'
This suggested package consists of data sets, the size of which is too
large to satisfy CRAN's constraints. I put this package in a repository
on github, from which it can be accessed by users.
My DESCRIPTION file contains the line:
Additional_repositories: https://rolfturner.r-universe.dev
The given URL seems to work, in that users can indeed load the
ionChannelData package via the command
install.packages("ionChannelData",repos="https://rolfturner.r-universe.dev;)
I was under the impression that this was all that I needed to do. The
CRAN checking process acknowledges the existence of the repository in
question:
Suggests or Enhances not in mainstream repositories:
ionChannelData
Availability using Additional_repositories specification:
ionChannelData yes https://rolfturner.r-universe.dev
>
So CRAN knows about this repository. Why can it not make use of it?
What can/should I do to resolve this problem?
I guess I could simply *not* Suggest ionChannelData. But what then, is
the point of the option of including an Additional_repositories field in
the DESCRIPTION file?
cheers,
Rolf Turner
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Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
package.
Specifically, include this line in your DESCRIPTION file:
VignetteBuilder: R.rsp
Let's say the pdf file is called "myfile.pdf". Create a file called
"myfile.pdf.asis" that contains the vignette instructions. Put it in the
vignette directory along with the PDF file. Mine looks like:
%\VignetteIndexEntry{PUT VIGNETTE TITLE HERE}
%\VignetteKeywords{PUT KEYWORDS HERE}
%\VignetteDepends{PACKAGE_NAME}
%\VignettePackage{PACKAGE_NAME}
%\VignetteEngine{R.rsp::asis}
I am not certain if this works for an HTML vignette, but I see no reason
why it shouldn't.
Best,
Kevin
On 10/16/2023 10:14 AM, John Fox wrote:
Dear list members,
I believe that this issue has been discussed previously, but I'm not
sure that I have the solution right.
Georges Monette and I have developed a package that we intend to
submit soon to CRAN which has a vignette including code that takes a
long time to run. The sources for the package are available at
.
We figure that we have to suppress running the code the vignette when
CRAN checks the package or the check time will be excessive.
The vignette is written as a .Rmd file to be compiled by knitr,
producing an HTML vignette. The top of the .Rmd file looks like this:
--- snip ---
---
title: "Cross-validation of regression models"
author: "John Fox and Georges Monette"
date: "`r Sys.Date()`"
package: cv
output:
rmarkdown::html_vignette:
fig_caption: yes
bibliography: ["cv.bib"]
csl: apa.csl
vignette: >
%\VignetteIndexEntry{Cross-validation of regression models}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
message = TRUE,
warning = TRUE,
fig.align = "center",
fig.height = 6,
fig.width = 7,
fig.path = "fig/",
dev = "png",
comment = "#>",
eval = nzchar(Sys.getenv("REBUILD_CV_VIGNETTES"))
)
### other irrelevant setup code not shown ###
```
--- snip ---
So (near the bottom), if the environment variable REBUILD_CV_VIGNETTES
isn't empty, the code blocks in the vignette are evaluated, otherwise
not. To build the tarball for the package to be submitted to CRAN, we
will set REBUILD_CV_VIGNETTES to "true". That works as intended.
If we submit the tarball to CRAN, I believe that the package as
distributed by CRAN will include the HTML vignette from our tarball,
showing the evaluated code blocks, but when CRAN checks the package,
these long-running code blocks will not be executed (because
REBUILD_CV_VIGNETTES will not exist on the CRAN check machines).
My questions:
Is that correct?
If not, how can we ensure that the complete vignette is distributed by
CRAN without causing an overly long CRAN check time?
In particular, we don't want CRAN to rebuild and distribute the
vignette, because the resulting HTML file won't show the evaluated code.
Any assistance would be appreciated.
Thank you,
John
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Re: [R-pkg-devel] Problem with "additional repository".
Whoops, I just read the next line. Sorry!
On 15/10/2023 9:34 p.m., Rolf Turner wrote:
I have submitted a new package to CRAN, and this package has been
knocked back on the basis of a NOTE:
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ionChannelData'
This suggested package consists of data sets, the size of which is too
large to satisfy CRAN's constraints. I put this package in a repository
on github, from which it can be accessed by users.
My DESCRIPTION file contains the line:
Additional_repositories: https://rolfturner.r-universe.dev
The given URL seems to work, in that users can indeed load the
ionChannelData package via the command
install.packages("ionChannelData",repos="https://rolfturner.r-universe.dev;)
I was under the impression that this was all that I needed to do. The
CRAN checking process acknowledges the existence of the repository in
question:
Suggests or Enhances not in mainstream repositories:
ionChannelData
Availability using Additional_repositories specification:
ionChannelData yes https://rolfturner.r-universe.dev
So CRAN knows about this repository. Why can it not make use of it?
What can/should I do to resolve this problem?
I guess I could simply *not* Suggest ionChannelData. But what then, is
the point of the option of including an Additional_repositories field in
the DESCRIPTION file?
cheers,
Rolf Turner
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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Problem with "additional repository".
On 15/10/2023 9:34 p.m., Rolf Turner wrote:
I have submitted a new package to CRAN, and this package has been
knocked back on the basis of a NOTE:
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ionChannelData'
This suggested package consists of data sets, the size of which is too
large to satisfy CRAN's constraints. I put this package in a repository
on github, from which it can be accessed by users.
My DESCRIPTION file contains the line:
Additional_repositories: https://rolfturner.r-universe.dev
Is that web site set up as a repository? My impression was that it
needed to be, so people could do
install.packages("ionChannelData", repos =
"https://rolfturner.r-universe.dev;)
You can use the "drat" package to set up a tiny repository quickly.
Duncan
The given URL seems to work, in that users can indeed load the
ionChannelData package via the command
install.packages("ionChannelData",repos="https://rolfturner.r-universe.dev;)
I was under the impression that this was all that I needed to do. The
CRAN checking process acknowledges the existence of the repository in
question:
Suggests or Enhances not in mainstream repositories:
ionChannelData
Availability using Additional_repositories specification:
ionChannelData yes https://rolfturner.r-universe.dev
So CRAN knows about this repository. Why can it not make use of it?
What can/should I do to resolve this problem?
I guess I could simply *not* Suggest ionChannelData. But what then, is
the point of the option of including an Additional_repositories field in
the DESCRIPTION file?
cheers,
Rolf Turner
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