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v1.9.0 release candidate (#4105)

Browse Source 
* Start v1.9.0 release candidate

* Check-in revdep results

* `yarn build` (GitHub Actions)

* Sync package version (GitHub Actions)

* `yarn build` (GitHub Actions)

* ran revdepcheck on cloud. 2 errors reported. Both seem like false positives

* Fix R CMD check note about Rd links targets missing package anchors

---------

Co-authored-by: cpsievert <cpsievert@users.noreply.github.com>
Co-authored-by: Barret Schloerke <barret@posit.co>
Co-authored-by: schloerke <schloerke@users.noreply.github.com>
This commit is contained in:
Carson Sievert
2024-07-29 17:10:38 -05:00
committed by GitHub
parent 599209a036
commit 56ab530d87
21 changed files with 194 additions and 59 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
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@@ -1,7 +1,7 @@
Package: shiny
Type: Package
Title: Web Application Framework for R
Version: 1.8.1.9001
Version: 1.9.0
Authors@R: c(
person("Winston", "Chang", role = c("aut", "cre"), email = "winston@posit.co", comment = c(ORCID = "0000-0002-1576-2126")),
person("Joe", "Cheng", role = "aut", email = "joe@posit.co"),

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NEWS.md
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# shiny (development version)
# shiny 1.9.0
## New busy indication feature

7
R/bootstrap.R
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@@ -172,9 +172,10 @@ setCurrentTheme <- function(theme) {
#' Register a theme dependency
#'
#' This function registers a function that returns an [htmlDependency()] or list
#' of such objects. If `session$setCurrentTheme()` is called, the function will
#' be re-executed, and the resulting html dependency will be sent to the client.
#' This function registers a function that returns an
#' [htmltools::htmlDependency()] or list of such objects. If
#' `session$setCurrentTheme()` is called, the function will be re-executed, and
#' the resulting html dependency will be sent to the client.
#'
#' Note that `func` should **not** be an anonymous function, or a function which
#' is defined within the calling function. This is so that,

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R/reactives.R
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@@ -951,7 +951,10 @@ Observable <- R6Class(
#' See the [Shiny tutorial](https://shiny.rstudio.com/tutorial/) for
#' more information about reactive expressions.
#'
#' @param x For `is.reactive()`, an object to test. For `reactive()`, an expression. When passing in a [`quo()`]sure with `reactive()`, remember to use [`rlang::inject()`] to distinguish that you are passing in the content of your quosure, not the expression of the quosure.
#' @param x For `is.reactive()`, an object to test. For `reactive()`, an
#' expression. When passing in a [`rlang::quo()`]sure with `reactive()`,
#' remember to use [`rlang::inject()`] to distinguish that you are passing in
#' the content of your quosure, not the expression of the quosure.
#' @template param-env
#' @templateVar x x
#' @templateVar env env

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R/utils-lang.R
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@@ -53,8 +53,8 @@ formalsAndBody <- function(x) {
#' @describeIn createRenderFunction convert a quosure to a function.
#' @param q Quosure of the expression `x`. When capturing expressions to create
#' your quosure, it is recommended to use [`enquo0()`] to not unquote the
#' object too early. See [`enquo0()`] for more details.
#' your quosure, it is recommended to use [`rlang::enquo0()`] to not unquote
#' the object too early. See [`rlang::enquo0()`] for more details.
#' @inheritParams installExprFunction
#' @export
quoToFunction <- function(

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inst/www/shared/busy-indicators/busy-indicators.css
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@@ -1,2 +1,2 @@
/*! shiny 1.8.1.9001 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
/*! shiny 1.9.0 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
:where([data-shiny-busy-spinners] .recalculating){position:relative}[data-shiny-busy-spinners] .recalculating:after{position:absolute;content:"";--_shiny-spinner-url: var(--shiny-spinner-url, url(spinners/ring.svg));--_shiny-spinner-color: var(--shiny-spinner-color, var(--bs-primary, #007bc2));--_shiny-spinner-size: var(--shiny-spinner-size, 32px);--_shiny-spinner-delay: var(--shiny-spinner-delay, 1s);background:var(--_shiny-spinner-color);width:var(--_shiny-spinner-size);height:var(--_shiny-spinner-size);inset:calc(50% - var(--_shiny-spinner-size) / 2);mask-image:var(--_shiny-spinner-url);-webkit-mask-image:var(--_shiny-spinner-url);opacity:0;animation-delay:var(--_shiny-spinner-delay);animation-name:fade-in;animation-duration:.25s;animation-fill-mode:forwards}[data-shiny-busy-spinners] .recalculating:has(>*),[data-shiny-busy-spinners] .recalculating:empty{opacity:1}[data-shiny-busy-spinners] .recalculating>*:not(.recalculating){opacity:var(--_shiny-fade-opacity);transition:opacity .25s ease var(--shiny-spinner-delay, 1s)}[data-shiny-busy-spinners] .recalculating.shiny-html-output:after{display:none}[data-shiny-busy-spinners][data-shiny-busy-pulse].shiny-busy:after{--_shiny-pulse-background: var( --shiny-pulse-background, linear-gradient( 120deg, var(--bs-body-bg, #fff), var(--bs-indigo, #4b00c1), var(--bs-purple, #74149c), var(--bs-pink, #bf007f), var(--bs-body-bg, #fff) ) );--_shiny-pulse-height: var(--shiny-pulse-height, 5px);--_shiny-pulse-speed: var(--shiny-pulse-speed, 1.85s);position:fixed;top:0;left:0;height:var(--_shiny-pulse-height);background:var(--_shiny-pulse-background);z-index:9999;animation-name:busy-page-pulse;animation-duration:var(--_shiny-pulse-speed);animation-iteration-count:infinite;animation-timing-function:ease-in-out;content:""}[data-shiny-busy-spinners][data-shiny-busy-pulse].shiny-busy:has(.recalculating):after{display:none}[data-shiny-busy-spinners][data-shiny-busy-pulse].shiny-busy:has(#shiny-disconnected-overlay):after{display:none}[data-shiny-busy-pulse]:not([data-shiny-busy-spinners]).shiny-busy:after{--_shiny-pulse-background: var( --shiny-pulse-background, linear-gradient( 120deg, var(--bs-body-bg, #fff), var(--bs-indigo, #4b00c1), var(--bs-purple, #74149c), var(--bs-pink, #bf007f), var(--bs-body-bg, #fff) ) );--_shiny-pulse-height: var(--shiny-pulse-height, 5px);--_shiny-pulse-speed: var(--shiny-pulse-speed, 1.85s);position:fixed;top:0;left:0;height:var(--_shiny-pulse-height);background:var(--_shiny-pulse-background);z-index:9999;animation-name:busy-page-pulse;animation-duration:var(--_shiny-pulse-speed);animation-iteration-count:infinite;animation-timing-function:ease-in-out;content:""}[data-shiny-busy-pulse]:not([data-shiny-busy-spinners]).shiny-busy:has(#shiny-disconnected-overlay):after{display:none}@keyframes fade-in{0%{opacity:0}to{opacity:1}}@keyframes busy-page-pulse{0%{left:-75%;width:75%}50%{left:100%;width:75%}to{left:-75%;width:75%}}.shiny-spinner-output-container{--shiny-spinner-size: 0px}

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inst/www/shared/shiny-autoreload.js
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inst/www/shared/shiny-showcase.css
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/*! shiny 1.8.1.9001 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
/*! shiny 1.9.0 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
#showcase-well{border-radius:0}.shiny-code{background-color:#fff;margin-bottom:0}.shiny-code code{font-family:Menlo,Consolas,Courier New,monospace}.shiny-code-container{margin-top:20px;clear:both}.shiny-code-container h3{display:inline;margin-right:15px}.showcase-header{font-size:16px;font-weight:400}.showcase-code-link{text-align:right;padding:15px}#showcase-app-container{vertical-align:top}#showcase-code-tabs{margin-right:15px}#showcase-code-tabs pre{border:none;line-height:1em}#showcase-code-tabs .nav,#showcase-code-tabs ul{margin-bottom:0}#showcase-code-tabs .tab-content{border-style:solid;border-color:#e5e5e5;border-width:0px 1px 1px 1px;overflow:auto;border-bottom-right-radius:4px;border-bottom-left-radius:4px}#showcase-app-code{width:100%}#showcase-code-position-toggle{float:right}#showcase-sxs-code{padding-top:20px;vertical-align:top}.showcase-code-license{display:block;text-align:right}#showcase-code-content pre{background-color:#fff}

2
inst/www/shared/shiny-showcase.js
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2
inst/www/shared/shiny-testmode.js
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@@ -1,3 +1,3 @@
/*! shiny 1.8.1.9001 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
/*! shiny 1.9.0 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
"use strict";(function(){var a=eval;window.addEventListener("message",function(i){var e=i.data;e.code&&a(e.code)});})();
//# sourceMappingURL=shiny-testmode.js.map

4
inst/www/shared/shiny.js
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@@ -1,4 +1,4 @@
/*! shiny 1.8.1.9001 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
/*! shiny 1.9.0 | (c) 2012-2024 RStudio, PBC. | License: GPL-3 | file LICENSE */
"use strict";
(function() {
var __create = Object.create;
@@ -25084,7 +25084,7 @@
_defineProperty23(this, "initializeInputs", void 0);
_defineProperty23(this, "initializedPromise", void 0);
_defineProperty23(this, "oncustommessage", void 0);
this.version = "1.8.1.9001";
this.version = "1.9.0";
var _initInputBindings = initInputBindings(), inputBindings = _initInputBindings.inputBindings, fileInputBinding2 = _initInputBindings.fileInputBinding;
var _initOutputBindings = initOutputBindings(), outputBindings = _initOutputBindings.outputBindings;
setFileInputBinding(fileInputBinding2);

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inst/www/shared/shiny.min.js vendored
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2
inst/www/shared/shiny.min.js.map
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4
man/createRenderFunction.Rd
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@@ -72,8 +72,8 @@ example, some render functions call \code{\link[=createWebDependency]{createWebD
is able to serve JS and CSS resources.}
\item{q}{Quosure of the expression \code{x}. When capturing expressions to create
your quosure, it is recommended to use \code{\link[=enquo0]{enquo0()}} to not unquote the
object too early. See \code{\link[=enquo0]{enquo0()}} for more details.}
your quosure, it is recommended to use \code{\link[rlang:defusing-advanced]{rlang::enquo0()}} to not unquote
the object too early. See \code{\link[rlang:defusing-advanced]{rlang::enquo0()}} for more details.}
\item{label}{A label for the object to be shown in the debugger. Defaults to
the name of the calling function.}

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man/reactive.Rd
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@@ -18,7 +18,10 @@ reactive(
is.reactive(x)
}
\arguments{
\item{x}{For \code{is.reactive()}, an object to test. For \code{reactive()}, an expression. When passing in a \code{\link[=quo]{quo()}}sure with \code{reactive()}, remember to use \code{\link[rlang:inject]{rlang::inject()}} to distinguish that you are passing in the content of your quosure, not the expression of the quosure.}
\item{x}{For \code{is.reactive()}, an object to test. For \code{reactive()}, an
expression. When passing in a \code{\link[rlang:defusing-advanced]{rlang::quo()}}sure with \code{reactive()},
remember to use \code{\link[rlang:inject]{rlang::inject()}} to distinguish that you are passing in
the content of your quosure, not the expression of the quosure.}
\item{env}{The parent environment for the reactive expression. By default,
this is the calling environment, the same as when defining an ordinary

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man/registerThemeDependency.Rd
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@@ -12,9 +12,10 @@ registerThemeDependency(func)
of them.}
}
\description{
This function registers a function that returns an \code{\link[=htmlDependency]{htmlDependency()}} or list
of such objects. If \code{session$setCurrentTheme()} is called, the function will
be re-executed, and the resulting html dependency will be sent to the client.
This function registers a function that returns an
\code{\link[htmltools:htmlDependency]{htmltools::htmlDependency()}} or list of such objects. If
\code{session$setCurrentTheme()} is called, the function will be re-executed, and
the resulting html dependency will be sent to the client.
}
\details{
Note that \code{func} should \strong{not} be an anonymous function, or a function which

2
package.json
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@@ -3,7 +3,7 @@
"homepage": "https://shiny.rstudio.com",
"repository": "github:rstudio/shiny",
"name": "@types/rstudio-shiny",
"version": "1.8.1-alpha.9001",
"version": "1.9.0",
"license": "GPL-3.0-only",
"main": "",
"browser": "",

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revdep/README.md
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# Revdeps
## Failed to check (18)
## Failed to check (29)
|package |version |error |warning |note |
|:------------------|:-------|:-----|:-------|:----|
|bigPint |? | | | |
|bioCancer |? | | | |
|ctsem |3.9.1 |1 | | |
|diveR |? | | | |
|EBImage |? | | | |
|g3viz |? | | | |
|GeneNetworkBuilder |? | | | |
|grandR |? | | | |
|InterCellar |? | | | |
|LACE |? | | | |
|loon.shiny |? | | | |
|MatrixQCvis |? | | | |
|modchart |? | | | |
|multilevelcoda |1.2.3 |1 | | |
|omicsViewer |? | | | |
|RQuantLib |0.4.21 |1 | | |
|rstanarm |2.32.1 |1 | | |
|Seurat |? | | | |
|package |version |error |warning |note |
|:---------------|:-------|:-----|:-------|:----|
|alevinQC |? | | | |
|animalEKF |1.2 |1 | | |
|animaltracker |? | | | |
|antaresViz |? | | | |
|AovBay |0.1.0 |1 | | |
|bdclean |? | | | |
|chipPCR |1.0-2 |1 | | |
|ctsem |3.10.0 |1 | | |
|diveR |? | | | |
|DynNom |5.1 |1 | | |
|hydflood |? | | | |
|loon.shiny |? | | | |
|modchart |? | | | |
|MODIStsp |? | | | |
|protGear |? | | | |
|robmedExtra |0.1.0 |1 | | |
|RQuantLib |0.4.23 |1 | | |
|rstanarm |2.32.1 |1 | | |
|scPipe |? | | | |
|sen2r |? | | | |
|SensMap |0.7 |1 | | |
|Seurat |5.1.0 |1 | | |
|shinyTempSignal |0.0.8 |1 | | |
|Signac |1.13.0 |1 | | |
|simplevis |? | | | |
|statsr |0.3.0 |1 | | |
|teachingApps |? | | | |
|tidyvpc |1.5.1 |1 | | |
|TVTB |? | | | |
## New problems (2)
|package |version |error |warning |note |
|:-------|:-------|:--------|:-------|:------|
|[EgoCor](problems.md#egocor)|1.2.0 |1 __+1__ | |-1 |
|[mxfda](problems.md#mxfda)|0.2.1 | | |__+1__ |

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revdep/cran.md
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## revdepcheck results
We checked 1201 reverse dependencies (1191 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
We checked 1221 reverse dependencies (1208 from CRAN + 13 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
* We saw 0 new problems
* We failed to check 8 packages
* We saw 2 new problems
* We failed to check 16 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
* EgoCor
checking running R code from vignettes ... ERROR
* mxfda
checking installed package size ... NOTE
### Failed to check
* ctsem (NA)
* diveR (NA)
* grandR (NA)
* loon.shiny (NA)
* multilevelcoda (NA)
* RQuantLib (NA)
* rstanarm (NA)
* Seurat (NA)
* animalEKF (NA)
* AovBay (NA)
* chipPCR (NA)
* ctsem (NA)
* diveR (NA)
* DynNom (NA)
* loon.shiny (NA)
* robmedExtra (NA)
* RQuantLib (NA)
* rstanarm (NA)
* SensMap (NA)
* Seurat (NA)
* shinyTempSignal (NA)
* Signac (NA)
* statsr (NA)
* tidyvpc (NA)

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revdep/problems.md
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@@ -1 +1,93 @@
*Wow, no problems at all. :)*
# EgoCor
<details>
* Version: 1.2.0
* GitHub: https://github.com/julia-dyck/EgoCor
* Source code: https://github.com/cran/EgoCor
* Date/Publication: 2024-03-28 18:10:02 UTC
* Number of recursive dependencies: 74
Run `revdepcheck::cloud_details(, "EgoCor")` for more info
</details>
## Newly broken
* checking running R code from vignettes ... ERROR
```
Errors in running code in vignettes:
when running code in ‘Intro_to_EgoCor.Rmd’
...
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
linear model has singular covariance matrix
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
linear model has singular covariance matrix
Warning in gstat::fit.variogram(emp.sv, model = v, fit.sills = TRUE, fit.ranges = TRUE, :
No convergence after 200 iterations: try different initial values?
When sourcing ‘Intro_to_EgoCor.R’:
Error: missing value where TRUE/FALSE needed
Execution halted
‘Intro_to_EgoCor.Rmd’ using ‘UTF-8’... failed
```
## Newly fixed
* checking re-building of vignette outputs ... NOTE
```
Error(s) in re-building vignettes:
--- re-building ‘Intro_to_EgoCor.Rmd’ using rmarkdown
```
## In both
* checking examples ... ERROR
```
Running examples in ‘EgoCor-Ex.R’ failed
The error most likely occurred in:
> ### Name: vario.reg.prep
> ### Title: Adjustment for covariates before semi-variogram model fitting
> ### Aliases: vario.reg.prep
>
> ### ** Examples
>
> ## Example 1
...
+ }
Warning in check_dep_version() :
ABI version mismatch:
lme4 was built with Matrix ABI version 1
Current Matrix ABI version is 0
Please re-install lme4 from source or restore original ‘Matrix’ package
Error in initializePtr() :
function 'cholmod_factor_ldetA' not provided by package 'Matrix'
Calls: <Anonymous> ... initialize -> <Anonymous> -> initializePtr -> .Call
Execution halted
```
# mxfda
<details>
* Version: 0.2.1
* GitHub: https://github.com/julia-wrobel/mxfda
* Source code: https://github.com/cran/mxfda
* Date/Publication: 2024-05-08 11:00:02 UTC
* Number of recursive dependencies: 220
Run `revdepcheck::cloud_details(, "mxfda")` for more info
</details>
## Newly broken
* checking installed package size ... NOTE
```
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 4.0Mb
```