Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document #1420

schloerke · 2018-08-03T21:23:57Z

By keeping track of the package version, we can force a new render if the user does not have the same package versions as the pre-rendered document.

This solves the error where a pre-rendered resource can not be mounted (because it doesn't exist!).

NEWS item
test?
when in Shiny Server and RSC env set in learnr

behavior: * return false if there is a prerender_option = 0 or yell if not 0 or 1 * if the original file is newer than the compiled file, return true * if any external resource is newer, return true * NEW: if any htmldep's package version is different than the installed, return true * return false

…exist

jjallaire · 2018-08-04T11:02:09Z

This LGTM and will be a huge improvement on what we have currently (which is obviously much too fragile).

rich-iannone · 2018-08-07T17:41:19Z

Based on a code-pairing between me and Barret, there are some changes that incorporate R package dependencies. One thing that Barret noted was that the package dependencies (in the current form below) will incorporate packages like graphics and methods where their versions mirror the R version. It could be argued that these packages don't change much between different R versions so we shouldn't invalidate based on these specific packages.

Here are the changes per file:

util.R

add:

get_loaded_packages <- function() {

  packages <- setdiff(loadedNamespaces(), "base")
  loadedversion <- vapply(packages, getNamespaceVersion, "")
  attached <- paste0("package:", packages) %in% search()

  data.frame(packages = packages[attached], loadedversion = loadedversion[attached],
             row.names = NULL, stringsAsFactors = FALSE)
}

render.R

change (ln 362):

output_options$dependency_resolver <- function(deps) {
  shiny_prerendered_dependencies <<- list(deps = deps, packages = get_loaded_packages())
  list()
}

shiny_prerendered.R

change (ln 184):

dependencies <- lapply(shiny_prerendered_dependencies$deps, function(dependency) {

add (after ln 228):

dependencies_pkgs_json <- jsonlite::serializeJSON(shiny_prerendered_dependencies$packages, pretty = FALSE)
shiny_prerendered_append_context(con, "package_dependencies", dependencies_pkgs_json)

yihui · 2018-08-07T20:09:14Z

I think it is fine to ignore base R packages. The original problem was caused by packages that ship HTML dependencies. Base R packages don't have such things.

rich-iannone · 2018-08-07T21:21:49Z

Thanks, Yihui. To ignore the base R packages, the function get_loaded_packages() in util.R would change to:

get_loaded_packages <- function() {

  base_r_packages <-
    c("base", "compiler", "datasets", "graphics", "grDevices",
      "grid", "methods", "parallel", "splines",  
      "stats", "stats4", "tcltk", "tools", "utils")
  
  packages <- sort(setdiff(loadedNamespaces(), base_r_packages))
  loadedversion <- vapply(packages, getNamespaceVersion, "")
  attached <- paste0("package:", packages) %in% search()

  data.frame(packages = packages[attached], loadedversion = loadedversion[attached],
             row.names = NULL, stringsAsFactors = FALSE)
}

schloerke · 2018-08-08T00:55:56Z

Documenting decision towards using loaded packages (after execution) vs detecting library and :: calls in the code (without execution)

There were two main approaches:

It was already solved in packrat and to use something similar to packrat::findDependencies. This function boils down to regular expressions and the name of the function calls. This can easily be tricked, but can not be poisoned by the user workspace.
We could detect the loaded packages after executing all the R code in the document. Looking at attached packages would only give results for library or require calls. Looking at the search path would give all packages that have been loaded or used. This can not be fooled like packrat, but can be poisoned by external user packages that were not a part of the knitting of the document.

We decided to go with the loaded packages, as it can not be easily fooled and most renderings of a document are done within RStudio's clean environment and on hosted sites, which will compile in a clean environment. The only caveat are with console users, where rendering is known to not be in a clean environment by default.

The good part about being aggressive with the execution package version matching is that users will get a cohesive experience. The worst interaction of not matching the execution packages is having to re-render the shiny prerendered document. This will be the first interaction of most any pre-render documents, but after re-rendering, it wont happen until the user (or service) updates their local packages.

yihui · 2018-08-08T04:52:54Z

That sounds reasonable to me.

@rich-iannone

…in prerender calculation Thanks @rich-iannone for the help!

yihui · 2018-08-08T16:01:06Z

R/util.R

+    "base", "compiler", "datasets", "graphics", "grDevices",
+    "grid", "methods", "parallel", "splines",
+    "stats", "stats4", "tcltk", "tools", "utils"
+  )


You can use rownames(installed.packages(priority = 'base')) instead of hardcoding the package names.

Aha! I thought there was a better way (but I couldn't find it). Thanks!

wch · 2018-08-13T19:57:15Z

R/shiny_prerendered.R

+  # check that the major R versions match
+  if (!identical(R.version$major, execution_info$rMajorVersion)) {
+    return(TRUE)
+  }


Remove -- we can use exact version matching for base packages.

wch · 2018-08-13T20:08:29Z

R/util.R

+
+  packages <- sort(setdiff(loadedNamespaces(), base_r_packages))
+  version <- vapply(packages, get_package_version_string, character(1))
+  attached <- paste0("package:", packages) %in% search()


We need to look at all loaded packages, not just the attached ones. For example, if someone does library(shiny), then this will only record the version of shiny, but not dependencies like htmltools.

Another case is if they do htmltools::div(), it will not attach htmltools, and this code will also not record the version.

wch · 2018-08-13T20:54:03Z

R/util.R

+# find all loaded packages.
+# May contain extra packages, but contains all packages used while knitting
+get_loaded_packages <- function() {
+  base_r_packages <- rownames(installed.packages(priority = 'base'))


This can be removed -- we might as well look at the base R packages as well, since it's (marginally) safer to use them, and the code will be slightly simpler without excluding them. It also lets us not record the R major version because that comes along with these packages.

wch · 2018-08-13T20:59:26Z

R/shiny_prerendered.R

+    f = function(package, version) {
+      !identical(get_package_version_string(package), version)
+    }
+  ))


Change to for loop with a short-circuit return.

wch

See comments.

wch · 2018-08-16T17:24:34Z

R/shiny_prerendered.R

@@ -298,7 +293,8 @@ shiny_prerendered_append_dependencies <- function(input, # always UTF-8

  # write r major version and execution package dependencies
  execution_json <- jsonlite::serializeJSON(
-    shiny_prerendered_dependencies[c("rMajorVersion", "packages")],
+    # visibly display what is being stored
+    shiny_prerendered_dependencies[c("packages")],


Don't need c() here

jjallaire · 2018-08-24T05:52:03Z

We just need to make sure that Shiny Server and RSC run these in a way that ensures that no render occurs (on the assumption that they are in read-only directories). They can I believe do this via an environment variable (which they may or may not already be setting, worth checking on).

schloerke · 2018-09-06T19:22:39Z

@jjallaire The original envvar check of RMARKDOWN_RUN_PRERENDER is still honored inside rmarkdown.

rstudio/learnr@942df45 now checks if the learnr::run_tutorial is being executed on a SS or RSC.

If learnr::run_tutorial is on a server, it will behave like it currently does (never attempt to rerender). If learnr::run_tutorial is now on a personal machine, it'll attempt to attempt to rerender aggressively.

schloerke · 2018-09-06T19:46:45Z

@yihui removed [WIP], ready for merge when you're ready. Thank you!

yihui

This is excellent. Thanks!

…, shiny-prerendered document (rstudio#1420) Fixes rstudio/learnr#169

schloerke added 3 commits August 3, 2018 17:11

fix typo

e0651c0

Store the pkgVersion in the html deps json

d2a7252

schloerke mentioned this pull request Aug 3, 2018

error when running a tutorial rstudio/learnr#169

Closed

check if the pkg field is there. otherwise check for the src file to …

fc9de14

…exist

add some comments

6281c12

schloerke added 2 commits August 8, 2018 11:48

store execution pacakges in shiny-prerendered documents and check it …

e7615ef

…in prerender calculation Thanks @rich-iannone for the help!

added news item

ff9b16c

yihui reviewed Aug 8, 2018

View reviewed changes

schloerke added 2 commits August 8, 2018 12:44

get standard packages by using installed.packages

26c84b0

merged from master

d04941f

schloerke mentioned this pull request Aug 10, 2018

Aggressive Prerender checks within rmarkdown rstudio/learnr#179

Merged

wch reviewed Aug 13, 2018

View reviewed changes

wch suggested changes Aug 13, 2018

View reviewed changes

schloerke added 3 commits August 14, 2018 10:55

remove r major version

8456c80

use all loaded pkgs

ffd19cb

short circuit the exec pkg check

de86f8e

wch approved these changes Aug 16, 2018

View reviewed changes

schloerke added 3 commits August 23, 2018 18:13

close broken code

a47129e

remove unnecessary c()

ad406f3

merged master

07f4a86

fix unknown execution_pkgs

9b9f1d8

schloerke changed the title ~~[WIP] Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document~~ Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document Sep 6, 2018

yihui mentioned this pull request Sep 11, 2018

No chapter on shiny_prerendered runtime. Should there be one ? rstudio/rmarkdown-book#37

Open

yihui approved these changes Oct 8, 2018

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yihui added this to the v1.11 milestone Oct 8, 2018

yihui merged commit 427724f into rstudio:master Oct 8, 2018

yihui added a commit that referenced this pull request Oct 8, 2018

add Barret to ctb (#1420), and bump version

dcc7d37

schloerke deleted the htmldep_version branch October 8, 2018 20:08

yihui pushed a commit to RLesur/rmarkdown that referenced this pull request Apr 1, 2019

Force a render when user pkgs don't match the pkgs used in a rendered…

e117ec4

…, shiny-prerendered document (rstudio#1420) Fixes rstudio/learnr#169

yihui added a commit to RLesur/rmarkdown that referenced this pull request Apr 1, 2019

add Barret to ctb (rstudio#1420), and bump version

50885fd

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Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document #1420

Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document #1420

schloerke commented Aug 3, 2018 •

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Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document #1420

Force a render when user pkgs don't match the pkgs used in a rendered, shiny-prerendered document #1420

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