本地存储库中的 RStudio Connect、Packrat 和自定义包

Question

We have recently got RStudio Connect in my office. For our work, we have made custom packages, which we have updated amongst ourselves by opening the project and build+reloading.

I understand the only way I can get our custom packages to work within apps with RSConnect is to get up a local repo and set our options(repos) to include this.

Currently I have the following:

library(drat)

RepoAddress <- "C:/<RepoPath>" # High level path

drat::insertPackage(<sourcePackagePath>, repodir = RepoAddress)

# Add this new repo to Rs knowledge of repos.
options(repos = c(options("repos")$repos,LocalCurrent = paste0("file:",RepoAddress)))

# Install <PackageName> from the local repo :)
install.packages("<PackageName>")

Currently this works nicely and I can install my custom package from the local repo. This indicates to me that the local repo is set up correctly.

As an additional aside, I have changed the DESCRIPTION file to have an extra line saying repository:LocalCurrent .

However when I try to deploy a Shiny app or Rmd which references , I get the following error on my deploy:

Error in findLocalRepoForPkg(pkg, repos, fatal = fatal) : 
  No package '<PackageName> 'found in local repositories specified

I understand this is a problem with packrat being unable to find my local repos during the deploy process (I believe at a stage where it uses packrat::snapshot() ).This is confusing since I would have thought packrat would use my option("repos") repos similar to install.packages . If I follow through the functions, I can see the particular point of failure is packrat:::findLocalRepoForPkg("<PackageName", repos = packrat::get_opts("local.repos")) , which fails even after I define packrat::set_opts("local.repos" = c(CurrentRepo2 = paste0("file:",RepoAddress)))

If I drill into packrat:::findLocalRepoForPkg , it fails because it can't find a file/folder called: "C://". I would have thought this is guaranteed to fail, because repos follow the C://bin/windows/contrib/3.3/ structure. At no point would a repo have the structure it's looking for?

I think this last part is showing I'm materially misunderstanding something. Any guidance on configuring my repo so packrat can understand it would be great.

Answer 1

One should always check what options RStudio connect supports at the moment: https://docs.rstudio.com/connect/admin/r/package-management/#private-packages

Personally I dislike all options for including local/private packages, as it defeats the purpose of having a nice easy target for deploying shiny apps. In many cases, I can't just set up local repositories in the organization because, I do not have clearance for that. It is also inconvenient that I have to email IT-support to make them manually install new packages. Overall I think RS connect is great product because it is simple, but when it comes to local packages it is really not.

I found a nice alternative/Hack to Rstudio official recommendations. I suppose thise would also work with shinyapps.io, but I have not tried. The solution goes like:

1. add to global.R if(!require(local_package) ) devtools::load_all("./local_package")

2. Write a script that copies all your source files, such that you get a shinyapp with a source directory for a local package inside, you could call the directory for ./inst/shinyconnect/ or what ever and local package would be copied to ./inst/shinyconnect/local_package manifest.

3. add script ./shinyconnect/packrat_sees_these_dependencies.R to shiny folder, this will be picked up by packrat-manifest

4. Hack rsconnet/packrat to ignore specifically named packages when building

(1)

#start of global.R...
#load more packages for shiny
library(devtools) #need for load_all
library(shiny)
library(htmltools) #or what ever you need


#load already built local_package or for shiny connection pseudo-build on-the-fly and load
if(!require(local_package)) {
  #if local_package here, just build on 2 sec with devtools::load_all()
  if(file.exists("./DESCRIPTION")) load_all(".") #for local test on PC/Mac, where the shinyapp is inside the local_package
  if(file.exists("./local_package/DESCRIPTION")) load_all("./local_package/") #for shiny conenct where local_package is inside shinyapp
}
library(local_package) #now local_package must load

(3) make script loading all the dependencies of your local package. Packrat will see this. The script will never be actually be executed. Place it at ./shinyconnect/packrat_sees_these_dependencies.R

#these codelines will be recognized by packrat and package will be added to manifest
library(randomForest)
library(MASS)
library(whateverpackageyouneed)

(4) During deployment, manifest generator (packrat) will ignore the existence of any named local_package. This is an option in packrat, but rsconnect does not expose this option. A hack is to load rsconnect to memory and and modify the sub-sub-sub-function performPackratSnapshot() to allow this. In script below, I do that and deploy a shiny app.

library(rsconnect)


orig_fun = getFromNamespace("performPackratSnapshot", pos="package:rsconnect")

#packages you want include manually, and packrat to ignore
ignored_packages = c("local_package")

#highjack rsconnect
local({
  assignInNamespace("performPackratSnapshot",value =  function (bundleDir) {
      owd <- getwd()
      on.exit(setwd(owd), add = TRUE)
      setwd(bundleDir)
      srp <- packrat::opts$snapshot.recommended.packages()
      packrat::opts$snapshot.recommended.packages(TRUE, persist = FALSE)
      packrat::opts$ignored.packages(get("ignored_packages",envir = .GlobalEnv)) #ignoreing packages mentioned here
      print("ignoring following packages")
      print(get("ignored_packages",envir = .GlobalEnv))
      on.exit(packrat::opts$snapshot.recommended.packages(srp,persist = FALSE), add = TRUE)
      packages <- c("BiocManager", "BiocInstaller")
      for (package in packages) {
        if (length(find.package(package, quiet = TRUE))) {
          requireNamespace(package, quietly = TRUE)
          break
        }
      }
      suppressMessages(packrat::.snapshotImpl(project = bundleDir,
                                              snapshot.sources = FALSE, fallback.ok = TRUE, verbose = FALSE,
                                              implicit.packrat.dependency = FALSE))
      TRUE
    },
    pos = "package:rsconnect"
  )},
envir = as.environment("package:rsconnect")
)


new_fun = getFromNamespace("performPackratSnapshot", pos="package:rsconnect")
rsconnect::deployApp(appDir="./inst/shinyconnect/",appName ="shinyapp_name",logLevel = "verbose",forceUpdate = TRUE)

Answer 2

The problem is one of nomenclature.

I have set up a repo in the CRAN sense. It works fine and is OK. When packrat references a local repo , it is referring to a local git-style repo.

This solves why findlocalrepoforpkg doesn't look like it will work - it is designed to work with a different kind of repo.

Answer 3

Feel free to also reach out to support@rstudio.com

I believe the local package code path is triggered in packrat because of the missing Repository: value line in the Description file of the package. You mentioned you added this line, could you try the case-sensitive version?

That said, RStudio Connect will not be able to install the package from the RepoAddress as you've specified it (hardcoded on the Windows share). We'd recommend hosting your repo over https from a server that both your Dev environment and RStudio Connect have access to. To make this type of repo setup much easier we just released RStudio Package Manager which you (and IT!) may find a compelling alternative to manually managing releases of your internal packages via drat.