add continue_on_error feature in `switchTo()`

[NBRAYKO]

TL;DR: when creating a library, switchTo() will quit with an error if the manifest is not carefully checked (e.g., if asking for some weird version that does not exist). Any way to issue a message instead of throwing an error? Some sort of force or continue_on_error? It takes a while to download 100s of libraries only to have to start all over on error.

I'm trying to recreate an environment used on a Dev R server to train a model into a Prod server. I don't have root access to the latter's default repository and it's ruining my life. Hoping your package is the answer. Here's the code I run

library(switchr, lib.loc = lib_loc)
package_manifest_gh <- GithubManifest("hadley/secure", 
                        "hadley/multidplyr",
                        "PhilippPro/vimp", 
                        "gsk3/taRifx.geo")
#capture packages in current env (get about 410)
package_manifest <- libManifest(known_manifest = package_manifest_gh)
#clean up manifest df and versions
temp_df <- manifest_df(package_manifest) 
manifest_df(package_manifest)<-temp_df[which(!is.na(temp_df$type)),]
temp_df <- versions_df(package_manifest)
versions_df(package_manifest)<-subset(temp_df, name %in% manifest_df(package_manifest)$name)

#create switch library
switchrBaseDir("/usr/share/R/library")
switchTo(paste0("NoShowPackage",format(Sys.Date(),"%m_%Y")),
                seed = package_manifest)

and error I end up with. I just had to go in, manually edit the manifest for multidplyr and start over. Perhaps there's a smarter way to avoid redownloading by using lazyRepo(), but I couldn't find in documentation

downloaded 0 bytes

sh: svn: command not found
Error in innerFun(src, pkg, version = vers, dir = dir, param = param,  : 
  Unable to locate the specified version  of packagemultidplyr

[gmbecker]

Thanks for the report. I will respond in more detail later, but to get things moving, can you attach the manifest you get (or just the part with multidplyr and its dependencies) that breaks things?

[NBRAYKO]

Sure, thanks! I'd already removed multidplyr since production code was not using it, but here's the version and package dfs for the PKI package which also threw an error

> package_manifest <- libManifest(record_versions = TRUE)

> package_manifest@pkg_versions %>% filter(name =="PKI")
  name version
1  PKI   0.1-5

> package_manifest@pkg_manifest@manifest %>% filter(name =="PKI")
  name                                  url type branch subdir extra
1  PKI https://cran.rstudio.com/src/contrib CRAN  trunk      .  <NA>
> 

The stable version in CRAN is 0.1-3. I think I had downloaded 0.1-5 from GitHub because it had a patch I needed. Did not remember that when I was creating the manifest. It would be convenient if whenever a version cannot be found by switchTo(), it would just install any available version. So like having record_versions = FALSE, but only for the problematic packages.

[gmbecker]

It would be convenient if whenever a version cannot be found by switchTo(), it would just install any available version. So like having record_versions = FALSE, but only for the problematic packages.

I'm hesitant to support this because this could easily give rise to a broken package library where, for example, a versioned dependency is not met. Even worse, the versioned dependency might not be explicitly declared by the package, and things might just be broken. I suppose I could just warn on that, although, alternatively you can

I will look into supporting this, perhaps only in cases where there are no reverse dependencies for the package.