Fix/install GitHub submodule warn

[ashander]

Add warning when downloading from github repo that uses submodules
(assessed through presence of .gitsubmodules file).

Help for install_github updated to suggest use of install_git with proper args in this case.

Limited testing (with mock responses from download and attempt to download .gitsubmodules).

Partially responsive to #737

[ashander]

Travis CI fails with message below. Seems like a separate issue.

Warning message:

package ‘BiocInstaller’ is not available (for R version 3.1.3)

The command "Rscript -e 'options(repos = "http://cran.rstudio.com"); tryCatch({ deps <- devtools::install_deps(dependencies = TRUE) }, error = function(e) { message(e); q(status=1) }); if (!all(deps %in% installed.packages())) { q(status = 1, save = "no") }'" failed and exited with 1 during .

[ashander]

Yes looks like @jimhester has a fix in PR #746

[hadley]

1. I think the comment is extraneous (given how simple the code is)
2. Can you please use a space after if
3. warning() looks like it's indented too much
4. I always use call. = FALSE with warning
5. I think it would be easier to understand if src_submodules was defined in front of this block

[ashander]

Thanks! Sorry for missing the indent and if-paren style with this PR. 

I've made the changes, and also fixed indent style in changes the tests

- Jaime

On Tue, Apr 21, 2015 at 6:51 AM, Hadley Wickham [email protected]
wrote:

@@ -98,6 +106,10 @@ remote_download.github_remote <- function(x, quiet = FALSE) {
} else {
auth <- NULL
}

• if repo uses submodules warn user

• I think the comment is extraneous (given how simple the code is)
• Can you please use a space after if
• warning() looks like it's indented too much

4. I always use call. = FALSE with warning

Reply to this email directly or view it on GitHub:
https://github.com/hadley/devtools/pull/751/files#r28778939

[hadley]

Looks good! Could you please add a bullet point to NEWS, thanking your github username?

(FYI github only notifies me about comments, not commits, so when done please add a comment like "PTAL")

[ashander]

Done! PTAL

- Jaime

On Tue, Apr 28, 2015 at 6:18 AM, Hadley Wickham [email protected]
wrote:

Looks good! Could you please add a bullet point to NEWS, thanking your github username?

(FYI github only notifies me about comments, not commits, so when done please add a comment like "PTAL")

Reply to this email directly or view it on GitHub:
#751 (comment)

[hadley]

Thanks!

[jonkeane]

I'm attempting to install from a github repository that has a submodule. I've tried to use install_git('[url to repo]", args="--recursive") but I get a warning that args is deprecated. Is there a new prefered method for installing submodules? Now that args is deprecated with install_git()?

Sorry if reviving this issue is inappropriate, I'm happy to start a new one if that is preferred.

[ashander]

I can't say for certain. But, it seems adopting git2r traded stability for the args. See 1b7e67a

Rather than commenting here, it's probably better to open a new issue regarding git2r and args (unless that discussion has already happened -- I haven't searched). In that issue you could reference this PR.

In any case, the suggestion to use install_git with --args should be removed from the docs to install-github.r

[jimhester]

@jonkeane install_git() uses libgit2 rather than the git client to clone the git repository. git2r the R client to the libgit2 library does not look it has an interface for submodules on cursory inspection.

Probably the easiest thing to do assuming you do have the command line git client installed is define a simple helper function to clone the repository locally and install from there.

install_submodule_git <- function(x, ...) {
  install_dir <- tempfile()
  system(paste("git clone --recursive", shQuote(x), shQuote(install_dir)))
  devtools::install(install_dir, ...)
}
install_submodule_git("https://github.com/jonkeane/mocapGrip")
list.files(system.file(package = "mocapGrip", "python", "pyelan"))
#> [1] "__init__.py"      "elanGen.py"       "elanSkeleton.eaf" "pyelan.py"        "README.md"        "relPathFix.py"