Upkeep

[dunkenwg]

No description provided.

[dunkenwg]

When I run the check/documentation for this package I get:

══ Documenting ══════════════════════════════════════════════════════════════════════════════════════
ℹ Updating embr documentation
Writing NAMESPACE
ℹ Loading embr
✖ pars.R:105: S3 method `pars.character` needs @export or @exportS3method tag.
Writing NAMESPACE

Should pars.character() be exported?

[joethorley]

Can you talk to Ayla when she is back about the NOTE around exporting S3 tags? I don't think it should be exported as it will likely break things in this case but we should suppress the NOTE if we can.

[dunkenwg]

Can you talk to Ayla when she is back about the NOTE around exporting S3 tags? I don't think it should be exported as it will likely break things in this case but we should suppress the NOTE if we can.

I'm also going to wait until Ayla is back to discuss why the Mac OS R-CMD-check is failing due to a segmentation fault as I'm quite lost.

[aylapear]

Can you talk to Ayla when she is back about the NOTE around exporting S3 tags? I don't think it should be exported as it will likely break things in this case but we should suppress the NOTE if we can.

This seems to be a new thing the documentation is requiring us to do. For now ignore the issue as we are working out what to do for this across the board. Please make an internal-infrastructure issue about this and list this repo in the comments and once we figure out the appropriate fix we can apply it to the relevant repositories.

[aylapear]

I'm also going to wait until Ayla is back to discuss why the Mac OS R-CMD-check is failing due to a segmentation fault as I'm quite lost.

I am not familiar with this specific issue, give me a call next time you are working on it and we can chat through some things to test to dig into the issue further.

[aylapear]

Changes look good but we need to figure out the failing action before we can merge in the changes.

[dunkenwg]

Check if action runs on no tests then add tests back

[joethorley]

We are getting a segfault.

I suspect the action is failing when it tries to install JAGS for macos

> test_check("embr")

 *** caught segfault ***
address 0x6e6f432f34366d72, cause 'invalid permissions'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
 5: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
 6: asNamespace(ns)
 7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
 8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
 9: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
10: loadNamespace(x)
11: ggplot_data(x, y, x_name, y_name)
12: plot_data.factor(x = x[[x_name]], y = x[[y_name]], x_name = x_name,     y_name = y_name)
13: plot_data(x = x[[x_name]], y = x[[y_name]], x_name = x_name,     y_name = y_name)
14: plot_data.data.frame(data)
15: plot_data(data)
16: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
17: withCallingHandlers(code, warning = function(condition) {    if (ignore_deprecation && is_deprecation(condition)) {        return()    }    out$push(condition)    maybe_restart("muffleWarning")})
18: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),     ...)
19: quasi_capture(enquo(object), label, capture_warnings, ignore_deprecation = identical(regexp,     NA))
20: expect_warning(x <- plot_data(data))
21: eval(code, test_env)
22: eval(code, test_env)
23: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
31: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
32: test_that("plot_data", {    data <- data.frame(x = 1:10, y = rep(2, 10), y2 = c(1, 4,         6, 7, 9, 11, 2, 2, 1, 5), str = paste0("txt", 1:10),         factor = factor(10:1), stringsAsFactors = FALSE)    expect_warning(x <- plot_data(data))    expect_identical(length(x), 6L)    expect_true(all(vapply(x, inherits, TRUE, what = "ggplot")))})
33: eval(code, test_env)
34: eval(code, test_env)
35: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
41: tryCatchList(expr, classes, parentenv, handlers)
42: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
Error: Error: R CMD check found ERRORs
Execution halted
43: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
44: source_file(path, env = env(env), desc = desc, error_call = error_call)
45: FUN(X[[i]], ...)
46: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
47: doTryCatch(return(expr), name, parentenv, handler)
48: tryCatchOne(expr, names, parentenv, handlers[[1L]])
49: tryCatchList(expr, classes, parentenv, handlers)
50: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
51: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
52: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
53: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
54: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
55: test_check("embr")
An irrecoverable exception occurred. R is aborting now ...

[joethorley]

Note there is this related issue that Kirill filed for jmbr

poissonconsulting/jmbr#45

[dunkenwg]

Fixed the macOS R-CMD-check by following this repo's action:

- name: Install JAGS (if macOS)
   if: runner.os == 'macOS'
      # This worked before R 4.3: brew install jags
      run: |
         curl -o wjags.pkg -L0 -k --url https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.2.pkg
         sudo installer -pkg wjags.pkg -target /
         rm wjags.pkg

brew install jags no longer works because Homebrew's library path has changed from /usr/local/lib/ to /opt/homebrew/. A .pkg installer works though!

[joethorley]

Awesome - well done!

[joethorley]

@dunkenwg - can you do the same fix for jmbr?

[dunkenwg]

@aylapear, would you review this when you have a chance?

[aylapear]

Awesome job on figuring that fix out!

[dunkenwg]

@joethorley or @aylapear, how do I update the status of this pull request so that the rcc action will run and I can merge?