remove system file inst

[nikolas-burkoff]

Closes #81

This function is only used in .onLoad

FYI @arkadiuszbeer

[nikolas-burkoff]

@gogonzo do we actually need inst_file? Or should I remove lines 79 + 83 + 84 ?

[Polkas]

agree, remove them as in the compiled package there is no inst directory.

[github-actions]

Code Coverage Summary

Filename                                 Stmts    Miss  Cover    Missing
-------------------------------------  -------  ------  -------  -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/as_cdisc.R                                39       4  89.74%   107-110
R/Callable.R                                45       0  100.00%
R/CallableCode.R                            36       2  94.44%   26, 63
R/CallableFunction.R                        88       3  96.59%   160-162
R/CallablePythonCode.R                      58      58  0.00%    21-223
R/CDISCTealData.R                           79      12  84.81%   41, 47-50, 55, 128, 131, 134, 266-268
R/CDISCTealDataConnector.R                  20       3  85.00%   31, 36, 49
R/CDISCTealDataset.R                        46      11  76.09%   108-115, 208-210
R/CDISCTealDatasetConnector.R               26       1  96.15%   116
R/CodeClass.R                              111       1  99.10%   157
R/data_label.R                              32       9  71.88%   35-39, 58-61, 101
R/deep_clone_r6.R                            9       0  100.00%
R/get_attrs.R                                2       2  0.00%    12-47
R/get_code.R                               173      21  87.86%   87, 140-143, 196-197, 201, 207-208, 212, 266, 297, 333, 337, 372, 381-385
R/get_dataname.R                             4       0  100.00%
R/get_dataset_label.R                        3       0  100.00%
R/get_dataset.R                             13       8  38.46%   37, 54, 80-86
R/get_datasets.R                            10       5  50.00%   85, 107-111
R/get_key_duplicates.R                      37       7  81.08%   42-48, 55-56
R/get_keys.R                                15       7  53.33%   72-73, 130-150
R/get_raw_data.R                            24      11  54.17%   109-122
R/include_css_js.R                           9       1  88.89%   20
R/is_pulled.R                                4       0  100.00%
R/JoinKeys.R                               128       4  96.88%   219, 282-321
R/load_dataset.R                            25      18  28.00%   60-65, 89-222
R/MAETealDataset.R                         137      57  58.39%   57, 118, 156-211, 227-232, 239-248, 285, 326-342
R/mutate_dataset.R                          18       0  100.00%
R/set_args.R                                10       5  50.00%   42-46
R/teal_data.R                               21       3  85.71%   101-103
R/TealData.R                               271     116  57.20%   87, 99, 236, 248-316, 330, 333, 389-396, 426-431, 433, 435-440, 442, 459-504
R/TealDataAbstract.R                       231      13  94.37%   86-89, 214-217, 428, 453-457, 479, 485
R/TealDataConnection.R                     296     179  39.53%   58-59, 64, 67, 70, 106-162, 182, 185-187, 193-199, 204-206, 232, 237, 253-276, 286, 299, 320, 324-329, 332-335, 357-359, 363-370, 373-376, 391-405, 424-425, 445-516, 534-542, 544, 548-563, 566-569, 601, 607-611, 625, 660-662, 671-673
R/TealDataConnector.R                      195     101  48.21%   167, 179, 183, 196, 199-208, 210, 218-227, 310-314, 372-476
R/TealDataset.R                            376      23  93.88%   148-158, 432-436, 492-501, 551
R/TealDatasetConnector_constructors.R      300      53  82.33%   176-212, 262, 830-835, 1033-1109
R/TealDatasetConnector.R                   341      90  73.61%   122, 179, 248, 262, 267, 281, 473, 496-534, 565, 580-610, 700, 710, 719-726, 739, 754-781
R/to_relational_data.R                      54       7  87.04%   35-36, 40, 99, 106, 112, 127
R/topological_sort.R                        32       4  87.50%   53-56
R/utils.R                                   49       9  81.63%   22-23, 27, 76-83
R/validate_data_args.R                      34       0  100.00%
R/zzz.R                                      6       6  0.00%    4-12
TOTAL                                     3407     854  74.93%

Results for commit: e9a974b

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

       1 files       27 suites   51s ⏱️
   319 tests    319 ✔️ 0 💤 0 ❌
1 098 runs  1 098 ✔️ 0 💤 0 ❌

Results for commit 045b3eb.

♻️ This comment has been updated with latest results.

[Polkas]

The base::system.file is overwritten (e.g. when devtools::load_all is used) by the pkgdown version:

> system.file
function (..., package = "base", lib.loc = NULL, mustWork = FALSE) 
{
    if (!(package %in% dev_packages())) {
        return(base::system.file(..., package = package, lib.loc = lib.loc, 
            mustWork = mustWork))
    }
    if (dots_n(...) && is_string(..1)) {
        if (is_string("inst", ..1) || grepl("^inst/", ..1)) {
            cli::cli_abort(c("Paths can't start with `inst`", 
                i = "Files in `inst` are installed at top-level."))
        }
    }
    pkg_path <- find.package(package)
    files_inst <- file.path(pkg_path, "inst", ...)
    present_inst <- file.exists(files_inst)
    files_top <- file.path(pkg_path, ...)
    present_top <- file.exists(files_top)
    files <- files_top
    files[present_inst] <- files_inst[present_inst]
    files <- files[present_inst | present_top]
    if (length(files) > 0) {
        normalizePath(files, winslash = "/")
    }
    else {
        if (mustWork) {
            cli::cli_abort("Can't find package file.", call = NULL)
        }
        ""
    }
}
<bytecode: 0x1374fa068>
<environment: namespace:pkgload>

There are at least two solutions:

• remove the lines suggested by Nick
• add base:: prefix to system.file calls
• remove the function :)

[Polkas]

Suggested change

inst_file <- file.path(system.file(package = pkg), file_name)

[Polkas]

Suggested change

	base_file <- system.file(file_name, package = pkg)
	base_file <- base::system.file(file_name, package = pkg)