Bioc Checks passed with some warnings remaining

[shaniAmare]

@Shians , Please check it on a local copy first. The built should work now.

The warnings due to not having runnable examples will be fixed in the next PR.

[Shians]

I'm still having 2 errors when I tried to check shaniAmare:master.

The first is in the example of sc_atac_bam_tagging(). https://github.com/shaniAmare/scPipe/blob/master/R/sc_atac_bam_tagging.R#L21-L24 The file requested by inbam <- system.file("extdata", "tiny_sample.bam", package="scPipe") does not exist.

The second is that multiple unit tests are failing. The most concerning being the stack usage warning.

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"gene_id"` instead of `.data$gene_id`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::rename.data.frame(...)
 10. tidyselect::eval_rename(expr(c(...)), .data)
 11. tidyselect:::rename_impl(...)
 12. tidyselect:::eval_select_impl(...)
 16. tidyselect:::vars_select_eval(...)
 17. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 18. tidyselect:::eval_c(expr, data_mask, context_mask)
 19. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 20. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 21. tidyselect:::expr_kind(expr, context_mask, error_call)
 22. tidyselect:::call_kind(expr, context_mask, error_call)

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"seqnames"` instead of `.data$seqnames`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::rename.data.frame(...)
 10. tidyselect::eval_rename(expr(c(...)), .data)
 11. tidyselect:::rename_impl(...)
 12. tidyselect:::eval_select_impl(...)
 16. tidyselect:::vars_select_eval(...)
 17. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 18. tidyselect:::eval_c(expr, data_mask, context_mask)
 19. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 20. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 21. tidyselect:::expr_kind(expr, context_mask, error_call)
 22. tidyselect:::call_kind(expr, context_mask, error_call)

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"start"` instead of `.data$start`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::rename.data.frame(...)
 10. tidyselect::eval_rename(expr(c(...)), .data)
 11. tidyselect:::rename_impl(...)
 12. tidyselect:::eval_select_impl(...)
 16. tidyselect:::vars_select_eval(...)
 17. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 18. tidyselect:::eval_c(expr, data_mask, context_mask)
 19. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 20. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 21. tidyselect:::expr_kind(expr, context_mask, error_call)
 22. tidyselect:::call_kind(expr, context_mask, error_call)

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"end"` instead of `.data$end`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::rename.data.frame(...)
 10. tidyselect::eval_rename(expr(c(...)), .data)
 11. tidyselect:::rename_impl(...)
 12. tidyselect:::eval_select_impl(...)
 16. tidyselect:::vars_select_eval(...)
 17. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 18. tidyselect:::eval_c(expr, data_mask, context_mask)
 19. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 20. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 21. tidyselect:::expr_kind(expr, context_mask, error_call)
 22. tidyselect:::call_kind(expr, context_mask, error_call)

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"strand"` instead of `.data$strand`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::rename.data.frame(...)
 10. tidyselect::eval_rename(expr(c(...)), .data)
 11. tidyselect:::rename_impl(...)
 12. tidyselect:::eval_select_impl(...)
 16. tidyselect:::vars_select_eval(...)
 17. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 18. tidyselect:::eval_c(expr, data_mask, context_mask)
 19. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 20. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 21. tidyselect:::expr_kind(expr, context_mask, error_call)
 22. tidyselect:::call_kind(expr, context_mask, error_call)

Warning (test-anno_import.R:14): ENSEMBL gtf annotation can be imported
Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"GeneID"` instead of `.data$GeneID`
Backtrace:
  1. testthat::expect_identical(anno_import(anno_path), expected)
       at test-anno_import.R:14:2
  9. dplyr:::select.data.frame(., .data$GeneID, dplyr::everything())
 12. tidyselect::eval_select(expr(c(...)), .data)
 13. tidyselect:::eval_select_impl(...)
 17. tidyselect:::vars_select_eval(...)
 18. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 19. tidyselect:::eval_c(expr, data_mask, context_mask)
 20. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 21. tidyselect:::walk_data_tree(new, data_mask, context_mask)
 22. tidyselect:::expr_kind(expr, context_mask, error_call)
 23. tidyselect:::call_kind(expr, context_mask, error_call)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
✖ | 3       0 | Check Barcode Reads before Trimming                                                            
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-check_barcode_reads.R:6): Correct input positions are accepted
Error in `check_barcode_reads(fastq, barcode_file, barcode_file_realname, 
    bstart, blength, search_lines, threshold)`: argument "threshold" is missing, with no default
Backtrace:
 1. testthat::expect_true(...)
      at test-check_barcode_reads.R:6:4
 4. scPipe:::check_barcode_start_position(...)
 5. scPipe:::check_barcode_reads(...)
      at scPipe-Shani/R/check_barcode_start.R:20:2

Error (test-check_barcode_reads.R:13): Bad input position causes rejection
Error in `check_barcode_reads(fastq, barcode_file, barcode_file_realname, 
    bstart, blength, search_lines, threshold)`: argument "threshold" is missing, with no default
Backtrace:
 1. testthat::expect_false(...)
      at test-check_barcode_reads.R:13:4
 4. scPipe:::check_barcode_start_position(...)
 5. scPipe:::check_barcode_reads(...)
      at scPipe-Shani/R/check_barcode_start.R:20:2

Error (test-check_barcode_reads.R:20): Bad match rate causes rejection
Error in `check_barcode_reads(fastq, barcode_file, barcode_file_realname, 
    bstart, blength, search_lines, threshold)`: argument "threshold" is missing, with no default
Backtrace:
 1. testthat::expect_false(...)
      at test-check_barcode_reads.R:20:4
 4. scPipe:::check_barcode_start_position(...)
 5. scPipe:::check_barcode_reads(...)
      at scPipe-Shani/R/check_barcode_start.R:20:2
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
✖ | 2       0 | Catch                                                                                          
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
Failure (???): 
C stack usage  394134749724 is too close to the limit

Error (test-cpp.R:1): (code run outside of `test_that()`)
Error: '' does not exist in current working directory ('/home/shians/Programs/R/scPipe-Shani/tests/testthat').
Backtrace:
 1. testthat::run_cpp_tests("scPipe")
      at test-cpp.R:1:0
 3. xml2:::read_xml.character(paste(output, collapse = "\n"))
 4. xml2:::path_to_connection(x)
 5. xml2:::check_path(path)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ |         5 | Read structure helper                                                                          

══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════
Duration: 2.7 s

[ FAIL 5 | WARN 6 | SKIP 0 | PASS 28 ]

Exited with status 139.