Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(parsemsf)
  > 
  > test_check("parsemsf")
  ── Warning (test_make_area_table.R:16:3): make_area_table creates a data frame w
  `select_()` is deprecated as of dplyr 0.7.0.
  Please use `select()` instead.
  This warning is displayed once every 8 hours.
  Call `lifecycle::last_warnings()` to see where this warning was generated.
  
  ── ERROR (test_make_area_table.R:16:3): make_area_table creates a data frame wit
  Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
  Backtrace:
       █
    1. ├─testthat::expect_equal(...) test_make_area_table.R:16:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::colnames(make_area_table(parsemsf_example("test_db.msf")))
    5. │ └─base::is.data.frame(x)
    6. └─parsemsf::make_area_table(parsemsf_example("test_db.msf"))
    7.   └─`%>%`(...)
    8.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    9.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   10.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   11.         └─parsemsf:::`_fseq`(`_lhs`)
   12.           └─magrittr::freduce(value, `_function_list`)
   13.             ├─base::withVisible(function_list[[k]](value))
   14.             └─function_list[[k]](value)
   15.               └─dplyr::select_(...)
  
  ── ERROR (test_make_pep_table.R:13:3): make_pep_table creates a data frame with 
  Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
  Backtrace:
       █
    1. ├─testthat::expect_equal(...) test_make_pep_table.R:13:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::colnames(make_pep_table(parsemsf_example("test_db.msf")))
    5. │ └─base::is.data.frame(x)
    6. └─parsemsf::make_pep_table(parsemsf_example("test_db.msf"))
    7.   └─tbl(my_db, "SchemaInfo") %>% select_(~SoftwareVersion) %>% collect()
    8.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    9.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   10.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   11.         └─parsemsf:::`_fseq`(`_lhs`)
   12.           └─magrittr::freduce(value, `_function_list`)
   13.             └─function_list[[i]](value)
   14.               └─dplyr::select_(., ~SoftwareVersion)
  
  ── ERROR (test_map_peptides.R:16:3): map_peptides creates a data frame with the 
  Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
  Backtrace:
       █
    1. ├─testthat::expect_equal(...) test_map_peptides.R:16:2
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::colnames(map_peptides(parsemsf_example("test_db.msf")))
    5. │ └─base::is.data.frame(x)
    6. └─parsemsf::map_peptides(parsemsf_example("test_db.msf"))
    7.   ├─`%>%`(...)
    8.   │ └─base::eval(lhs, parent, parent)
    9.   │   └─base::eval(lhs, parent, parent)
   10.   └─parsemsf::make_pep_table(msf_file, min_conf, collapse = FALSE)
   11.     └─tbl(my_db, "SchemaInfo") %>% select_(~SoftwareVersion) %>% collect()
   12.       ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
   13.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   14.         └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
   15.           └─parsemsf:::`_fseq`(`_lhs`)
   16.             └─magrittr::freduce(value, `_function_list`)
   17.               └─function_list[[i]](value)
   18.                 └─dplyr::select_(., ~SoftwareVersion)
  
  ── ERROR (???): (code run outside of `test_that()`) ────────────────────────────
  Error: no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
  Backtrace:
       █
    1. └─parsemsf::make_area_table(parsemsf_example("test_db.msf"))
    2.   └─`%>%`(...)
    3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
    5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
    6.         └─parsemsf:::`_fseq`(`_lhs`)
    7.           └─magrittr::freduce(value, `_function_list`)
    8.             ├─base::withVisible(function_list[[k]](value))
    9.             └─function_list[[k]](value)
   10.               └─dplyr::select_(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  Warning (test_make_area_table.R:16:3): make_area_table creates a data frame with the correct column names
  ERROR (test_make_area_table.R:16:3): make_area_table creates a data frame with the correct column names
  ERROR (test_make_pep_table.R:13:3): make_pep_table creates a data frame with the correct column names
  ERROR (test_map_peptides.R:16:3): map_peptides creates a data frame with the correct column names
  ERROR (???): (code run outside of `test_that()`)
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted