Clean up tests outputs/prints/messages/etc

Testthat produces a lot of noise which make it hard to parse out problems.  could we look at reducing the artifacts being spit out here?  @kodesiba, @parmsam-pfizer,  @nicholas-masel do you all see the same thing when running logrx tests

=> devtools::test()

ℹ Testing logrx
✔ | F W  S  OK | Context
⠏ |          0 | axecute                                                 [1] "hello logrx"
⠹ |          3 | axecute                                                 hello logrx
⠸ |         14 | axecute                                                 hello logrx
⠇ |         19 | axecute                                                 hello logrx
⠏ |         20 | axecute                                                 hello logrx
⠹ |         23 | axecute                                                 hello logrx
this is output
Warning: closing unused connection 4 (/tmp/RtmpREIYgA/log_out_nested.Rds)
⠧ |         28 | axecute                                                 hello logrx
⠋ |         31 | axecute                                                 hello logrx
⠼ |         35 | axecute                                                 

processing file: ex1.Rmd
1/7                  
2/7 [cars]           
3/7                  
4/7 [pressure]       
5/7                  
6/7 [unnamed-chunk-1]
7/7                  
[1] "print"
output file: ex1.knit.md

/usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/pandoc +RTS -K512m -RTS ex1.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output ex1.html --lua-filter /cloud/lib/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /cloud/lib/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /cloud/lib/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /cloud/lib/x86_64-pc-linux-gnu-library/4.2/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpREIYgA/rmarkdown-str20fb4679b1ee.html 

Output created: ex1.html


processing file: ref/ex1.Rmd
1/7                  
2/7 [cars]           
3/7                  
4/7 [pressure]       
5/7                  
6/7 [unnamed-chunk-1]
7/7                  
output file: /tmp/RtmpREIYgA/file20fb63d12062.R

✔ |         46 | axecute [10.8s]                                         
⠇ |          9 | get                                                     Rows: 3
Columns: 2
$ cyl  <dbl> 4, 6, 8
$ mean <dbl> 26.66364, 19.74286, 15.10000
⠋ |         11 | get                                                     [1] "hello logrx"
Error: ref/ex4.R:5:0: unexpected end of input
3: 
4: print("hello logrx"
  ^
⠼ |         15 | get                                                     [1] 1
⠧ |         18 | get                                                     [1] 1


processing file: ref/ex1.Rmd
1/7                  
2/7 [cars]           
3/7                  
4/7 [pressure]       
5/7                  
6/7 [unnamed-chunk-1]
7/7                  
output file: /tmp/RtmpREIYgA/file20fb28e71d07.R

[1] "print"
✔ |         21 | get [3.7s]                                              
⠏ |          0 | interact                                                [1] "log print"
[1] "log print 2"
log catlog cat 2log inform
log inform 2
log message
log message 2
⠋ |   3      8 | interact                                                Error: log error
⠦ |   4     13 | interact                                                
Attaching package: 'magrittr'

The following object is masked from 'package:logrx':

    set_names

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

✔ |   4     18 | interact [2.1s]
─────────────────────────────────────────────────────────────────────────
Warning (test-interact.R:85:3): setting log name works
log_path already assigned, will not be overwritten
Backtrace:
    ▆
 1. ├─testthat::expect_warning(set_log_name_path(log_name = "test_log_name2")) at test-interact.R:85:3
 2. │ └─testthat:::expect_condition_matching(...)
 3. │   └─testthat:::quasi_capture(...)
 4. │     ├─testthat (local) .capture(...)
 5. │     │ └─base::withCallingHandlers(...)
 6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 7. └─logrx:::set_log_name_path(log_name = "test_log_name2")

Warning (test-interact.R:113:3): setting path name works
log_path already assigned, will not be overwritten
Backtrace:
    ▆
 1. ├─testthat::expect_warning(set_log_name_path(log_path = ".")) at test-interact.R:113:3
 2. │ └─testthat:::expect_condition_matching(...)
 3. │   └─testthat:::quasi_capture(...)
 4. │     ├─testthat (local) .capture(...)
 5. │     │ └─base::withCallingHandlers(...)
 6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 7. └─logrx:::set_log_name_path(log_path = ".")

Warning (test-interact.R:123:3): run_safely_loudly works for warnings, errors, messages, and output
log warning
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-interact.R:123:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)

Warning (test-interact.R:123:3): run_safely_loudly works for warnings, errors, messages, and output
log warning2
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-interact.R:123:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)
─────────────────────────────────────────────────────────────────────────
⠹ |          3 | log                                                     Removing existing log.rx environment and proceeding...

A log.rx environment already exists and cannot be used for a new execution.

This typically happens when:
  - A previous logrx execution did not complete properly
  - The log.rx environment was not cleaned up after a previous run

To resolve this issue, you have the following options:
  1. Allow logrx to remove the environment and proceed with execution
  2. Manually remove the environment using log_remove() or restart your R session

⠋ |         11 | log                                                     
A log.rx environment already exists and cannot be used for a new execution.

This typically happens when:
  - A previous logrx execution did not complete properly
  - The log.rx environment was not cleaned up after a previous run

To resolve this issue, you have the following options:
  1. Allow logrx to remove the environment and proceed with execution
  2. Manually remove the environment using log_remove() or restart your R session


A log.rx environment already exists and cannot be used for a new execution.

This typically happens when:
  - A previous logrx execution did not complete properly
  - The log.rx environment was not cleaned up after a previous run

To resolve this issue, you have the following options:
  1. Allow logrx to remove the environment and proceed with execution
  2. Manually remove the environment using log_remove() or restart your R session


A log.rx environment already exists and cannot be used for a new execution.

This typically happens when:
  - A previous logrx execution did not complete properly
  - The log.rx environment was not cleaned up after a previous run

To resolve this issue, you have the following options:
  1. Allow logrx to remove the environment and proceed with execution
  2. Manually remove the environment using log_remove() or restart your R session


A log.rx environment already exists and cannot be used for a new execution.

This typically happens when:
  - A previous logrx execution did not complete properly
  - The log.rx environment was not cleaned up after a previous run

To resolve this issue, you have the following options:
  1. Allow logrx to remove the environment and proceed with execution
  2. Manually remove the environment using log_remove() or restart your R session

Removing existing log.rx environment and proceeding...
✔ |         19 | log [1.3s]                                              
⠋ |          1 | parse                                                   [1] "hello logrx"
✔ |   1      6 | parse [1.3s]                                            
─────────────────────────────────────────────────────────────────────────
Warning (test-parse.R:15:3): read_log_file will parse a logrx log file and create the necessary object
5 parsing failures.
row col  expected    actual         file
 27  -- 7 columns 5 columns literal data
 68  -- 7 columns 2 columns literal data
 69  -- 7 columns 2 columns literal data
 70  -- 7 columns 2 columns literal data
 72  -- 7 columns 6 columns literal data

Backtrace:
    ▆
 1. ├─logrx::read_log_file(filePath) at test-parse.R:15:3
 2. │ └─flines %>% reformat_subsections() %>% nest_log() %>% ... at project/R/read_log_file.R:328:3
 3. ├─logrx:::parse_log(.)
 4. │ └─... %>% readr::read_table(skip = 1, col_names = FALSE) at project/R/read_log_file.R:194:5
 5. └─readr::read_table(., skip = 1, col_names = FALSE)
 6.   └─readr:::read_delimited(...)
 7.     └─readr:::warn_problems(out)
─────────────────────────────────────────────────────────────────────────
⠋ |          1 | sha1                                                    hello logrx
⠙ |          2 | sha1                                                    hello again logrx
⠹ |          3 | sha1                                                    hello logrx
✔ |          4 | sha1 [4.3s]                                             
✔ |          2 | utils                                                   
⠸ |         14 | writer                                                  [1] "log print"
[1] "log print 2"
log catlog cat 2log inform
log inform 2
log message
log message 2
⠼ |   1     14 | writer                                                  Error: log error
⠦ |   2     15 | writer                                                  [1] "log print"
[1] "log print 2"
log catlog cat 2log inform
log inform 2
log message
log message 2
⠧ |   3     15 | writer                                                  Error: log error
⠋ |   4     17 | writer                                                  [1] 1
⠙ |   4     18 | writer                                                  [1] 1
✔ |   4     24 | writer [11.0s]                                          
─────────────────────────────────────────────────────────────────────────
Warning (test-writer.R:189:3): write_output will return a formatted log output element
log warning
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-writer.R:189:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)

Warning (test-writer.R:189:3): write_output will return a formatted log output element
log warning2
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-writer.R:189:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)

Warning (test-writer.R:201:3): write_messages will return a formatted log messages element
log warning
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-writer.R:201:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)

Warning (test-writer.R:201:3): write_messages will return a formatted log messages element
log warning2
Backtrace:
     ▆
  1. └─logrx:::run_safely_loudly(fp) at test-writer.R:201:3
  2.   ├─logrx:::loudly(run_safely(file)) at project/R/interact.R:152:3
  3.   │ └─base::withCallingHandlers(code, warning = wHandler, message = mHandler) at project/R/utils-execution.R:31:3
  4.   └─purrr (local) run_safely(file) at project/R/utils-execution.R:31:3
  5.     ├─purrr:::capture_error(.f(...), otherwise, quiet)
  6.     │ └─base::tryCatch(...)
  7.     │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.     │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.     │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.     └─logrx (local) .f(...)
 11.       └─base::source(file, local = exec_env) at project/R/interact.R:136:5
 12.         ├─base::withVisible(eval(ei, envir))
 13.         └─base::eval(ei, envir)
 14.           └─base::eval(ei, envir)
─────────────────────────────────────────────────────────────────────────

══ Results ══════════════════════════════════════════════════════════════
Duration: 34.9 s

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 140 ]

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Clean up tests outputs/prints/messages/etc #284

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Clean up tests outputs/prints/messages/etc #284

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