Running 'testthat.R' [108s/123s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("RaMS")
  Loading required package: RaMS
  -- Attaching packages --------------------------------------- tidyverse 1.3.2 --
  v ggplot2 3.4.0      v purrr   0.3.5 
  v tibble  3.1.8      v dplyr   1.0.10
  v tidyr   1.2.1      v stringr 1.4.1 
  v readr   2.1.3      v forcats 0.5.2 
  -- Conflicts ------------------------------------------ tidyverse_conflicts() --
  x dplyr::between()       masks RaMS::between()
  x readr::edition_get()   masks testthat::edition_get()
  x dplyr::filter()        masks stats::filter()
  x purrr::is_null()       masks testthat::is_null()
  x dplyr::lag()           masks stats::lag()
  x readr::local_edition() masks testthat::local_edition()
  x dplyr::matches()       masks tidyr::matches(), testthat::matches()
  
  Attaching package: 'data.table'
  
  The following objects are masked from 'package:dplyr':
  
      between, first, last
  
  The following object is masked from 'package:purrr':
  
      transpose
  
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzML.gz... 0.64 secs 
  Reading MS1 data...1.15 secs 
  Reading MS2 data...0.44 secs 
  Reading BPC...0.37 secs 
  Reading TIC...0.39 secs 
  Reading file metadata...0.73 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzML.gz... 0.31 secs 
  Reading MS1 data...0.53 secs 
  Reading MS2 data...0.03 secs 
  Reading BPC...0.33 secs 
  Reading TIC...0.2 secs 
  Reading file metadata...0.35 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 5.5 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 5.23 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzXML.gz... 0.14 secs 
  Reading MS1 data...0.55 secs 
  Reading MS2 data...0.11 secs 
  Reading BPC...0.16 secs 
  Reading TIC...0.14 secs 
  Reading file metadata...0.44 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzXML.gz... 0.02 secs 
  Reading MS1 data...0.27 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.07 secs 
  Reading TIC...0.08 secs 
  Reading file metadata...0.2 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 2.98 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |=======================                                               |  33%
    |                                                                            
    |===============================================                       |  67%
    |                                                                            
    |======================================================================| 100%
  Total time: 3.4 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzML.gz... 0.79 secs 
  Extracting EIC...0.98 secs 
  Extracting EIC MS2...0.28 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzML.gz... 0.3 secs 
  Extracting EIC...0.35 secs 
  Extracting EIC MS2...0.02 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 2.72 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzXML.gz... 0.06 secs 
  Extracting EIC...0.49 secs 
  Extracting EIC MS2...0.12 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzXML.gz... 0.02 secs 
  Extracting EIC...0.15 secs 
  Extracting EIC MS2...0 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 0.85 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.29 secs 
  
  Reading file DDApos_2.mzXML.gz... 0.06 secs 
  Reading MS1 data...0.16 secs 
  Reading MS2 data...0.03 secs 
  Reading BPC...0.23 secs 
  Reading TIC...0.17 secs 
  Total time: 0.66 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Some data seem to have incorrect names: MS1
  Total time: 2.17 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.28 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.79 secs 
  
  Reading file uv_test_mini.mzML.gz... 0.01 secs 
  Reading MS1 data...0.03 secs 
  Reading MS2 data...0 secs 
  Reading DAD data...0 secs 
  Reading BPC...0.01 secs 
  Reading TIC...0.01 secs 
  Reading file metadata...0.02 secs 
  Total time: 0.1 secs 
  
  Reading file uv_test_mini.mzML.gz... 0.02 secs 
  Reading DAD data...0 secs 
  Total time: 0.03 secs 
  
  Reading file LB12HL_AB.mzXML.gz... 0.04 secs 
  Total time: 0.04 secs 
  
  Reading file wk_chrom.mzML.gz... 0.02 secs 
  Reading chromatograms...0.01 secs 
  Total time: 0.03 secs 
  
  Reading file wk_chrom.mzML.gz... 0 secs 
  Reading MS1 data...0 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0 secs 
  Reading TIC...0 secs 
  Reading chromatograms...0.01 secs 
  Reading file metadata...0 secs 
  Total time: 0.02 secs 
  
  Reading file LB12HL_AB.mzXML.gz... 0.02 secs 
  Total time: 0.02 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file LB12HL_AB.mzML.gz... 0.34 secs 
  Reading MS1 data...0.43 secs 
  Reading MS2 data...0.03 secs 
  Reading BPC...0.14 secs 
  Reading TIC...0.25 secs 
  Reading file metadata...0.32 secs 
  Total time: 1.51 secs 
  
  Reading file LB12HL_AB.mzML.gz... 0.32 secs 
  Reading MS1 data...0.38 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.17 secs 
  Reading TIC...0.28 secs 
  Reading file metadata...0.36 secs 
  Total time: 1.54 secs 
  
  Reading file Rtmpk4hRnn\mini_mzML.mzML... 0.18 secs 
  Reading MS1 data...0.28 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.14 secs 
  Reading TIC...0.13 secs 
  Reading file metadata...0.19 secs 
  Total time: 1 secs 
  
  Reading file Rtmpk4hRnn\mini_mzML.mzML... 0.21 secs 
  Reading MS1 data...0.3 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.2 secs 
  Reading TIC...0.14 secs 
  Reading file metadata...0.2 secs 
  Total time: 1.07 secs 
  
  Reading file Rtmpk4hRnn\mini_mzXML.mzXML... 0.03 secs 
  Reading MS1 data...0.16 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.09 secs 
  Reading TIC...0.05 secs 
  Reading file metadata...0.12 secs 
  Total time: 0.45 secs 
  
  Reading file Rtmpk4hRnn\mini_mzXML.mzXML... 0.03 secs 
  Reading MS1 data...0.15 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.09 secs 
  Reading TIC...0.07 secs 
  Reading file metadata...0.09 secs 
  Total time: 0.43 secs 
  
    |                                                                            
    |                                                                      |   0%Total time: 9.8 secs 
  
  Reading file DDApos_2.mzML.gz... 0.73 secs 
  Reading MS1 data...0.81 secs 
  Reading MS2 data...0.32 secs 
  Reading BPC...0.37 secs 
  Reading TIC...0.35 secs 
  Reading file metadata...0.71 secs 
  Total time: 4.14 secs 
  
  Reading file Rtmpk4hRnn\mini_DDA.mzML... 0.49 secs 
  Reading MS1 data...0.91 secs 
  Reading MS2 data...0.08 secs 
  Reading BPC...0.36 secs 
  Reading TIC...0.35 secs 
  Reading file metadata...0.88 secs 
  Total time: 3.07 secs 
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 208 ]
  
  == Failed tests ================================================================
  -- Error ('test_minify.R:174'): Warn on overwrite ------------------------------
  Error in `open.connection(file, "wb")`: cannot open the connection
  Backtrace:
       x
    1. +-testthat::expect_warning(...) at test_minify.R:174:2
    2. | \-testthat:::quasi_capture(...)
    3. |   +-testthat (local) .capture(...)
    4. |   | \-base::withCallingHandlers(...)
    5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. \-RaMS::minifyMSdata(files = mzML_filenames[2:4], ppm = 5, mz_include = include_mzs)
    7.   \-RaMS:::minifyMzml(...)
    8.     +-xml2::write_xml(x = xml_data, file = output_filename)
    9.     \-xml2:::write_xml.xml_document(x = xml_data, file = output_filename)
   10.       +-base::open(file, "wb")
   11.       \-base::open.connection(file, "wb")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 208 ]
  Error: Test failures
  Execution halted