Running ‘testthat.R’ [86s/97s]
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 ──
  ✔ ggplot2 3.4.0      ✔ purrr   0.3.5 
  ✔ tibble  3.1.8      ✔ dplyr   1.0.10
  ✔ tidyr   1.2.1      ✔ stringr 1.4.1 
  ✔ readr   2.1.3      ✔ forcats 0.5.2 
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ dplyr::between()       masks RaMS::between()
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ 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... 0.77 secs 
  Reading MS1 data...0.65 secs 
  Reading MS2 data...0.26 secs 
  Reading BPC...0.39 secs 
  Reading TIC...0.45 secs 
  Reading file metadata...0.63 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzML.gz... 0.2 secs 
  Reading MS1 data...0.41 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.12 secs 
  Reading TIC...0.11 secs 
  Reading file metadata...0.19 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 4.23 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 3.92 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzXML.gz... 0.22 secs 
  Reading MS1 data...0.45 secs 
  Reading MS2 data...0.09 secs 
  Reading BPC...0.07 secs 
  Reading TIC...0.06 secs 
  Reading file metadata...0.19 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzXML.gz... 0.03 secs 
  Reading MS1 data...0.11 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.03 secs 
  Reading TIC...0.03 secs 
  Reading file metadata...0.06 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 1.35 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |=======================                                               |  33%
    |                                                                            
    |===============================================                       |  67%
    |                                                                            
    |======================================================================| 100%
  Total time: 3.23 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzML.gz... 0.79 secs 
  Extracting EIC...0.82 secs 
  Extracting EIC MS2...0.27 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzML.gz... 0.19 secs 
  Extracting EIC...0.33 secs 
  Extracting EIC MS2...0.02 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 2.43 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file DDApos_2.mzXML.gz... 0.07 secs 
  Extracting EIC...0.37 secs 
  Extracting EIC MS2...0.11 secs 
  
    |                                                                            
    |===================================                                   |  50%
  Reading file LB12HL_AB.mzXML.gz... 0.02 secs 
  Extracting EIC...0.24 secs 
  Extracting EIC MS2...0 secs 
  
    |                                                                            
    |======================================================================| 100%
  Total time: 0.82 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.56 secs 
  
  Reading file DDApos_2.mzXML.gz... 0.06 secs 
  Reading MS1 data...0.1 secs 
  Reading MS2 data...0.05 secs 
  Reading BPC...0.19 secs 
  Reading TIC...0.07 secs 
  Total time: 0.48 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Some data seem to have incorrect names: MS1
  Total time: 1.96 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.42 secs 
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  Total time: 2.54 secs 
  
  Reading file uv_test_mini.mzML.gz... 0.01 secs 
  Reading MS1 data...0.02 secs 
  Reading MS2 data...0 secs 
  Reading DAD data...0 secs 
  Reading BPC...0.02 secs 
  Reading TIC...0 secs 
  Reading file metadata...0.01 secs 
  Total time: 0.07 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... 0.02 secs 
  Total time: 0.02 secs 
  
  Reading file wk_chrom.mzML.gz... 0.01 secs 
  Reading chromatograms...0.01 secs 
  Total time: 0.02 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... 0.04 secs 
  Total time: 0.04 secs 
  
    |                                                                            
    |                                                                      |   0%
  Reading file LB12HL_AB.mzML.gz... 0.2 secs 
  Reading MS1 data...0.33 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.12 secs 
  Reading TIC...0.12 secs 
  Reading file metadata...0.19 secs 
  Total time: 0.99 secs 
  
  Reading file LB12HL_AB.mzML.gz... 0.18 secs 
  Reading MS1 data...0.3 secs 
  Reading MS2 data...0.03 secs 
  Reading BPC...0.14 secs 
  Reading TIC...0.13 secs 
  Reading file metadata...0.19 secs 
  Total time: 0.99 secs 
  
  Reading file Rtmp9BmglH\mini_mzML.mzML... 0.19 secs 
  Reading MS1 data...0.3 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.17 secs 
  Reading TIC...0.16 secs 
  Reading file metadata...0.2 secs 
  Total time: 1.05 secs 
  
  Reading file Rtmp9BmglH\mini_mzML.mzML... 0.16 secs 
  Reading MS1 data...0.36 secs 
  Reading MS2 data...0.02 secs 
  Reading BPC...0.11 secs 
  Reading TIC...0.12 secs 
  Reading file metadata...0.2 secs 
  Total time: 0.97 secs 
  
  Reading file Rtmp9BmglH\mini_mzXML.mzXML... 0.01 secs 
  Reading MS1 data...0.12 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.03 secs 
  Reading TIC...0.03 secs 
  Reading file metadata...0.07 secs 
  Total time: 0.27 secs 
  
  Reading file Rtmp9BmglH\mini_mzXML.mzXML... 0.01 secs 
  Reading MS1 data...0.19 secs 
  Reading MS2 data...0 secs 
  Reading BPC...0.04 secs 
  Reading TIC...0.03 secs 
  Reading file metadata...0.08 secs 
  Total time: 0.36 secs 
  
    |                                                                            
    |                                                                      |   0%Total time: 7.67 secs 
  
  Reading file DDApos_2.mzML.gz... 0.58 secs 
  Reading MS1 data...0.78 secs 
  Reading MS2 data...0.29 secs 
  Reading BPC...0.33 secs 
  Reading TIC...0.3 secs 
  Reading file metadata...0.6 secs 
  Total time: 2.87 secs 
  
  Reading file Rtmp9BmglH\mini_DDA.mzML... 0.38 secs 
  Reading MS1 data...0.6 secs 
  Reading MS2 data...0.08 secs 
  Reading BPC...0.28 secs 
  Reading TIC...0.33 secs 
  Reading file metadata...0.47 secs 
  Total time: 2.14 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:
       ▆
    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
  In addition: Warning message:
  closing unused connection 4 (/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RaMS/extdata/LB12HL_AB_mini.mzML.gz) 
  Execution halted