Running 'testthat.R' [196s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(GCalignR)
  > 
  > test_check("GCalignR")
  Run GCalignR
  Start: 2024-03-23 07:30:52
  
  Data for 3 samples loaded.
  Start correcting linear shifts with "M2" as a reference ...
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   Remove contaminations and remove blanks ... done
  
  Alignment completed!
  Time: 2024-03-23 07:30:55 
  
  Run GCalignR
  Start: 2024-03-23 07:30:55
  
  Data for 3 samples loaded.
  Apply retention time cut-offs ... done
  No reference was specified. Hence, a reference will be selected automatically ...
   
  'C3' was selected on the basis of highest average similarity to all samples (score = 0.02).
  Start correcting linear shifts with "C3" as a reference ...
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   remove single peaks ... 36 have been removed
  
  Alignment completed!
  Time: 2024-03-23 07:30:58 
  
  All checks passed!
  
  [1] "RT is not a valid variable name. Data contains: time & area"
  Computing chromatograms ...
  
    |                                                  | 0 % elapsed=00s   
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  Run GCalignR
  Start: 2024-03-23 07:31:16
  
  Data for 5 samples loaded.
  Start correcting linear shifts with "M2" as a reference ...
  
    |                                                  | 0 % elapsed=00s   
    |++++++++++                                        | 20% elapsed=00s, remaining~00s
    |++++++++++++++++++++                              | 40% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++                    | 60% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++          | 80% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   Remove contaminations and remove blanks ... done
  
  Alignment completed!
  Time: 2024-03-23 07:31:16 
  
  Run GCalignR
  Start: 2024-03-23 07:31:16
  
  Data for 5 samples loaded.
  Start correcting linear shifts with "M2" as a reference ...
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   Remove contaminations and remove blanks ... done
  
  Alignment completed!
  Time: 2024-03-23 07:31:16 
  
  Run GCalignR
  Start: 2024-03-23 07:31:16
  
  Data for 5 samples loaded.
  Start correcting linear shifts with "M2" as a reference ...
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   Remove contaminations and remove blanks ... done
  
  Alignment completed!
  Time: 2024-03-23 07:31:17 
  
  Run GCalignR
  Start: 2024-03-23 07:31:17
  
  Data for 5 samples loaded.
  No reference was specified. Hence, a reference will be selected automatically ...
   
    |                                                  | 0 % elapsed=00s   
    |++++++++++                                        | 20% elapsed=00s, remaining~00s
    |++++++++++++++++++++                              | 40% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++                    | 60% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++          | 80% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  'C2' was selected on the basis of highest average similarity to all samples (score = 0.02).
  Start correcting linear shifts with "C2" as a reference ...
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   Remove contaminations and remove blanks ... done
  
  Alignment completed!
  Time: 2024-03-23 07:31:17 
  
  
    |                                                  | 0 % elapsed=00s   
    |+++++++++++++                                     | 25% elapsed=00s, remaining~00s
    |+++++++++++++++++++++++++                         | 50% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++            | 75% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  Run GCalignR
  Start: 2024-03-23 07:31:18
  
  Data for 4 samples loaded.
  No reference was specified. Hence, a reference will be selected automatically ...
   
    |                                                  | 0 % elapsed=00s   
    |+++++++++++++                                     | 25% elapsed=00s, remaining~00s
    |+++++++++++++++++++++++++                         | 50% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++            | 75% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  'C2' was selected on the basis of highest average similarity to all samples (score = 0.15).
  Start correcting linear shifts with "C2" as a reference ...
  
    |                                                  | 0 % elapsed=00s   
    |+++++++++++++                                     | 25% elapsed=00s, remaining~00s
    |+++++++++++++++++++++++++                         | 50% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++            | 75% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   
  Alignment completed!
  Time: 2024-03-23 07:31:18 
  
  Summary of Peak Alignment running align_chromatograms
  Input: peak_data
  Start:  2017-07-19 16:31:47 	Finished:  2017-07-19 17:30:47 
  
  Call:
    GCalignR::align_chromatograms(data=peak_data, rt_col_name=time,
    max_linear_shift=0.05, max_diff_peak2mean=0.02, min_diff_peak2peak=0.08,
    blanks=(C2, C3), delete_single_peak=T, sep=\t, rt_cutoff_low=NULL,
    rt_cutoff_high=NULL, reference=NULL)
  
  Summary of scored substances:
     total   blanks singular retained 
       494      171       45      278 
  
  In total 494 substances were identified among all samples. 171 substances were
    present in blanks. The corresponding peaks as well as the blanks were removed
    from the data. 45 substances were present in just one single sample and were
    removed. 278 substances are retained after all filtering steps.
  
  Sample overview:
    The following 84 samples were aligned to the reference 'P20':
    M2, M3, M4, M5, M6, M7, M8, M9, M10, M12, M14, M15, M16, M17, M18, M19, M20,
    M21, M23, M24, M25, M26, M27, M28, M29, M30, M31, M33, M35, M36, M37, M38,
    M39, M40, M41, M43, M44, M45, M46, M47, M48, P2, P3, P4, P5, P6, P7, P8, P9,
    P10, P12, P14, P15, P16, P17, P18, P19, P20, P21, P23, P24, P25, P26, P27,
    P28, P29, P30, P31, P33, P35, P36, P37, P38, P39, P40, P41, P43, P44, P45,
    P46, P47, P48
  
  For further details type:
    'gc_heatmap(aligned_peak_data)' to retrieve heatmaps
    'plot(aligned_peak_data)' to retrieve further diagnostic plotsRun GCalignR
  Start: 2024-03-23 07:31:18
  
  Data for 5 samples loaded.
  No reference was specified. Hence, a reference will be selected automatically ...
   
    |                                                  | 0 % elapsed=00s   
    |++++++++++                                        | 20% elapsed=00s, remaining~00s
    |++++++++++++++++++++                              | 40% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++                    | 60% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++          | 80% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  'M3' was selected on the basis of highest average similarity to all samples (score = 0.08).
  Start correcting linear shifts with "M3" as a reference ...
  
    |                                                  | 0 % elapsed=00s   
    |++++++++++                                        | 20% elapsed=00s, remaining~00s
    |++++++++++++++++++++                              | 40% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++                    | 60% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++          | 80% elapsed=00s, remaining~00s
    |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s, remaining~00s
  
  Start aligning peaks ...  this might take a while!
  
  Merge redundant rows ...
   
  Alignment completed!
  Time: 2024-03-23 07:31:20 
  
  [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-align_peaks.R:26:1'
  
  [ FAIL 0 | WARN 3 | SKIP 1 | PASS 33 ]
  > 
  > proc.time()
     user  system elapsed 
    27.65    0.65   28.35