Running ‘testthat.R’ [12s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(AMR)
  > 
  > test_check("AMR")
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (no changes)
  Enterococcus (no changes)
  Streptococcus groups A, B, C, G (no changes)
  Streptococcus pneumoniae (no changes)
  Viridans group streptococci (no changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (no changes)
  Anaerobic Gram negatives (no changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (no changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (no changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 1,980 out of 2,000 rows -> changed 0 test results.
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (no changes)
  Enterococcus (no changes)
  Streptococcus groups A, B, C, G (no changes)
  Streptococcus pneumoniae (no changes)
  Viridans group streptococci (no changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (no changes)
  Anaerobic Gram negatives (no changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (no changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (2 changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (1 change)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 3 out of 3 rows -> changed 3 test results.
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (no changes)
  Enterococcus (no changes)
  Streptococcus groups A, B, C, G (no changes)
  Streptococcus pneumoniae (no changes)
  Viridans group streptococci (no changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (no changes)
  Anaerobic Gram negatives (no changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (no changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (2 changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (1 change)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 3 out of 3 rows -> changed 3 test results.
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (45 changes)
  Enterococcus (14 changes)
  Streptococcus groups A, B, C, G (no changes)
  Streptococcus pneumoniae (no changes)
  Viridans group streptococci (4 changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (17 changes)
  Anaerobic Gram negatives (20 changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (no changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (no changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (2 changes)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (657 changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (7 changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (139 changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 2,000 out of 2,000 rows -> changed 905 test results.
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (1090 changes)
  Enterococcus (no changes)
  Streptococcus groups A, B, C, G (146 changes)
  Streptococcus pneumoniae (214 changes)
  Viridans group streptococci (no changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (no changes)
  Anaerobic Gram negatives (no changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (2 changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (no changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (168 changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 1,894 out of 2,000 rows -> changed 1,620 test results.
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v8.1, 2018)
  Enterobacteriales (Order) (no changes)
  Staphylococcus (no changes)
  Enterococcus (no changes)
  Streptococcus groups A, B, C, G (no changes)
  Streptococcus pneumoniae (no changes)
  Viridans group streptococci (no changes)
  Haemophilus influenzae (no changes)
  Moraxella catarrhalis (no changes)
  Anaerobic Gram positives (no changes)
  Anaerobic Gram negatives (no changes)
  Pasteurella multocida (no changes)
  Campylobacter jejuni and C. coli (no changes)
  Aerococcus sanguinicola and A. urinae (no changes)
  Kingella kingae (no changes)
  
  EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
  Table 1:  Intrinsic resistance in Enterobacteriaceae (no changes)
  Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)
  Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
  Table 4:  Intrinsic resistance in Gram-positive bacteria (no changes)
  Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
  Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
  Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
  Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
  Table 12: Interpretive rules for aminoglycosides (no changes)
  Table 13: Interpretive rules for quinolones (no changes)
  
  Other rules
  Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
  Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
  Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
  Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
  Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
  Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
  
  => EUCAST rules affected 756 out of 2,000 rows -> changed 0 test results.
  
  [Criteria] Inclusion based on key antibiotics, ignoring I.
  [Criteria] Inclusion based on key antibiotics, not ignoring I.
  [Criteria] Inclusion based on key antibiotics, using points threshold of 2.
  Terminated