Running 'tinytest.R' [168s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if ( requireNamespace("tinytest", quietly = TRUE) ){
  +   tinytest::test_package("chem16S")
  + }
  
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    0 tests    
  test-calc_metrics.R...........    1 tests [0;32mOK[0m 
  test-calc_metrics.R...........    2 tests [0;32mOK[0m 
  test-calc_metrics.R...........    3 tests [0;32mOK[0m 
  test-calc_metrics.R...........    3 tests [0;32mOK[0m 
  test-calc_metrics.R...........    3 tests [0;32mOK[0m 
  test-calc_metrics.R...........    3 tests [0;32mOK[0m 
  test-calc_metrics.R...........    3 tests [0;32mOK[0m 
  test-calc_metrics.R...........    4 tests [0;32mOK[0m 
  test-calc_metrics.R...........    4 tests [0;32mOK[0m 
  test-calc_metrics.R...........    4 tests [0;32mOK[0m 
  test-calc_metrics.R...........    4 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    5 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    6 tests [0;32mOK[0m 
  test-calc_metrics.R...........    7 tests [0;32mOK[0m 
  test-calc_metrics.R...........    8 tests [0;32mOK[0m 
  test-calc_metrics.R...........    9 tests [0;32mOK[0m 
  test-calc_metrics.R...........   10 tests [0;32mOK[0m [0;36m96ms[0m
  
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    0 tests    
  test-get_metadata.R...........    1 tests [0;32mOK[0m 
  test-get_metadata.R...........    2 tests [0;32mOK[0m [0;34m0.3s[0m
  
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    0 tests    
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    1 tests [0;32mOK[0m 
  test-get_metrics.R............    2 tests [0;32mOK[0m 
  test-get_metrics.R............    2 tests [0;32mOK[0m 
  test-get_metrics.R............    3 tests [0;32mOK[0m [0;34m0.6s[0m
  
  test-map_taxa.R...............    0 tests    
  test-map_taxa.R...............    0 tests    
  test-map_taxa.R...............    0 tests    
  test-map_taxa.R...............    0 tests    
  test-map_taxa.R...............    1 tests [0;32mOK[0m 
  test-map_taxa.R...............    1 tests [0;32mOK[0m 
  test-map_taxa.R...............    1 tests [0;32mOK[0m 
  test-map_taxa.R...............    1 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    2 tests [0;32mOK[0m 
  test-map_taxa.R...............    3 tests [0;32mOK[0m 
  test-map_taxa.R...............    4 tests [0;32mOK[0m 
  test-map_taxa.R...............    5 tests [0;32mOK[0m 
  test-map_taxa.R...............    5 tests [0;32mOK[0m 
  test-map_taxa.R...............    5 tests [0;32mOK[0m 
  test-map_taxa.R...............    5 tests [0;32mOK[0m [1] "map_taxa [SMS+12.tab.xz]: using these manual mapping(s) to NCBI RefSeq:"
  [1] "map_taxa [SMS+12.tab.xz]: can't map groups genus_Diapherotrites Incertae Sedis AR10 (17%), genus_Armatimonadetes_gp7 (5.08%), 6 others (2.32%)"
  [1] "map_taxa [SMS+12.tab.xz]: mapping rate to RefSeq taxonomy is 75.6%"
  
  test-map_taxa.R...............    6 tests [0;32mOK[0m 
  test-map_taxa.R...............    7 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m [1] "read_RDP [HLA+16.tab.xz]: 38% of classifications at genus level"
  [1] "read_RDP [HLA+16.tab.xz]: removing genus_Bacillariophyta (1.4%)"
  [1] "read_RDP [HLA+16.tab.xz]: removing genus_Chlorophyta (0.2%)"
  [1] "read_RDP [HLA+16.tab.xz]: removing family_Chloroplast (0.3%)"
  [1] "read_RDP [HLA+16.tab.xz]: removing domain_Bacteria (2.9%)"
  [1] "read_RDP [HLA+16.tab.xz]: removing rootrank_Root (0.1%)"
  [1] "read_RDP [HLA+16.tab.xz]: range of counts is 699 to 3466"
  
  test-map_taxa.R...............    8 tests [0;32mOK[0m [1] "map_taxa [HLA+16.tab.xz]: using these manual mapping(s) to NCBI RefSeq:"
  class_Actinobacteria --> phylum_Actinobacteria (4.9%)
  genus_Spartobacteria_genera_incertae_sedis --> class_Spartobacteria (7%)
  genus_GpI --> genus_Nostoc (1.6%)
  genus_GpIIa --> genus_Synechococcus (8.1%)
  family_Family II --> family_Synechococcaceae (0.1%)
  class_Cyanobacteria --> phylum_Cyanobacteria (0.1%)
  phylum_Cyanobacteria/Chloroplast --> phylum_Cyanobacteria (0.8%)
  [1] "map_taxa [HLA+16.tab.xz]: can't map groups family_Thalassobaculaceae (0.96%), genus_Cryptomonadaceae (0.46%), 51 others (0.68%)"
  [1] "map_taxa [HLA+16.tab.xz]: mapping rate to RefSeq taxonomy is 97.9%"
  
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    8 tests [0;32mOK[0m 
  test-map_taxa.R...............    9 tests [0;32mOK[0m 
  test-map_taxa.R...............    9 tests [0;32mOK[0m 
  test-map_taxa.R...............   10 tests [0;32mOK[0m 
  test-map_taxa.R...............   11 tests [0;32mOK[0m [0;34m0.9s[0m
  
  test-read_RDP.R...............    0 tests    
  test-read_RDP.R...............    0 tests    
  test-read_RDP.R...............    0 tests    
  test-read_RDP.R...............    1 tests [0;32mOK[0m 
  test-read_RDP.R...............    2 tests [0;32mOK[0m 
  test-read_RDP.R...............    3 tests [0;32mOK[0m 
  test-read_RDP.R...............    4 tests [0;32mOK[0m 
  test-read_RDP.R...............    5 tests [0;32mOK[0m 
  test-read_RDP.R...............    5 tests [0;32mOK[0m 
  test-read_RDP.R...............    5 tests [0;32mOK[0m 
  test-read_RDP.R...............    5 tests [0;32mOK[0m 
  test-read_RDP.R...............    5 tests [0;32mOK[0m 
  test-read_RDP.R...............    6 tests [0;32mOK[0m 
  test-read_RDP.R...............    7 tests [0;32mOK[0m 
  test-read_RDP.R...............    8 tests [0;32mOK[0m [0;36m17ms[0m
  
  test_phyloseq_integration.R...    0 tests    
  test_phyloseq_integration.R...    0 tests    
  test_phyloseq_integration.R...    0 tests    
  test_phyloseq_integration.R...    0 tests    
  test_phyloseq_integration.R...    1 tests [0;32mOK[0m 
  test_phyloseq_integration.R...    1 tests [0;32mOK[0m 
  test_phyloseq_integration.R...    1 tests [0;32mOK[0m 
  test_phyloseq_integration.R...    1 tests [0;32mOK[0m 
  test_phyloseq_integration.R...    2 tests [0;32mOK[0m [0;34m8.2s[0m
  All ok, 36 results (10.1s)
  > 
  > proc.time()
     user  system elapsed 
    10.45    0.90   11.32