R Under development (unstable) (2025-01-15 r87581 ucrt) -- "Unsuffered Consequences"
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> if ( requireNamespace("tinytest", quietly = TRUE) ){
+   tinytest::test_package("chem16S")
+ }

test-chemlab.R................    0 tests    
test-chemlab.R................    1 tests OK 73ms

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 OK 
test-get_metadata.R...........    2 tests OK 0.2s

test-get_metric_byrank.R......    0 tests    [1] "read_RDP [BGPF13.tab.xz]: 27% of classifications at genus level"
[1] "read_RDP [BGPF13.tab.xz]: range of counts is 1332 to 9873"

test-get_metric_byrank.R......    0 tests    [1] "map_taxa [BGPF13.tab.xz]: using these manual mapping(s) to NCBI RefSeq:"
order_Rhizobiales --> order_Hyphomicrobiales (0.3%)
class_Cyanobacteria --> phylum_Cyanobacteria (3.1%)
genus_Subdivision3_genera_incertae_sedis --> family_Verrucomicrobia subdivision 3 (0.1%)
[1] "map_taxa [BGPF13.tab.xz]: can't map groups domain_Archaea (28.12%), domain_Bacteria (14.04%), 33 others (13.14%)"
[1] "map_taxa [BGPF13.tab.xz]: mapping rate to RefSeq_206 taxonomy is 44.7%"

test-get_metric_byrank.R......    0 tests    
test-get_metric_byrank.R......    0 tests    
test-get_metric_byrank.R......    0 tests    
test-get_metric_byrank.R......    0 tests    
test-get_metric_byrank.R......    1 tests OK 
test-get_metric_byrank.R......    1 tests OK 
test-get_metric_byrank.R......    1 tests OK 
test-get_metric_byrank.R......    1 tests OK 
test-get_metric_byrank.R......    1 tests OK 
test-get_metric_byrank.R......    2 tests OK 1.2s

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 OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    1 tests OK 
test-get_metrics.R............    2 tests OK 
test-get_metrics.R............    2 tests OK 
test-get_metrics.R............    3 tests OK 
test-get_metrics.R............    3 tests OK 
test-get_metrics.R............    3 tests OK 
test-get_metrics.R............    4 tests OK 
test-get_metrics.R............    4 tests OK 
test-get_metrics.R............    5 tests OK 1.0s

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 OK 
test-map_taxa.R...............    1 tests OK 
test-map_taxa.R...............    1 tests OK 
test-map_taxa.R...............    1 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    2 tests OK 
test-map_taxa.R...............    3 tests OK 
test-map_taxa.R...............    4 tests OK 
test-map_taxa.R...............    5 tests OK 
test-map_taxa.R...............    5 tests OK 
test-map_taxa.R...............    5 tests OK 
test-map_taxa.R...............    5 tests OK [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_206 taxonomy is 75.6%"

test-map_taxa.R...............    6 tests OK 
test-map_taxa.R...............    7 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK [1] "read_RDP [HLA+16.tab.xz]: 38% of classifications at genus level"
[1] "read_RDP [HLA+16.tab.xz]: range of counts is 733 to 3702"

test-map_taxa.R...............    8 tests OK [1] "map_taxa [HLA+16.tab.xz]: using these manual mapping(s) to NCBI RefSeq:"
class_Actinobacteria --> phylum_Actinobacteria (4.7%)
genus_Spartobacteria_genera_incertae_sedis --> class_Spartobacteria (6.6%)
genus_GpI --> genus_Nostoc (1.6%)
genus_GpIIa --> genus_Synechococcus (7.7%)
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 domain_Bacteria (2.85%), genus_Bacillariophyta (1.42%), 57 others (2.61%)"
[1] "map_taxa [HLA+16.tab.xz]: mapping rate to RefSeq_206 taxonomy is 93.0%"

test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    8 tests OK 
test-map_taxa.R...............    9 tests OK 
test-map_taxa.R...............    9 tests OK 
test-map_taxa.R...............   10 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   11 tests OK 
test-map_taxa.R...............   12 tests OK 
test-map_taxa.R...............   12 tests OK family_Koribacteraceae --> family_Korobacteraceae (0.022%)
order_Ammonifexales --> order_Ammonificales (0.011%)
family_Phormidesmiaceae --> family_Phormidesmidaceae (0.018%)
order_Hydrogenedentiales --> order_Hydrogenedentales (0.0063%)

test-map_taxa.R...............   13 tests OK 
test-map_taxa.R...............   14 tests OK 9.0s

test-read_RDP.R...............    0 tests    
test-read_RDP.R...............    0 tests    
test-read_RDP.R...............    0 tests    
test-read_RDP.R...............    1 tests OK 
test-read_RDP.R...............    2 tests OK 
test-read_RDP.R...............    3 tests OK 
test-read_RDP.R...............    4 tests OK 
test-read_RDP.R...............    5 tests OK 
test-read_RDP.R...............    5 tests OK 
test-read_RDP.R...............    5 tests OK 
test-read_RDP.R...............    5 tests OK 
test-read_RDP.R...............    5 tests OK 
test-read_RDP.R...............    6 tests OK 
test-read_RDP.R...............    7 tests OK 
test-read_RDP.R...............    8 tests OK 
test-read_RDP.R...............    8 tests OK 
test-read_RDP.R...............    8 tests OK 
test-read_RDP.R...............    9 tests OK 36ms

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 OK 
test_phyloseq_integration.R...    1 tests OK 
test_phyloseq_integration.R...    1 tests OK 
test_phyloseq_integration.R...    1 tests OK 
test_phyloseq_integration.R...    2 tests OK 3.6s
All ok, 35 results (15.0s)
> 
> proc.time()
   user  system elapsed 
  15.15    1.10   16.20