R Under development (unstable) (2024-06-30 r86854 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 68ms

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 0.3s

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 0.6s

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]: 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 OK [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_206 taxonomy is 97.9%"

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 0.4s

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 14ms

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 5.6s
All ok, 29 results (6.9s)
> 
> proc.time()
   user  system elapsed 
   7.35    0.54    7.85