R Under development (unstable) (2025-05-01 r88184 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(RAMClustR)
> 
> test_check("RAMClustR")
plotting findmain annotation results 
finished 
87.5% of features move forward
ma MSdata 
df phenoData 
Features which failed to demonstrate signal intensity of at least 3 -fold greater in QC samples than in blanks were removed from the feature dataset. 6 of 48 features were removed.MSdata :  33 passed the CV filter 
Features were filtered based on their qc sample CV values. Only features with CV values less than or equal to 0.5 in MSdata set were retained. 9 of 42 features were removed.Features were normalized by linearly regressing run order versus qc feature intensities to account for instrument signal intensity drift. Only features with a regression pvalue less than 0.05 and an r-squared greater than 0.1 were corrected.  Of 42 features, 0 was corrected for run order effects.replaced 12 of 192 total feature values ( 6 % ) 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 33 features into 4 spectra 
collapsing feature into spectral signal intensities 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 33 features into 6 spectra 
collapsing feature into spectral signal intensities 
replaced 12 of 192 total feature values ( 6 % ) 
87.5% of features move forward
ma MSdata 
df phenoData 
Features which failed to demonstrate signal intensity of at least 3 -fold greater in QC samples than in blanks were removed from the feature dataset. 6 of 48 features were removed.Features were normalized by linearly regressing run order versus qc feature intensities to account for instrument signal intensity drift. Only features with a regression pvalue less than 0.05 and an r-squared greater than 0.1 were corrected.  Of 42 features, 0 was corrected for run order effects.MSdata :  33 passed the CV filter 
Features were filtered based on their qc sample CV values. Only features with CV values less than or equal to 0.5 in MSdata set were retained. 9 of 42 features were removed.Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 33 features into 4 spectra 
collapsing feature into spectral signal intensities 
plotting findmain annotation results 
finished 
organizing dataset 
replaced 12 of 192 total feature values ( 6 % ) 
  normalizing dataset 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 48 features into 6 spectra 
collapsing feature into spectral signal intensities 
writing msp formatted spectra 
msp file complete 
replaced 12 of 192 total feature values ( 6 % ) 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 48 features into 6 spectra 
collapsing feature into spectral signal intensities 
organizing dataset 
replaced 12 of 192 total feature values ( 6 % ) 
  normalizing dataset 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 48 features into 6 spectra 
collapsing feature into spectral signal intensities 
writing msp formatted spectra 
msp file complete 
organizing dataset 
replaced 0 of 609 total feature values ( 0 % ) 
  normalizing dataset 
Calculating ramclustR similarity using 3 nblocks.
1  
 RAMClust feature similarity matrix calculated and stored.
fastcluster based clustering complete 
dynamicTreeCut based pruning complete 
RAMClust has condensed 203 features into 22 spectra 
collapsing feature into spectral signal intensities 
writing msp formatted spectra 
msp file complete 
[ FAIL 0 | WARN 22 | SKIP 0 | PASS 33 ]

[ FAIL 0 | WARN 22 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  40.15    1.28   41.43