Running examples in ‘otuSummary-Ex.R’ failed
The error most likely occurred in:

> ### Name: otuReport
> ### Title: Summarize the community structure and abundance with OTU table
> ### Aliases: otuReport
> ### Keywords: summarize
> 
> ### ** Examples
> 
> # summary the otu table in qiime format
> 
> data(otuqiime)
> summaryInfo <- otuReport(otutab = otuqiime, siteInCol = TRUE, taxhead = "taxonomy",
+     platform = "qiime", pattern = ";", prefix = TRUE, percent  =FALSE, level = "class")
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
Data checking ... 
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
This funciton is designed for OTU table
OTUs in rows with a column given taxonomy
The input OTUs is in QIIME format
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
The Summary Information at Rank of CLASS
Printing summary at Rank of CLASS below
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
> length(summaryInfo)
[1] 9
> names(summaryInfo)
[1] "whatTaxa"     "taxaFreqs"    "taxaFrac"     "reads"        "readSum"     
[6] "readFrac"     "readFracSum"  "Relabund"     "RelabundMean"
> summaryInfo[[1]]
 [1] "k__Bacteria->p__Verrucomicrobia->c__Spartobacteria"      
 [2] "k__Bacteria->p__Proteobacteria->c__Gammaproteobacteria"  
 [3] "k__Bacteria->p__Verrucomicrobia->c__Verrucomicrobiae"    
 [4] "k__Bacteria->p__Proteobacteria->c__Alphaproteobacteria"  
 [5] "k__Bacteria->p__Proteobacteria->c__Betaproteobacteria"   
 [6] "k__Bacteria->p__Proteobacteria->c__Deltaproteobacteria"  
 [7] "k__Bacteria->p__Bacteroidetes->c__Bacteroidia"           
 [8] "k__Bacteria->p__Firmicutes->c__Clostridia"               
 [9] "k__Bacteria->p__Spirochaetes->c__Spirochaetes"           
[10] "k__Bacteria->p__Bacteroidetes->c__Sphingobacteriia"      
[11] "k__Archaea->p__Euryarchaeota->c__Methanomicrobia"        
[12] "k__Bacteria->p__Bacteroidetes->c__Saprospirae"           
[13] "k__Bacteria->p__Spirochaetes->c__Leptospirae"            
[14] "k__Bacteria->p__Acidobacteria->c__Solibacteres"          
[15] "k__Bacteria->p__Verrucomicrobia->c__Opitutae"            
[16] "k__Bacteria->p__Chlamydiae->c__Chlamydiia"               
[17] "k__Bacteria->p__Acidobacteria->c__Acidobacteriia"        
[18] "k__Bacteria->p__Firmicutes->c__Bacilli"                  
[19] "k__Bacteria->p__Cyanobacteria->c__Synechococcophycideae" 
[20] "k__Bacteria->p__Actinobacteria->c__Actinobacteria"       
[21] "k__Bacteria->p__Armatimonadetes->c__Fimbriimonadia"      
[22] "k__Archaea->p__Euryarchaeota->c__Methanobacteria"        
[23] "k__Bacteria->p__Fusobacteria->c__Fusobacteriia"          
[24] "k__Bacteria->p__Actinobacteria->c__Thermoleophilia"      
[25] "k__Bacteria->p__Proteobacteria->c__Epsilonproteobacteria"
[26] "k__Bacteria->p__Bacteroidetes->c__Flavobacteriia"        
[27] "k__Bacteria->p__Planctomycetes->c__Planctomycetia"       
[28] "k__Bacteria->p__Chloroflexi->c__Anaerolineae"            
[29] "k__Bacteria->p__Firmicutes->c__Erysipelotrichi"          
[30] "k__Bacteria->p__Bacteroidetes->c__Cytophagia"            
[31] "k__Bacteria->p__Thermi->c__Deinococci"                   
[32] "k__Bacteria->p__Armatimonadetes->c__Armatimonadia"       
[33] "k__Bacteria->p__Deferribacteres->c__Deferribacteres"     
[34] "k__Bacteria->p__Acidobacteria->c__Holophagae"            
[35] "k__Bacteria->p__Cyanobacteria->c__Nostocophycideae"      
[36] "k__Bacteria->p__Verrucomicrobia->c__Pedosphaerae"        
> 
> # summary otu table in mothur format
> 
> data(otumothur)
> summaryInfo <- otuReport(otutab = otumothur, siteInCol = TRUE, taxhead = "taxonomy",
+     platform = "qiime", pattern = ";", percent = FALSE, level = "phylum", collap = ";")
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
Data checking ... 
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
This funciton is designed for OTU table
OTUs in rows with a column given taxonomy
The input OTUs is in QIIME format
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
The Summary Information at Rank of PHYLUM
Printing summary at Rank of PHYLUM below
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
> length(summaryInfo)
[1] 9
> names(summaryInfo)
[1] "whatTaxa"     "taxaFreqs"    "taxaFrac"     "reads"        "readSum"     
[6] "readFrac"     "readFracSum"  "Relabund"     "RelabundMean"
> summaryInfo[[1]]
 [1] "Bacteria->Verrucomicrobia" "Bacteria->Proteobacteria" 
 [3] "Bacteria->Bacteroidetes"   "Bacteria->Firmicutes"     
 [5] "Bacteria->Spirochaetes"    "Archaea->Euryarchaeota"   
 [7] "Bacteria->Acidobacteria"   "Bacteria->Chlamydiae"     
 [9] "Bacteria->Cyanobacteria"   "Bacteria->Actinobacteria" 
[11] "Bacteria->Armatimonadetes" "Bacteria->Fusobacteria"   
[13] "Bacteria->Planctomycetes"  "Bacteria->Chloroflexi"    
[15] "Bacteria->Thermi"          "Bacteria->Deferribacteres"
> bplot(summaryInfo[["taxaFreqs"]])
This function only works with numeric vector or table object
> 
> # summary otu table of relative abundance
> 
> per <- subOTU(otutab = otuqiime, siteInCol = TRUE, taxhead = "taxonomy",
+     percent = FALSE, choose = "all", outype = "Relabund", sort = TRUE)
You select to subset the all data
There is one column given taxonomy in the data set
Keep all biosphere, but the empty rows will be removed
The outype is the relative abundance data
The outype data have 591 rows and 454 columns
[1] 591 454
> 
> summaryInfo <- otuReport(otutab = per, siteInCol = TRUE, taxhead = "taxonomy",
+     platform = "qiime", pattern = ";", percent = TRUE, level = "class")
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
Data checking ... 
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
This funciton is designed for OTU table
OTUs in rows with a column given taxonomy
The input OTUs is in QIIME format
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Error in names(dn) <- dnn : attempt to set an attribute on NULL
Calls: otuReport -> sapply -> lapply -> FUN
Execution halted