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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PrioSubtypeDrug
> ### Title: Prioritization of candidate cancer subtype-specific drugs
> ###   (PrioSubtypeDrug)
> ### Aliases: PrioSubtypeDrug
> 
> ### ** Examples
> 
> require(GSVA)
Loading required package: GSVA
> require(parallel)
Loading required package: parallel
> ## Get simulated breast cancer gene expression profile data.
> Geneexp<-get("Geneexp")
> ## Obtain sample subtype data and calculate breast cancer subtype-specific drugs.
> Subtype<-system.file("extdata", "Subtype_labels.cls", package = "SubtypeDrug")
> 
> ## Subpathway list data and drug subpathway association data
> ## were stored in packet `SubtypeDrugData`.
> ## `SubtypeDrugData` has been uploaded to the github repository.
> ## If subpathway list data and drug subpathway association data are needed,
> ## users can download and install through `install_github` function and
> ## set parameter url=""hanjunwei-lab/SubtypeDrugData".
> ## After installing and loading package `SubtypeDrugData`,
> ## users can use the following command to get the data.
> ## Get subpathway list data.
> ## If the gene expression profile contains gene Symbol.
> ## data(SpwSymbolList)
> ## If the gene expression profile contains gene Entrezid.
> ## data(SpwEntrezidList)
> ## Get drug subpathway association data.
> ## data(DrugSpwData)
> 
> ## Identify breast subtype-specific drugs.
> ## Subtype_drugs<-PrioSubtypeDrug(Geneexp,Subtype,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ##                                       E_FDR=1,S_FDR=1)
> 
> ## Identify breast cancer-related drugs in only two types of samples: breast cancer and control.
> Cancer<-system.file("extdata", "Cancer_normal_labels.cls", package = "SubtypeDrug")
> ## Disease_drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",SpwSymbolList,drug.spw.data=DrugSpwData,
> ##                                       E_FDR=1,S_FDR=1)
> 
> ## The function PrioSubtypeDrug() can also support user-defined data.
> Geneexp<-get("GeneexpT")
> ## User-defined drug regulation data should resemble the structure below
> UserDS<-get("UserDST")
> str(UserDS)
List of 2
 $ chloramphenicol(1.24e-05M):List of 2
  ..$ Target_upregulation  : chr [1:5] "04060_26" "04610_11" "04670_6" "05162_13" ...
  ..$ Target_downregulation: chr [1:5] "04150_14" "04610_11" "04625_34" "04670_6" ...
 $ thioridazine(1e-06M)      :List of 2
  ..$ Target_upregulation  : chr [1:5] "04060_4" "04060_19" "04670_9" "05134_4" ...
  ..$ Target_downregulation: chr [1:5] "00790_8" "04060_8" "04064_14" "04390_10" ...
> ## Need to load gene set data consistent with drug regulation data.
> UserGS<-get("UserGST")
> str(UserGS)
List of 20
 $ 04060_26 : chr [1:3] "ACVR1" "AMHR2" "AMH"
 $ 04610_11 : chr [1:3] "C3" "CFB" "CFD"
 $ 04670_6  : chr [1:3] "ITGB2" "F11R" "ITGAL"
 $ 05162_13 : chr [1:3] "IL12A" "IL12B" "FCGR2B"
 $ 05206_112: chr [1:3] "MIR143" "ATM" "TP53"
 $ 04150_14 : chr [1:2] "SLC7A5" "SLC3A2"
 $ 04610_11 : chr [1:3] "C3" "CFB" "CFD"
 $ 04625_34 : chr [1:4] "MDM2" "IRF1" "IL12A" "IL12B"
 $ 04670_6  : chr [1:3] "ITGB2" "F11R" "ITGAL"
 $ 05162_13 : chr [1:3] "IL12A" "IL12B" "FCGR2B"
 $ 04060_4  : chr [1:4] "IL10RB" "IL22RA1" "IL22RA2" "IL22"
 $ 04060_19 : chr [1:3] "IL6ST" "IL11RA" "IL11"
 $ 04670_9  : chr [1:3] "ITGB2" "ITGAM" "JAM3"
 $ 05134_4  : chr [1:3] "ITGAM" "ITGB2" "C3"
 $ 00100_6  : chr [1:6] "DHCR24" "LSS" "TM7SF2" "MSMO1" ...
 $ 00790_8  : chr [1:4] "MOCS2" "MOCS1" "GPHN" "MOCOS"
 $ 04060_8  : chr [1:3] "IL2RG" "IL7R" "IL7"
 $ 04064_14 : chr [1:3] "PLCG1" "ZAP70" "LAT"
 $ 04390_10 : chr [1:4] "YAP1" "WWTR1" "TP73" "BBC3"
 $ 05165_16 : chr [1:3] "NFX1" "UBE3A" "TERT"
> Drugs<-PrioSubtypeDrug(Geneexp,Cancer,"Control",UserGS,spw.min.sz=1,
+                        drug.spw.data=UserDS,drug.spw.min.sz=1,
+                        nperm=10,E_FDR=1,S_FDR=1)
Error in ..Internal(is.unsorted(x, FALSE)) : 
  2 arguments passed to .Internal(is.unsorted) which requires 3
Calls: PrioSubtypeDrug ... fast_path_FUN -> <Anonymous> -> .numeric2end -> <Anonymous>
Execution halted