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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SubSEA
> ### Title: Subtype Set Enrichment Analysis (SubSEA)
> ### Aliases: SubSEA
> 
> ### ** Examples
> 
> # load depend package.
> require(GSVA)
Loading required package: GSVA
> require(parallel)
Loading required package: parallel
> # get breast cancer disease subtype gene expression profile.
> Bregenematrix<-get("Subgenematrix")
> # get path of the sample disease subtype files.
> Subtypelabels<- system.file("extdata", "Sublabels.cls", package = "psSubpathway")
> # get the result of the SubSEA function
> SubSEAresult<-get("Subspwresult")
> str(SubSEAresult)
List of 5
 $ Basal    :'data.frame':	15 obs. of  6 variables:
  ..$ SubpathwayID  : Factor w/ 15 levels "00120_19","00120_9",..: 2 1 3 4 5 6 7 8 9 10 ...
  ..$ PathwayName   : Factor w/ 14 levels "Apoptosis","C-type lectin receptor signaling pathway",..: 10 10 3 13 8 6 4 11 1 14 ...
  ..$ SubpathwayGene: Factor w/ 15 levels "AMACR ACOX2 HSD17B4 SCP2",..: 1 13 6 7 9 3 15 12 2 4 ...
  ..$ SES           : num [1:15] -0.885 -0.829 -0.848 -0.767 -0.665 ...
  ..$ Pvalue        : num [1:15] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ FDR           : num [1:15] 0 0 0 0 0 0 0 0 0 0 ...
 $ Her2     :'data.frame':	25 obs. of  6 variables:
  ..$ SubpathwayID  : Factor w/ 25 levels "00010_6","00020_4",..: 1 2 3 4 5 6 7 8 9 10 ...
  ..$ PathwayName   : Factor w/ 24 levels "Arginine and proline metabolism",..: 12 3 8 1 16 11 24 22 5 17 ...
  ..$ SubpathwayGene: Factor w/ 25 levels "ADCY1 ADCY2 ADCY3 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADCY4 PRKACA PRKACB PRKACG CREB1 ATF2 CREM ATF1 ATF3 ATF4 XBP1 "| __truncated__,..: 3 18 2 23 13 22 12 24 7 16 ...
  ..$ SES           : num [1:25] 0.704 0.681 0.725 0.817 0.711 ...
  ..$ Pvalue        : num [1:25] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ FDR           : num [1:25] 0 0 0 0 0 0 0 0 0 0 ...
 $ LumA     :'data.frame':	49 obs. of  6 variables:
  ..$ SubpathwayID  : Factor w/ 49 levels "00052_2","00340_5",..: 1 2 3 5 4 6 7 8 9 10 ...
  ..$ PathwayName   : Factor w/ 36 levels "Adipocytokine signaling pathway",..: 15 18 32 11 11 30 13 21 7 14 ...
  ..$ SubpathwayGene: Factor w/ 49 levels "ADCY1 ADCY2 ADCY3 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADCY4 PRKACA PRKACB PRKACG CREB1 ATF2 CREM ATF1 ATF3 ATF4 XBP1 "| __truncated__,..: 3 23 14 17 12 49 16 42 41 10 ...
  ..$ SES           : num [1:49] -0.731 0.773 -0.554 0.677 0.703 ...
  ..$ Pvalue        : num [1:49] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ FDR           : num [1:49] 0 0 0 0 0 0 0 0 0 0 ...
 $ LumB     :'data.frame':	22 obs. of  6 variables:
  ..$ SubpathwayID  : Factor w/ 22 levels "00350_2","00563_1",..: 1 2 3 4 5 6 7 8 9 10 ...
  ..$ PathwayName   : Factor w/ 22 levels "Amyotrophic lateral sclerosis (ALS)",..: 22 7 18 15 6 4 12 8 2 13 ...
  ..$ SubpathwayGene: Factor w/ 22 levels "ADAM17 HBEGF ADAM10 CXCL8 CXCR1 CXCR2 EGFR",..: 6 17 7 11 10 14 12 18 19 21 ...
  ..$ SES           : num [1:22] 0.576 0.559 0.608 0.627 -0.658 ...
  ..$ Pvalue        : num [1:22] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ FDR           : num [1:22] 0 0 0 0 0 0 0 0 0 0 ...
 $ spwmatrix: num [1:725, 1:67] 0.1892 0.0467 0.1907 0.0874 0.1993 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:725] "00010_1" "00010_2" "00010_5" "00010_6" ...
  .. ..$ : chr [1:67] "Her2" "LumA" "LumB" "LumA" ...
> head(SubSEAresult$Basal)
         SubpathwayID
00120_9       00120_9
00120_19     00120_19
00232_1       00232_1
00280_10     00280_10
00510_8       00510_8
00601_8       00601_8
                                                        PathwayName
00120_9                              Primary bile acid biosynthesis
00120_19                             Primary bile acid biosynthesis
00232_1                                         Caffeine metabolism
00280_10                 Valine, leucine and isoleucine degradation
00510_8                                       N-Glycan biosynthesis
00601_8  Glycosphingolipid biosynthesis - lacto and neolacto series
                                                                                                                                                                          SubpathwayGene
00120_9                                                                                                                                                         AMACR ACOX2 HSD17B4 SCP2
00120_19                                                                                                                                             SLC27A5 CYP27A1 AMACR ACOX2 HSD17B4
00232_1                                                                                                                                                      CYP1A2 XDH NAT2 NAT1 CYP2A6
00280_10                                                     EHHADH HADH ACADSB AOX1 ALDH2 ALDH1B1 ALDH9A1 ALDH3A2 ALDH7A1 ALDH6A1 ABAT HIBADH HIBCH ECHS1 HADHA ACADM ACADS ACAD8 AGXT2
00510_8                                                                                                   FUT8 MGAT3 MGAT2 MAN2A2 MAN2A1 MAN1A2 MAN1B1 MAN1A1 MAN1C1 MGAT4B MGAT4A MGAT1
00601_8  B4GALT4 B4GALT3 B4GALT2 FUT4 FUT7 FUT3 FUT5 FUT6 ST8SIA1 ST3GAL6 FUT9 B3GNT3 B3GNT2 B3GNT4 B4GALT1 ABO FUT1 FUT2 B3GNT5 B3GALT1 B3GALT2 B3GALT5 ST3GAL3 ST3GAL4 A4GALT B3GALNT1
              SES Pvalue FDR
00120_9  -0.88462      0   0
00120_19 -0.82945      0   0
00232_1  -0.84790      0   0
00280_10 -0.76735      0   0
00510_8  -0.66495      0   0
00601_8   0.74271      0   0
> 
> # Simulated gene matrix
> genematrix <- matrix(rnorm(500*40), nrow=500, dimnames=list(1:500, 1:40))
> # Construct subpathway list data.
> subpathwaylist <- as.list(sample(2:100, size=20, replace=TRUE))
> subpathwaylist <- lapply(subpathwaylist, function(n) sample(1:500, size=n, replace=FALSE))
> names(subpathwaylist)<-c(paste(rep("spw",20),c(1:20)))
> # Construct sample labels data.
> subtypelabel<-list(phen=c("subtype1","subtype2","subtype3","subtype4"),
+                    class.labes=c(rep("subtype1",10),rep("subtype2",10),
+                    rep("subtype3",10),rep("subtype4",10)))
> SubSEAcs<-SubSEA(genematrix,subtypelabel,subpathwaylist,nperm=10,parallel.sz=1)
Error in serverSocket(port = port) : 
  creation of server socket failed: port 11963 cannot be opened
Calls: SubSEA -> makeCluster -> makePSOCKcluster -> serverSocket
Execution halted