* using log directory ‘/srv/hornik/tmp/CRAN/psSubpathway.Rcheck’ * using R Under development (unstable) (2024-03-16 r86144) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘psSubpathway/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘psSubpathway’ version ‘0.1.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Junwei Han ’ Package has a VignetteBuilder field but no prebuilt vignette index. The Date field is over a month old. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... 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[8s/8s] ERROR 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") > # SubSEA(Bregenematrix,input.cls=Subtypelabels,nperm=50,fdr.th=0.01,parallel.sz=2) > # 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=0,parallel.sz=1) Error in .local(gSets, ...) : unused arguments (min.sz = 1, max.sz = Inf) Calls: SubSEA -> filterGeneSets -> filterGeneSets Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE