* 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 <hanjunwei1981@163.com>’

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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘psSubpathway’ can be installed ... [23s/23s] OK
* used C compiler: ‘Debian clang version 17.0.6 (5)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/6s] OK
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* checking whether the package can be unloaded cleanly ... [6s/6s] OK
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* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [30s/30s] OK
* checking Rd files ... [0s/0s] OK
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* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
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* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
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* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [7s/7s] ERROR
Running examples in ‘psSubpathway-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DCSA
> ### Title: Dynamic Changed Subpathway Analysis (DCSA)
> ### Aliases: DCSA
> 
> ### ** Examples
> 
> # load depend package.
> require(GSVA)
Loading required package: GSVA
> require(parallel)
Loading required package: parallel
> require(mpmi)
Loading required package: mpmi
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
> # get ACC disease stage gene expression profiling.
> # ACCgenematrix<-get("DCgenematrix")
> # get path of the sample disease stage phenotype files.
> # Stagelabels<-system.file("extdata", "DClabels.cls", package = "psSubpathway")
> # perform the DCSA method.
> # DCSA(ACCgenematrix,input.cls=Stagelabels,nperm=50,fdr.th=0.01,parallel.sz=2)
> # get the result of the SubSEA function
> # DCSAresult<-get("DCspwresult")
> # str(DCSAresult)
> # head(DCSAresult$DCSA)
> 
> # 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.
> stagelabel<-list(phen=c("stage1","stage2","stage3","stage4"),
+                    class.labes=c(rep("stage1",10),rep("stage2",10),
+                    rep("stage3",10),rep("stage4",10)))
> DCSAcs<-DCSA(genematrix,stagelabel,subpathwaylist,nperm=0,parallel.sz=1)
Error in .local(gSets, ...) : 
  unused arguments (min.sz = 5, max.sz = 1000)
Calls: DCSA -> filterGeneSets -> filterGeneSets
Execution halted
* checking PDF version of manual ... [3s/3s] OK
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* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE