* using log directory 'd:/RCompile/CRANincoming/R-devel/IndepthPathway.Rcheck' * using R Under development (unstable) (2023-09-26 r85226 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'IndepthPathway/DESCRIPTION' ... OK * this is package 'IndepthPathway' version '0.1.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: 'Sanghoon Lee ' New submission License components with restrictions and base license permitting such: MIT + file LICENSE Possibly misspelled words in DESCRIPTION: IndepthPathway (7:29) csea (7:83) gsea (7:99) uniConSig (7:58) wcsea (7:89) Package has a VignetteBuilder field but no prebuilt vignette index. Size of tarball: 39079954 bytes * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'IndepthPathway' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Invalid license file pointers: LICENSE * checking top-level files ... NOTE Non-standard files/directories found at top level: 'DS_Store' 'LICENSE.md' 'Rbuildignore' 'cran-comments.md' 'gitattributes' 'gitignore' 'news.md' * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... NOTE CSEA2: no visible global function definition for 'setNames' CSEA2: no visible binding for global variable 'uniConSigResult' batch_CalWeight: no visible binding for global variable 'compare.list' cal.uniConSig: no visible binding for global variable 'preCalmatrix_Part1' cal.uniConSig.ks: no visible binding for global variable 'preCalmatrix_Part1' cal_ES: no visible binding for global variable 'compare.list' disambiguationCSEA: no visible global function definition for 'setNames' disambiguationCSEA: no visible global function definition for 'p.adjust' disambiguationGSEA: no visible global function definition for 'p.adjust' limmaDEG: no visible binding for global variable 'var' mergePathway: no visible global function definition for 'setNames' pathway.heatmap: no visible global function definition for 'colorRampPalette' pathwayAssociation: no visible binding for global variable 'topPathwayUp' pathwayAssociation: no visible binding for global variable 'preCalmatrix_Part1' pathwayAssociation: no visible global function definition for 'setNames' weightedKS.batch: no visible global function definition for 'nthroot' Undefined global functions or variables: colorRampPalette compare.list nthroot p.adjust preCalmatrix_Part1 setNames topPathwayUp uniConSigResult var Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "p.adjust", "setNames", "var") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'CSEA2.Rd': \examples lines wider than 100 characters: CSEA2(targetScore=setNames(as.numeric(uniConSigResult$up.uniConSig), uniConSigResult$subjectID),compare.list,p.cut=1) Rd file 'cal.uniConSig.Rd': \examples lines wider than 100 characters: cal.uniConSig(targetList=targetList_Up,feature.list=feature.list,preCalmatrix=preCalmatrix_Part1,rm.overfit=FALSE) Rd file 'cal.uniConSig.ks.Rd': \examples lines wider than 100 characters: cal.uniConSig.ks(up.ks=ks.result[[1]],down.ks=ks.result[[2]],preCalmatrix=preCalmatrix_Part1,feature.list) Rd file 'disambiguationCSEA.Rd': \examples lines wider than 100 characters: disambiguationCSEA(GEA.result=down.CSEA.result,uniConSigResult=uniConSigResult,compare.list=compare.list,upPathways=FALSE,topn=30,p.cut ... [TRUNCATED] Rd file 'disambiguationGSEA.Rd': \examples lines wider than 100 characters: disambiguationGSEA(GEA.result=down.GSEA.result,weight=-weight,compare.list=compare.list,topn=30,p.cut=0.8,p.adjust.method="bonferroni") Rd file 'draw.network.Rd': \examples lines wider than 100 characters: draw.network(pathway.out=pathway.merge,assoc=pathwayMergeAssoc,NES.cut=2,node.size=1,line.thickness=1,font.size=0.4,wrap.string.width=1 ... [TRUNCATED] Rd file 'pathwayAssociation.Rd': \examples lines wider than 100 characters: pathwayAssociation(topPathway=topPathwayUp, compare.list, feature.list, preCalmatrix=preCalmatrix_Part1, minsize=10, rm.overfit=FALSE) Rd file 'preCalmatrix_Combine.Rd': \examples lines wider than 100 characters: preCalmatrix_Combine(preCalmatrix_Part1, preCalmatrix_Part2, preCalmatrix_Part3, preCalmatrix_Part4, preCalmatrix_Part5) Rd file 'run.weightedKS.Rd': \examples lines wider than 100 characters: run.weightedKS(weight,signed=TRUE,feature.list=feature.list,minsize=10,correct.outlier=FALSE,transformNegWeight=FALSE ) Rd file 'weightedKS.batch.Rd': \examples lines wider than 100 characters: weightedKS.batch(weight, feature.list=feature.list,high.enrich=TRUE,p.cut=0.05,correct.outlier=FALSE,minsize=5) These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... Check process probably crashed or hung up for 20 minutes ... killed Most likely this happened in the example checks (?), if not, ignore the following last lines of example output: [23728,] "LLCFC1\t1\tZBTB48@1" [23729,] "CENPBD1P1\t1\tZDHHC17@1" [23730,] "LNCRI\t1\tZDHHC17@1" [23731,] "LOC554206\t1\tZDHHC17@1" [23732,] "VN1R10P\t1\tZDHHC17@1" [23733,] "ZNF667-AS1\t1\tZDHHC17@1" [23734,] "MGC15885\t1\tZFP36L2@1" [23735,] "TPT1P8\t1\tZFP36L2@1" > > > > base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv") > base::cat("preCalmatrix_Combine", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t") > cleanEx() > nameEx("run.weightedKS") > ### * run.weightedKS > > flush(stderr()); flush(stdout()) > > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: run.weightedKS > ### Title: Title run weighted KS for a weighted subject list using > ### weightedKSV2 module > ### Aliases: run.weightedKS > > ### ** Examples > > run.weightedKS(weight,signed=TRUE,feature.list=feature.list,minsize=10,correct.outlier=FALSE,transformNegWeight=FALSE ) [1] "Using Weight to rank subjects" [1] "Pre-calculating 1000 ES permutations" ======== End of example output (where/before crash/hang up occured ?) ========