* using log directory ‘/srv/hornik/tmp/CRAN/IndepthPathway.Rcheck’ * using R Under development (unstable) (2023-09-26 r85226) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * 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 ... [3s/4s] 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: 39080085 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 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 ‘IndepthPathway’ can be installed ... [106s/106s] 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] 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 ... [0s/0s] 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 ... [6s/6s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [13m/13m] ERROR Running examples in ‘IndepthPathway-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: read_concepts > ### Title: Read molecular concepts or gene signature from gmt files > ### Aliases: read_concepts > > ### ** Examples > > read_concepts(GeneSigFile) Error in data.table::fread(GeneSigFile, sep = "") : File 'C:/Users/sal170/CCBR_XWANGLAB10/19_SymSim_wCSEA2/52_5_CRANSubmission_IndepthPathway/h.all.v7.5.1.symbols.gmt' does not exist or is non-readable. getwd()=='/srv/hornik/tmp/CRAN/IndepthPathway.Rcheck' Calls: read_concepts -> Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [1s/1s] OK Running ‘testthat.R’ [0s/0s] * checking PDF version of manual ... [4s/4s] WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... ! LaTeX Error: Something's wrong--perhaps a missing \item. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... * checking PDF version of manual without index ... ERROR * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... NOTE Found the following files/directories: ‘IndepthPathway-manual.tex’ * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs, 1 WARNING, 6 NOTEs