* using log directory ‘/srv/hornik/tmp/CRAN_pretest/EMTscore.Rcheck’ * using R Under development (unstable) (2024-09-15 r87152) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.8 (9) Debian flang-new version 18.1.8 (9) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘EMTscore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘EMTscore’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘haimei wen ’ New submission Possibly misspelled words in DESCRIPTION: EMTscore (7:1051, 7:1495) mesenchymal (7:25) omics (3:53, 7:611, 7:1325, 7:1588) No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = "haimei", family = "wen", role = c("aut", "cre"), email = "hudie.luoluo@gmail.com"), person(given = "tian", family = "hong", role = "aut")) as necessary. The Title field should be in title case. Current version is: ‘A toolbox for scoring multi-context EMT from omics data’ In title case that is: ‘A Toolbox for Scoring Multi-Context EMT from Omics Data’ This build time stamp is over a month old. Size of tarball: 13706170 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 ‘EMTscore’ can be installed ... [9s/9s] OK * 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 ... [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 ... [2s/2s] NOTE AUCellfunc: no visible global function definition for ‘AUCell_buildRankings’ AUCellfunc: no visible global function definition for ‘AUCell_calcAUC’ AUCellfunc: no visible global function definition for ‘getAUC’ Execute_nnPCA: no visible global function definition for ‘nsprcomp’ Execute_ssGSVA: no visible global function definition for ‘gsva’ Undefined global functions or variables: AUCell_buildRankings AUCell_calcAUC getAUC gsva nsprcomp * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘AUCellfunc’ ‘JASMINE’ ‘NormalizationJAS’ ‘ORCalculation’ ‘RankCalculation’ ‘SingleCellSigExplorer’ ‘stringsAsFactors’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'Execute_JAS.Rd' ‘data’ ‘Genesets’ Documented arguments not in \usage in Rd file 'Execute_JAS.Rd': ‘geneExp’ ‘geneList_E’ Undocumented arguments in Rd file 'Execute_SCSE.Rd' ‘data’ Documented arguments not in \usage in Rd file 'Execute_SCSE.Rd': ‘geneExp’ Undocumented arguments in Rd file 'Execute_nnPCA.Rd' ‘data’ ‘geneList’ ‘dimention’ ‘score_names’ Documented arguments not in \usage in Rd file 'Execute_nnPCA.Rd': ‘geneExp’ ‘geneList_E’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... WARNING LazyData DB of 13.1 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress geneExp.rda 13.1Mb 7.7Mb xz * checking examples ... [8s/8s] ERROR Running examples in ‘EMTscore-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Execute_ssGSVA > ### Title: ssGSVA methods to calculate EMT score > ### Aliases: Execute_ssGSVA > > ### ** Examples > > data(geneExp) > data(geneList_E) > library(GSVA) > Execute_ssGSVA(geneExp, geneList_E) Error in gsva(geneExp, geneslist, method = "ssgsea") : Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva'). Calls: Execute_ssGSVA -> gsva -> gsva -> .Defunct 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, 4 WARNINGs, 2 NOTEs