############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings oppar_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/oppar.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘oppar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘oppar’ version ‘1.30.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘oppar’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: data 5.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release * 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 startup messages can be suppressed ... 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 compute.gene.density : : no visible global function definition for ‘ecdf’ compute.geneset.es: no visible global function definition for ‘txtProgressBar’ compute.geneset.es: no visible global function definition for ‘setTxtProgressBar’ ks_test_m: no visible global function definition for ‘setTxtProgressBar’ plage: no visible global function definition for ‘txtProgressBar’ plage : : no visible global function definition for ‘sd’ plage : : no visible global function definition for ‘setTxtProgressBar’ plage: no visible global function definition for ‘setTxtProgressBar’ ssgsea: no visible global function definition for ‘txtProgressBar’ ssgsea : : no visible global function definition for ‘setTxtProgressBar’ ssgsea: no visible global function definition for ‘setTxtProgressBar’ zscore: no visible global function definition for ‘txtProgressBar’ zscore : : no visible global function definition for ‘sd’ zscore : : no visible global function definition for ‘setTxtProgressBar’ zscore: no visible global function definition for ‘setTxtProgressBar’ computeGeneSetsOverlap,list-ExpressionSet : : no visible global function definition for ‘na.omit’ computeGeneSetsOverlap,list-character : : no visible global function definition for ‘na.omit’ gsva,ExpressionSet-GeneSetCollection: no visible binding for global variable ‘sd’ gsva,ExpressionSet-GeneSetCollection : : no visible global function definition for ‘na.omit’ gsva,ExpressionSet-list: no visible binding for global variable ‘sd’ gsva,ExpressionSet-list : : no visible global function definition for ‘na.omit’ gsva,matrix-GeneSetCollection: no visible binding for global variable ‘sd’ gsva,matrix-GeneSetCollection : : no visible global function definition for ‘na.omit’ gsva,matrix-list: no visible binding for global variable ‘sd’ gsva,matrix-list : : no visible global function definition for ‘na.omit’ opa,matrix: no visible global function definition for ‘relevel’ opa,matrix : : no visible global function definition for ‘mad’ opa,matrix : : no visible global function definition for ‘median’ opa,matrix : : no visible binding for global variable ‘quantile’ opa,matrix : : no visible global function definition for ‘IQR’ show,OPPARList: no visible global function definition for ‘head’ Undefined global functions or variables: IQR ecdf head mad median na.omit quantile relevel sd setTxtProgressBar txtProgressBar Consider adding importFrom("stats", "IQR", "ecdf", "mad", "median", "na.omit", "quantile", "relevel", "sd") importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * 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 ... WARNING LazyData DB of 5.1 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘oppar-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getSampleOutlier > ### Title: Retrieving outlier genes in samples > ### Aliases: getSampleOutlier getSampleOutlier,OPPARList,nuchar-method > ### getSampleOutlier,matrix,nuchar-method > > ### ** Examples > > data(GSE46141) > library(Biobase) Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > group <- sapply(pData(bcm)$source_name_ch1, function(x){ ifelse(x == "breast",0,1)}) > group <- factor(group) > bcm.opa <- opa(bcm,group=group) * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/oppar.Rcheck/00check.log’ for details.