############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings bioCancer_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/bioCancer.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * 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 ‘bioCancer/DESCRIPTION’ ... OK * this is package ‘bioCancer’ version ‘1.32.0’ * package encoding: UTF-8 * 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 ‘bioCancer’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: app 3.4Mb extdata 2.6Mb * 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 ... OK * checking code 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... NOTE Invalid package aliases in Rd file 'bioCancer.Rd': ‘-package’ * 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘bioCancer-Ex.R’ failed The error occurred in: R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "bioCancer" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > base::assign(".ExTimings", "bioCancer-Ex.timings", pos = 'CheckExEnv') > base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv')) > base::assign(".format_ptime", + function(x) { + if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L] + if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L] + options(OutDec = '.') + format(x[1L:3L], digits = 7L) + }, + pos = 'CheckExEnv') > > ### * > library('bioCancer') Loading required package: radiant.data Loading required package: magrittr Loading required package: ggplot2 Loading required package: lubridate Attaching package: ‘lubridate’ The following objects are masked from ‘package:base’: date, intersect, setdiff, union Loading required package: tidyr Attaching package: ‘tidyr’ The following object is masked from ‘package:magrittr’: extract Loading required package: dplyr Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Attaching package: ‘radiant.data’ The following objects are masked from ‘package:lubridate’: month, wday The following object is masked from ‘package:ggplot2’: diamonds The following object is masked from ‘package:magrittr’: set_attr The following object is masked from ‘package:base’: date Loading required package: cBioPortalData Loading required package: AnVIL Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following object is masked from ‘package:radiant.data’: normalize The following objects are masked from ‘package:dplyr’: combine, intersect, setdiff, union The following objects are masked from ‘package:lubridate’: intersect, setdiff, union 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:dplyr’: first, rename The following object is masked from ‘package:tidyr’: expand The following objects are masked from ‘package:lubridate’: second, second<- The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following objects are masked from ‘package:dplyr’: collapse, desc, slice The following object is masked from ‘package:lubridate’: %within% Loading required package: GenomeInfoDb Attaching package: ‘GenomicRanges’ The following object is masked from ‘package:magrittr’: subtract Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: XML * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/bioCancer.Rcheck/00check.log’ for details.