############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings DEGreport_1.38.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DEGreport.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 ‘DEGreport/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DEGreport’ version ‘1.38.1’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DEGreport’ can be installed ... OK * checking installed package size ... OK * 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 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 dependencies in R code ... NOTE ':::' call which should be '::': ‘dendextend:::cutree’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .benckmark_cutoff: no visible binding for global variable ‘cutoff’ .benckmark_cutoff: no visible binding for global variable ‘cluster’ .convertIDs: no visible global function definition for ‘keys’ .correct_fdr: no visible global function definition for ‘fdrtool’ .generate_scatter_plot: no visible binding for global variable ‘compare’ .generate_scatter_plot: no visible binding for global variable ‘covar’ .get_counts: no visible global function definition for ‘counts’ .model: no visible global function definition for ‘lm’ .plot_raw: no visible binding for global variable ‘.x’ .plot_shrunken: no visible binding for global variable ‘.x’ .process: no visible binding for global variable ‘genes’ .process: no visible binding for global variable ‘cluster’ .reduce : : : no visible global function definition for ‘boxplot’ .reduce_covariates : : no visible binding for global variable ‘fdr’ .reduce_covariates : : no visible binding for global variable ‘compare’ .reduce_covariates : : no visible binding for global variable ‘r’ .reduce_covariates : : no visible binding for global variable ‘p.value’ .run_cluster_profiler: no visible global function definition for ‘enrichGO’ .run_cluster_profiler: no visible global function definition for ‘simplify’ .select_concensus_genes: no visible global function definition for ‘desc’ .select_concensus_genes: no visible binding for global variable ‘score’ .select_concensus_genes: no visible binding for global variable ‘k’ .select_concensus_genes: no visible binding for global variable ‘itemConsensus’ .summarise_res: no visible global function definition for ‘matches’ .summarise_res: no visible binding for global variable ‘comparison’ .summarise_res: no visible binding for global variable ‘gene’ .summarise_res: no visible binding for global variable ‘value_fdr’ .summarise_res: no visible binding for global variable ‘value_fc’ .table_w_fc: no visible binding for global variable ‘comp’ .table_w_fc: no visible binding for global variable ‘log2FoldChange’ degCheckFactors: no visible binding for global variable ‘ratios’ degCorCov: no visible binding for global variable ‘compare’ degCovariates: no visible binding for global variable ‘x’ degCovariates: no visible binding for global variable ‘y’ degCovariates: no visible binding for global variable ‘xend’ degCovariates: no visible binding for global variable ‘yend’ degCovariates: no visible binding for global variable ‘pvalue’ degMA: no visible binding for global variable ‘base_mean’ degMA: no visible binding for global variable ‘log2fc’ degMV: no visible binding for global variable ‘min_median’ degMV: no visible binding for global variable ‘max_sd’ degPatterns: no visible global function definition for ‘rowMedians’ degPatterns: no visible binding for global variable ‘genes’ degPatterns: no visible global function definition for ‘color_branches’ degPatterns: no visible global function definition for ‘set’ degPlotCluster: no visible binding for global variable ‘genes’ degPlotCluster: no visible binding for global variable ‘cluster’ degPlotWide : : no visible binding for global variable ‘count’ significants,TopTags: no visible binding for global variable ‘FDR’ significants,TopTags: no visible binding for global variable ‘logFC’ significants,list : : no visible global function definition for ‘matches’ Undefined global functions or variables: .x FDR base_mean boxplot cluster color_branches comp compare comparison count counts covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k keys lm log2FoldChange log2fc logFC matches max_sd min_median p.value pvalue r ratios rowMedians score set simplify value_fc value_fdr x xend y yend Consider adding importFrom("graphics", "boxplot") importFrom("stats", "lm") 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘DEGreport-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: degDefault > ### Title: Method to get the default table to use. > ### Aliases: degDefault degCorrect degDefault,DEGSet-method > ### degCorrect,DEGSet-method > > ### ** Examples > > library(DESeq2) Loading required package: S4Vectors Loading required package: stats4 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 Attaching package: ‘S4Vectors’ 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 Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats 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: 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 > library(dplyr) Attaching package: ‘dplyr’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:matrixStats’: count The following objects are masked from ‘package:GenomicRanges’: intersect, setdiff, union The following object is masked from ‘package:GenomeInfoDb’: intersect The following objects are masked from ‘package:IRanges’: collapse, desc, intersect, setdiff, slice, union The following objects are masked from ‘package:S4Vectors’: first, intersect, rename, setdiff, setequal, union The following objects are masked from ‘package:BiocGenerics’: combine, intersect, setdiff, union The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > dds <- makeExampleDESeqDataSet(betaSD=1) > colData(dds)[["treatment"]] <- sample(colData(dds)[["condition"]], 12) > design(dds) <- ~ condition + treatment > dds <- DESeq(dds) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing > res <- degComps(dds, contrast = list("treatment_B_vs_A")) Doing 1 element(s). Doing results() for each element. Doing lcfSrink() for each element. using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014). Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'. See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette. Reference: https://doi.org/10.1093/bioinformatics/bty895 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 914689 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > library(DEGreport) > > test_check("DEGreport") * 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: 2 ERRORs, 3 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DEGreport.Rcheck/00check.log’ for details.