############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BBCAnalyzer.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BBCAnalyzer_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BBCAnalyzer.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 ‘BBCAnalyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BBCAnalyzer’ version ‘1.32.0’ * 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 ‘BBCAnalyzer’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE analyzeBases: no visible global function definition for ‘read.table’ analyzeBasesPlotOnly: no visible global function definition for ‘read.table’ analyzeReads: no visible global function definition for ‘path’ analyzeReads: no visible global function definition for ‘write.table’ checkBamInput: no visible global function definition for ‘path’ checkVcfInput: no visible global function definition for ‘path’ frequencyAnalysis: no visible global function definition for ‘write.table’ frequencyAnalysisVcf: no visible global function definition for ‘read.table’ frequencyAnalysisVcf: no visible global function definition for ‘path’ frequencyAnalysisVcf: no visible global function definition for ‘write.table’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘par’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘rect’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘lines’ plotCountsPerSampleRelativeVcf_plot: no visible global function definition for ‘text’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘par’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘rect’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘lines’ plotCountsPerSampleRelative_plot: no visible global function definition for ‘text’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘par’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘rect’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘lines’ plotCountsPerSampleVcf_plot: no visible global function definition for ‘text’ plotCountsPerSample_plot: no visible global function definition for ‘par’ plotCountsPerSample_plot: no visible global function definition for ‘barplot’ plotCountsPerSample_plot: no visible global function definition for ‘rect’ plotCountsPerSample_plot: no visible global function definition for ‘lines’ plotCountsPerSample_plot: no visible global function definition for ‘text’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘par’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘rect’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘lines’ plotCountsPerTargetRelativeVcf_plot: no visible global function definition for ‘text’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘par’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘rect’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘lines’ plotCountsPerTargetRelative_plot: no visible global function definition for ‘text’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘par’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘barplot’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘rect’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘lines’ plotCountsPerTargetVcf_plot: no visible global function definition for ‘text’ plotCountsPerTarget_plot: no visible global function definition for ‘par’ plotCountsPerTarget_plot: no visible global function definition for ‘barplot’ plotCountsPerTarget_plot: no visible global function definition for ‘rect’ plotCountsPerTarget_plot: no visible global function definition for ‘lines’ plotCountsPerTarget_plot: no visible global function definition for ‘text’ processVcfFile: no visible global function definition for ‘read.table’ reportVariants: no visible global function definition for ‘write.table’ reportVariantsVcf: no visible global function definition for ‘write.table’ Undefined global functions or variables: barplot lines par path read.table rect text write.table Consider adding importFrom("graphics", "barplot", "lines", "par", "rect", "text") importFrom("utils", "read.table", "write.table") 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BBCAnalyzer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: analyzeBasesPlotOnly > ### Title: Plots the number of reads at all previously defined positions > ### Aliases: analyzeBasesPlotOnly 'analyze Bases Plot Only' > > ### ** Examples > > library("BSgenome.Hsapiens.UCSC.hg19") Loading required package: BSgenome 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 Loading required package: S4Vectors Loading required package: stats4 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: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: ‘rtracklayer’ The following object is masked from ‘package:BiocIO’: FileForFormat > ref_genome<-BSgenome.Hsapiens.UCSC.hg19 > > output<-analyzeBases(sample_names=system.file("extdata","SampleNames_small.txt",package="BBCAnalyzer"), + bam_input=system.file("extdata",package="BBCAnalyzer"), + target_regions=system.file("extdata","targetRegions_small.txt",package="BBCAnalyzer"), + vcf_input="", + output=system.file("extdata",package="BBCAnalyzer"), + output_pictures=system.file("extdata",package="BBCAnalyzer"), + known_file="", + genome=ref_genome, + MQ_threshold=60, + BQ_threshold=50, + frequency_threshold=0.01, + qual_lower_bound=58, + qual_upper_bound=63, + marks=c(0.01), + relative=TRUE, + per_sample=TRUE) Determine Target Analyze Reads Sample 1 out of 1 Position 1 out of 1 * 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 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/BBCAnalyzer.Rcheck/00check.log’ for details.