############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CNVfilteR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CNVfilteR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CNVfilteR.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 ‘CNVfilteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNVfilteR’ version ‘1.16.0’ * 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 ‘CNVfilteR’ 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 ... OK * 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 ‘CNVfilteR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotScoringModel > ### Title: plotVariantsForCNV > ### Aliases: plotScoringModel > > ### ** Examples > > # Load CNVs data > cnvs.file <- system.file("extdata", "DECoN.CNVcalls.csv", package = "CNVfilteR", mustWork = TRUE) > cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample") > > # Load VCFs data > vcf.files <- c(system.file("extdata", "variants.sample1.vcf.gz", package = "CNVfilteR", mustWork = TRUE), + system.file("extdata", "variants.sample2.vcf.gz", package = "CNVfilteR", mustWork = TRUE)) > vcfs <- loadVCFs(vcf.files, cnvs.gr = cnvs.gr) Scanning file /home/biocbuild/R/R-4.3.1/site-library/CNVfilteR/extdata/variants.sample1.vcf.gz... VarScan2 was found as source in the VCF metadata, RD will be used as ref allele depth field, AD will be used as alt allele depth field. Scanning file /home/biocbuild/tmp/RtmpJzZJyg/variants.sample2.vcf.gz... VarScan2 was found as source in the VCF metadata, RD will be used as ref allele depth field, AD will be used as alt allele depth field. * 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 See ‘/home/biocbuild/bbs-3.18-bioc/meat/CNVfilteR.Rcheck/00check.log’ for details.