############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:AneuFinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings AneuFinder_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘AneuFinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AneuFinder’ version ‘1.35.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘AneuFinder’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * 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 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 whether 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 Aneufinder: multiple local function definitions for ‘parallel.helper’ with different formal arguments * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Aneufinder.Rd: GRanges-class DNAcopy.findCNVs.Rd: GRanges-class HMM.findCNVs.Rd: GRanges-class, GRangesList aneuBiHMM.Rd: GRanges-class aneuHMM.Rd: GRanges-class annotateBreakpoints.Rd: GRanges-class bam2GRanges.Rd: GRanges-class bed2GRanges.Rd: GRanges-class bi.edivisive.findCNVs.Rd: e.divisive, GRanges-class biDNAcopy.findCNVs.Rd: GRanges-class biHMM.findCNVs.Rd: GRanges-class, GRangesList binReads.Rd: GRanges-class, GenomicRanges, GRangesList binned.data.Rd: GRanges-class blacklist.Rd: GRanges-class clusterByQuality.Rd: mclust clusterHMMs.Rd: GRanges-class edivisive.findCNVs.Rd: e.divisive, GRanges-class estimateComplexity.Rd: GRanges-class export.Rd: GRanges-class filterSegments.Rd: GRanges-class findCNVs.Rd: GRanges-class findCNVs.strandseq.Rd: GRanges-class findHotspots.Rd: GRanges-class fixedWidthBins.Rd: GRanges-class, GRangesList getBreakpoints.Rd: GRanges-class getQC.Rd: GRanges-class getSCEcoordinates.Rd: GRanges-class heatmapGenomewide.Rd: GRanges-class hotspotter.Rd: GRanges-class hotspotter.variable.Rd: GRanges-class importBed.Rd: GRanges-class karyotypeMeasures.Rd: GRanges-class loadFromFiles.Rd: GRanges-class, GRangesList mergeStrandseqFiles.Rd: GRanges-class plot.GRanges.Rd: GRanges-class plot.GRangesList.Rd: GRangesList plotHeterogeneity.Rd: GRanges-class plot_pca.Rd: GRanges-class refineBreakpoints.Rd: GRanges-class subsetByCNVprofile.Rd: GRanges-class transCoord.Rd: GRanges-class variableWidthBins.Rd: GRanges-class, GRangesList Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed simulateReads 49.124 4.344 53.469 refineBreakpoints 44.585 0.309 44.895 heatmapAneuploidies 40.042 0.251 40.294 correctGC 27.258 3.621 30.882 plotHeterogeneity 26.883 0.264 27.148 heatmapGenomewideClusters 21.675 0.135 21.811 karyotypeMeasures 19.982 0.130 20.112 heatmapGenomewide 18.640 0.061 18.743 annotateBreakpoints 14.051 0.923 15.368 getBreakpoints 9.818 0.167 9.985 consensusSegments 7.460 0.075 7.535 getSCEcoordinates 4.677 0.077 5.128 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/AneuFinder.Rcheck/00check.log’ for details.