############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:CNVrd2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings CNVrd2_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/CNVrd2.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘CNVrd2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CNVrd2’ version ‘1.41.0’ * 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 ‘CNVrd2’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * 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 ... NOTE Namespaces in Imports field not imported from: ‘DNAcopy’ ‘Rsamtools’ All declared Imports should be used. Packages in Depends field not imported from: ‘VariantAnnotation’ ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘parallel’ ‘rjags’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE groupCNVs,clusteringCNVs: warning in matrix(0, nr = length(x2), ncol = k - 2): partial argument match of 'nr' to 'nrow' segmentSamples,CNVrd2: warning in matrix(0, nr = nnn, ncol = dim(genes)[2]): partial argument match of 'nr' to 'nrow' calculateLDSNPandCNV: no visible global function definition for ‘TabixFile’ calculateLDSNPandCNV : readChunkVCF: no visible global function definition for ‘GRanges’ calculateLDSNPandCNV : readChunkVCF: no visible global function definition for ‘readVcf’ calculateLDSNPandCNV : readChunkVCF: no visible global function definition for ‘geno’ calculateLDSNPandCNV: no visible global function definition for ‘mclapply’ calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function definition for ‘fisher.test’ calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function definition for ‘chisq.test’ calculateLDSNPandCNV : calcPandR2: no visible global function definition for ‘p.adjust’ groupBayesianCNVs: no visible global function definition for ‘jags.model’ groupBayesianCNVs: no visible global function definition for ‘update’ groupBayesianCNVs: no visible global function definition for ‘coda.samples’ groupBayesianCNVs: no visible global function definition for ‘dnorm’ groupBayesianCNVs: no visible global function definition for ‘par’ groupBayesianCNVs: no visible global function definition for ‘hist’ countReadInWindow,CNVrd2: no visible global function definition for ‘readDNAStringSet’ countReadInWindow,CNVrd2 : countReadForBamFile: no visible global function definition for ‘write.table’ countReadInWindow,CNVrd2: no visible binding for global variable ‘objectCNVrd2’ countReadInWindow,CNVrd2: no visible global function definition for ‘ScanBamParam’ countReadInWindow,CNVrd2 : : no visible global function definition for ‘countBam’ countReadInWindow,CNVrd2 : gcContent: no visible global function definition for ‘unmasked’ countReadInWindow,CNVrd2 : gcContent: no visible binding for global variable ‘Hsapiens’ countReadInWindow,CNVrd2 : gcContent: no visible global function definition for ‘alphabetFrequency’ emnormalCNV,clusteringCNVs : loglk : : no visible global function definition for ‘dnorm’ emnormalCNV,clusteringCNVs : initialValues: no visible global function definition for ‘kmeans’ emnormalCNV,clusteringCNVs: no visible global function definition for ‘dnorm’ emnormalCNV,clusteringCNVs : : no visible global function definition for ‘dnorm’ groupCNVs,clusteringCNVs: no visible global function definition for ‘par’ groupCNVs,clusteringCNVs: no visible global function definition for ‘axis’ groupCNVs,clusteringCNVs: no visible global function definition for ‘abline’ groupCNVs,clusteringCNVs: no visible global function definition for ‘text’ groupCNVs,clusteringCNVs: no visible global function definition for ‘hist’ plotCNVrd2,CNVrd2: no visible global function definition for ‘rect’ plotCNVrd2,CNVrd2: no visible global function definition for ‘text’ plotCNVrd2,CNVrd2: no visible global function definition for ‘lines’ plotCNVrd2,CNVrd2: no visible global function definition for ‘abline’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘ggplot’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘geom_line’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘aes’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘x1’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘x2’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘Quantile’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘coord_cartesian’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘theme’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘ylab’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘geom_rect’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘xmin’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘xmax’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘ymin’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘ymax’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘geom_text’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘x’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘y’ plotPolymorphicRegion,CNVrd2: no visible binding for global variable ‘label’ plotPolymorphicRegion,CNVrd2: no visible global function definition for ‘grid.arrange’ segmentSamples,CNVrd2 : runFunction: no visible global function definition for ‘as’ segmentSamplesUsingPopInformation,CNVrd2: no visible global function definition for ‘fitted’ segmentSamplesUsingPopInformation,CNVrd2: no visible global function definition for ‘lm’ Undefined global functions or variables: GRanges Hsapiens Quantile ScanBamParam TabixFile abline aes alphabetFrequency as axis chisq.test coda.samples coord_cartesian countBam dnorm fisher.test fitted geno geom_line geom_rect geom_text ggplot grid.arrange hist jags.model kmeans label lines lm mclapply objectCNVrd2 p.adjust par readDNAStringSet readVcf rect text theme unmasked update write.table x x1 x2 xmax xmin y ylab ymax ymin Consider adding importFrom("graphics", "abline", "axis", "hist", "lines", "par", "rect", "text") importFrom("methods", "as") importFrom("stats", "chisq.test", "dnorm", "fisher.test", "fitted", "kmeans", "lm", "p.adjust", "update") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) identifyPolymorphicRegion.Rd:15-16: Lost braces 15 | \code{polymorphicRegionObject}{An object obtained from the process of | ^ checkRd: (-1) plotPolymorphicRegion.Rd:18-19: Lost braces 18 | \code{polymorphicRegionObject}{An object obtained from the process of | ^ * 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 ... 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/CNVrd2.Rcheck/00check.log’ for details.