############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDOC_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HiCDOC.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiCDOC/DESCRIPTION’ ... OK * this is package ‘HiCDOC’ version ‘1.9.0’ * package encoding: UTF-8 * 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 ‘HiCDOC’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 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 .checkCompartmentAssignment: no visible binding for global variable ‘chromosome’ .checkPca : f: no visible binding for global variable ‘compartment’ .checkResults: no visible binding for global variable ‘assignment.check’ .computePValues: no visible binding for global variable ‘condition’ .computePValues: no visible binding for global variable ‘chromosome’ .computePValues: no visible binding for global variable ‘index’ .computePValues: no visible global function definition for ‘.’ .computePValues: no visible binding for global variable ‘concordance’ .computePValues: no visible binding for global variable ‘condition.1’ .computePValues: no visible binding for global variable ‘condition.2’ .computePValues: no visible binding for global variable ‘concordance.1’ .computePValues: no visible binding for global variable ‘concordance.2’ .computePValues: no visible binding for global variable ‘compartment’ .computePValues: no visible binding for global variable ‘compartment.1’ .computePValues: no visible binding for global variable ‘compartment.2’ .computePValues: no visible binding for global variable ‘H0_value’ .computePValues: no visible binding for global variable ‘difference’ .computePValues : : no visible binding for global variable ‘difference’ .computePValues: no visible binding for global variable ‘pvalue’ .computePValues: no visible binding for global variable ‘pvalue.adjusted’ .computePValues: no visible binding for global variable ‘direction’ .computePca: no visible binding for global variable ‘chromosome’ .computePca: no visible global function definition for ‘.’ .computePca: no visible binding for global variable ‘condition’ .computePca: no visible binding for global variable ‘compartment’ .computePca: no visible binding for global variable ‘centroid’ .computeSelfInteractionRatios: no visible global function definition for ‘.’ .computeSelfInteractionRatios: no visible binding for global variable ‘index’ .computeSelfInteractionRatios: no visible binding for global variable ‘ratio’ .computeSelfInteractionRatios: no visible binding for global variable ‘variable’ .computeSelfInteractionRatios: no visible binding for global variable ‘chromosome’ .computeSelfInteractionRatios: no visible binding for global variable ‘condition’ .determineChromosomeSizes: no visible binding for global variable ‘minIndex’ .determineChromosomeSizes: no visible binding for global variable ‘index’ .determineChromosomeSizes: no visible global function definition for ‘.’ .determineChromosomeSizes: no visible binding for global variable ‘minStart’ .filterWeakPositionsOfChromosome: no visible global function definition for ‘.’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index1’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index2’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘value’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘variable’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index’ .formatDetectCompartment: no visible binding for global variable ‘chromosome’ .formatDetectCompartment: no visible global function definition for ‘.’ .formatDetectCompartment: no visible binding for global variable ‘index’ .formatDetectCompartment: no visible binding for global variable ‘condition’ .formatDetectCompartment: no visible binding for global variable ‘compartment’ .formatDetectCompartment: no visible binding for global variable ‘concordance’ .formatDetectCompartment: no visible binding for global variable ‘significance’ .formatDetectCompartment: no visible binding for global variable ‘pvalue.adjusted’ .formatDetectCompartment: no visible binding for global variable ‘condition.1’ .formatDetectCompartment: no visible binding for global variable ‘condition.2’ .formatDetectCompartment: no visible binding for global variable ‘pvalue’ .formatDetectCompartment: no visible binding for global variable ‘direction’ .formatDetectCompartment: no visible binding for global variable ‘centroid.check’ .formatDetectCompartment: no visible binding for global variable ‘PC1.check’ .formatDetectCompartment: no visible binding for global variable ‘assignment.check’ .messageCheck: no visible binding for global variable ‘chromosome’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘value’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘logvalue’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘logdistance’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘bias’ .parseOneCool: no visible binding for global variable ‘chromosome’ .parseOneCool: no visible binding for global variable ‘index’ .parseOneCool: no visible binding for global variable ‘id1’ .parseOneCool: no visible binding for global variable ‘id2’ .parseOneHiCPro: no visible binding for global variable ‘chromosome’ .parseOneHiCPro: no visible binding for global variable ‘index’ .parseOneHiCPro: no visible binding for global variable ‘startIndex’ .parseOneHiCPro: no visible binding for global variable ‘stopIndex’ .plotInteractionsGrid: no visible binding for global variable ‘start1’ .plotInteractionsGrid: no visible binding for global variable ‘start2’ .plotInteractionsWrap: no visible binding for global variable ‘start1’ .plotInteractionsWrap: no visible binding for global variable ‘start2’ .predictCompartmentsAB: no visible binding for global variable ‘offDiagonal’ .predictCompartmentsAB: no visible binding for global variable ‘ratio’ .predictCompartmentsAB: no visible global function definition for ‘.’ .predictCompartmentsAB: no visible binding for global variable ‘chromosome’ .predictCompartmentsAB: no visible binding for global variable ‘cluster’ .predictCompartmentsAB: no visible binding for global variable ‘A’ .predictCompartmentsAB: no visible binding for global variable ‘1’ .predictCompartmentsAB: no visible binding for global variable ‘2’ .predictCompartmentsAB: no visible binding for global variable ‘compartment’ .predictCompartmentsAB: no visible binding for global variable ‘change’ .predictCompartmentsAB: no visible binding for global variable ‘concordance’ .reduceHiCDOCChromosomes: no visible binding for global variable ‘chromosome’ .reduceHiCDOCConditions: no visible binding for global variable ‘condition’ .setFromTabular: no visible binding for global variable ‘chromosome’ .setFromTabular: no visible binding for global variable ‘position 1’ .setFromTabular: no visible binding for global variable ‘position 2’ .setFromTabular: no visible global function definition for ‘.’ .setFromTabular: no visible binding for global variable ‘bin.1’ .setFromTabular: no visible binding for global variable ‘bin.2’ .setFromTabular: no visible binding for global variable ‘variable’ .setFromTabular: no visible binding for global variable ‘indexC’ .setFromTabular: no visible binding for global variable ‘index’ .tieCentroids: no visible binding for global variable ‘cluster’ .tieCentroids: no visible binding for global variable ‘condition’ .tieCentroids: no visible binding for global variable ‘chromosome’ .tieCentroids: no visible global function definition for ‘.’ .tieCentroids: no visible binding for global variable ‘centroid’ .tieCentroids: no visible binding for global variable ‘cluster.1’ .tieCentroids: no visible binding for global variable ‘cluster.2’ .tieCentroids: no visible binding for global variable ‘change’ .tieCentroids: no visible binding for global variable ‘concordance’ .tieCentroids: no visible binding for global variable ‘compartment’ normalizeTechnicalBiases: no visible global function definition for ‘.’ normalizeTechnicalBiases: no visible binding for global variable ‘seqnames1’ normalizeTechnicalBiases: no visible binding for global variable ‘start1’ normalizeTechnicalBiases: no visible binding for global variable ‘start2’ normalizeTechnicalBiases: no visible binding for global variable ‘chromosome’ plotCentroids: no visible binding for global variable ‘PC1’ plotCentroids: no visible binding for global variable ‘PC2’ plotCentroids: no visible binding for global variable ‘compartment’ plotCentroids: no visible binding for global variable ‘condition’ plotCompartments: no visible binding for global variable ‘position’ plotCompartments: no visible binding for global variable ‘compartment’ plotCompartments: no visible binding for global variable ‘condition’ plotConcordanceDifferences: no visible binding for global variable ‘changed’ plotConcordanceDifferences: no visible binding for global variable ‘compartment.1’ plotConcordanceDifferences: no visible binding for global variable ‘compartment.2’ plotConcordanceDifferences: no visible binding for global variable ‘difference’ plotConcordances: no visible binding for global variable ‘condition’ plotConcordances: no visible binding for global variable ‘pvalue.adjusted’ plotConcordances: no visible binding for global variable ‘concordance’ plotInteractions: no visible global function definition for ‘.’ plotInteractions: no visible binding for global variable ‘seqnames1’ plotInteractions: no visible binding for global variable ‘start1’ plotInteractions: no visible binding for global variable ‘start2’ plotInteractions: no visible binding for global variable ‘variable’ plotInteractions: no visible binding for global variable ‘condition’ plotSelfInteractionRatios: no visible global function definition for ‘.’ plotSelfInteractionRatios: no visible binding for global variable ‘condition’ plotSelfInteractionRatios: no visible binding for global variable ‘index’ plotSelfInteractionRatios: no visible binding for global variable ‘compartment’ plotSelfInteractionRatios: no visible binding for global variable ‘ratio’ concordances,HiCDOCDataSet: no visible binding for global variable ‘centroid.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘PC1.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘assignment.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘chromosome’ Undefined global functions or variables: . 1 2 A H0_value PC1 PC1.check PC2 assignment.check bias bin.1 bin.2 centroid centroid.check change changed chromosome cluster cluster.1 cluster.2 compartment compartment.1 compartment.2 concordance concordance.1 concordance.2 condition condition.1 condition.2 difference direction id1 id2 index index1 index2 indexC logdistance logvalue minIndex minStart offDiagonal position position 1 position 2 pvalue pvalue.adjusted ratio seqnames1 significance start1 start2 startIndex stopIndex value variable * checking Rd files ... NOTE checkRd: (-1) HiCDOC.Rd:28-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:31-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:34-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:55-58: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: HiCDOC.Rd: BiocParallel 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 HiCDOC 49.203 5.618 55.093 normalizeTechnicalBiases 47.028 7.220 54.563 plotDistanceEffect 11.601 1.132 12.757 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/HiCDOC.Rcheck/00check.log’ for details.