############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TADCompare_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/TADCompare.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TADCompare/DESCRIPTION’ ... OK * this is package ‘TADCompare’ version ‘1.4.0’ * 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 ‘TADCompare’ 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘cluster’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .Make_Triangles: no visible binding for global variable ‘start’ .Make_Triangles: no visible binding for global variable ‘end’ .Make_Triangles: no visible global function definition for ‘na.omit’ .Make_Triangles: no visible binding for global variable ‘boundary_start’ .Make_Triangles: no visible binding for global variable ‘orig_regx’ .Make_Triangles: no visible binding for global variable ‘start1’ .Make_Triangles: no visible binding for global variable ‘boundary_end’ ConsensusTADs : : no visible binding for global variable ‘Coordinate’ ConsensusTADs: no visible binding for global variable ‘Sample’ ConsensusTADs: no visible binding for global variable ‘Boundary’ ConsensusTADs: no visible binding for global variable ‘Diff_Score’ ConsensusTADs: no visible global function definition for ‘sd’ ConsensusTADs: no visible binding for global variable ‘Differential’ ConsensusTADs: no visible binding for global variable ‘Coordinate’ ConsensusTADs: no visible binding for global variable ‘TAD_Score’ ConsensusTADs: no visible binding for global variable ‘.’ ConsensusTADs: no visible binding for global variable ‘median’ DiffPlot: no visible binding for global variable ‘Type’ DiffPlot: no visible binding for global variable ‘Differential’ DiffPlot: no visible binding for global variable ‘Boundary’ DiffPlot: no visible binding for global variable ‘Enriched_In’ DiffPlot: no visible global function definition for ‘na.omit’ DiffPlot: no visible binding for global variable ‘boundary_start’ DiffPlot: no visible binding for global variable ‘orig_regx’ DiffPlot: no visible binding for global variable ‘start1’ DiffPlot: no visible binding for global variable ‘boundary_end’ DiffPlot: no visible binding for global variable ‘start2’ DiffPlot: no visible binding for global variable ‘TAD_Score1’ DiffPlot: no visible binding for global variable ‘TAD_Score2’ DiffPlot: no visible binding for global variable ‘Gap_Score’ DiffPlot: no visible binding for global variable ‘variable’ DiffPlot: no visible binding for global variable ‘value’ DiffPlot: no visible binding for global variable ‘line_spot’ DiffPlot: no visible global function definition for ‘complete.cases’ DiffPlot: no visible binding for global variable ‘.’ DiffPlot: no visible binding for global variable ‘x’ DiffPlot: no visible binding for global variable ‘y’ DiffPlot: no visible binding for global variable ‘orig_regy’ TADCompare: no visible global function definition for ‘sd’ TADCompare: no visible binding for global variable ‘Boundary’ TADCompare: no visible binding for global variable ‘Gap_Score’ TADCompare: no visible binding for global variable ‘Differential’ TADCompare: no visible binding for global variable ‘Bound_Dist’ TADCompare: no visible binding for global variable ‘Enriched_In’ TADCompare: no visible binding for global variable ‘Type’ TADCompare: no visible binding for global variable ‘Count’ TimeCompare : : no visible binding for global variable ‘Coordinate’ TimeCompare: no visible binding for global variable ‘Sample’ TimeCompare: no visible binding for global variable ‘Groups’ TimeCompare: no visible binding for global variable ‘Coordinate’ TimeCompare: no visible binding for global variable ‘Boundary’ TimeCompare: no visible global function definition for ‘median’ TimeCompare: no visible binding for global variable ‘Diff_Score’ TimeCompare: no visible global function definition for ‘sd’ TimeCompare: no visible binding for global variable ‘Differential’ TimeCompare: no visible binding for global variable ‘TAD_Score’ TimeCompare: no visible binding for global variable ‘.’ TimeCompare: no visible binding for global variable ‘median’ TimeCompare: no visible binding for global variable ‘Sample 1’ TimeCompare: no visible binding for global variable ‘Consensus_Score’ TimeCompare: no visible binding for global variable ‘Category’ TimeCompare: no visible binding for global variable ‘Count’ Undefined global functions or variables: . Bound_Dist Boundary Category Consensus_Score Coordinate Count Diff_Score Differential Enriched_In Gap_Score Groups Sample Sample 1 TAD_Score TAD_Score1 TAD_Score2 Type boundary_end boundary_start complete.cases end line_spot median na.omit orig_regx orig_regy sd start start1 start2 value variable x y Consider adding importFrom("stats", "complete.cases", "end", "median", "na.omit", "sd", "start") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... 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 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/TADCompare.Rcheck/00check.log’ for details.