############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetaNeighbor_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetaNeighbor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaNeighbor’ version ‘1.12.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘MetaNeighbor’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: data 8.1Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE MetaNeighbor : : no visible binding for global variable ‘cell_type’ ggPlotHeatmap: no visible binding for global variable ‘target_ct’ ggPlotHeatmap: no visible binding for global variable ‘ref_ct’ ggPlotHeatmap: no visible binding for global variable ‘auroc’ is_reciprocal_top_hit: no visible binding for global variable ‘auroc’ is_reciprocal_top_hit: no visible binding for global variable ‘ref_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘target_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘reciprocal_cell_type’ is_reciprocal_top_hit: no visible binding for global variable ‘is_reciprocal’ plotDotPlot: no visible binding for global variable ‘cluster’ plotDotPlot: no visible binding for global variable ‘gene’ plotDotPlot: no visible binding for global variable ‘cell_type’ plotDotPlot: no visible binding for global variable ‘average_expression’ plotDotPlot: no visible binding for global variable ‘percent_expressing’ plotMetaClusters: no visible global function definition for ‘order_sym_matrix’ topHitsByStudy: no visible binding for global variable ‘ref_cell_type’ topHitsByStudy: no visible binding for global variable ‘target_cell_type’ topHitsByStudy: no visible binding for global variable ‘ref_study’ topHitsByStudy: no visible binding for global variable ‘target_study’ topHitsByStudy: no visible binding for global variable ‘.’ topHitsByStudy: no visible binding for global variable ‘pair_id’ topHitsByStudy: no visible binding for global variable ‘is_reciprocal’ topHitsByStudy: no visible global function definition for ‘desc’ topHitsByStudy: no visible binding for global variable ‘Match_type’ variableGenes: no visible binding for global variable ‘gene’ variableGenes: no visible binding for global variable ‘is_hvg’ variableGenes: no visible binding for global variable ‘var_quant’ variableGenes: no visible binding for global variable ‘recurrence’ variableGenes: no visible global function definition for ‘desc’ variableGenes: no visible binding for global variable ‘score’ variable_genes_single_exp: no visible binding for global variable ‘bin_med’ variable_genes_single_exp: no visible binding for global variable ‘variance’ variable_genes_single_exp: no visible binding for global variable ‘var_quant’ Undefined global functions or variables: . Match_type auroc average_expression bin_med cell_type cluster desc gene is_hvg is_reciprocal order_sym_matrix pair_id percent_expressing reciprocal_cell_type recurrence ref_cell_type ref_ct ref_study score target_cell_type target_ct target_study var_quant variance * 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 ... WARNING LazyData DB of 7.1 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed MetaNeighbor 25.316 0.927 26.262 plotBPlot 17.605 0.375 17.997 neighborVoting 16.822 0.425 17.264 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetaNeighbor.Rcheck/00check.log’ for details.