############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MetaNeighbor.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MetaNeighbor_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MetaNeighbor.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetaNeighbor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetaNeighbor’ version ‘1.24.0’ * 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 ‘MetaNeighbor’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... 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 ... NOTE checkRd: (-1) extractMetaClusters.Rd:25: Lost braces; missing escapes or markup? 25 | if 1<->2 and 1<->3 are reciprocal top hits, {1, 2, 3} is a meta-cluster, | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed MetaNeighbor 219.963 0.988 221.275 plotBPlot 210.325 0.353 210.967 neighborVoting 209.474 0.213 210.075 MetaNeighborUS 21.452 0.076 21.559 topHitsByStudy 20.573 0.035 20.659 plotHeatmapPretrained 20.542 0.056 20.652 topHits 20.033 0.028 20.112 plotHeatmap 20.007 0.016 20.064 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/MetaNeighbor.Rcheck/00check.log’ for details.