############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:InterCellar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings InterCellar_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/InterCellar.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 ‘InterCellar/DESCRIPTION’ ... OK * this is package ‘InterCellar’ version ‘2.13.0’ * 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' INFO Imports includes 35 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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: .dockerignore 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 ‘InterCellar’ 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 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 buildPairsbyFunctionMatrix: warning in dcast(as.data.table(functions_df), int_pair ~ functional_term, fun = function(x) min(sum(x), 1), value.var = "value"): partial argument match of 'fun' to 'fun.aggregate' annotateGO: no visible binding for global variable ‘go_linkage_type’ annotateGO: no visible binding for global variable ‘domain’ annotateGO: no visible binding for global variable ‘int_pair’ annotateGO: no visible binding for global variable ‘geneA’ annotateGO: no visible binding for global variable ‘geneB’ annotateGO: no visible binding for global variable ‘gene_symbol’ annotateGO: no visible binding for global variable ‘go_id’ annotateGO: no visible binding for global variable ‘geneA.1’ annotateGO: no visible binding for global variable ‘geneB.4’ annotatePathways: no visible binding for global variable ‘int_pair’ annotatePathways: no visible binding for global variable ‘geneA’ annotatePathways: no visible binding for global variable ‘geneB’ combineAnnotations: no visible binding for global variable ‘int_pair’ combineAnnotations: no visible binding for global variable ‘functional_term’ createBarPlot1_ggplot: no visible binding for global variable ‘cluster_names’ createBarPlot1_ggplot: no visible binding for global variable ‘n_int’ createBarPlot1_ggplot: no visible binding for global variable ‘type’ createBarPlot2_ggplot: no visible binding for global variable ‘Clusters’ createBarPlot2_ggplot: no visible binding for global variable ‘Num_int’ getBack2BackBarplot: no visible binding for global variable ‘n_int’ getBack2BackBarplot: no visible binding for global variable ‘cluster_names’ getBack2BackBarplot: no visible binding for global variable ‘type’ getBack2BackBarplot: no visible binding for global variable ‘diff_c1_c2’ getBarplotDF : : no visible binding for global variable ‘clustA’ getBarplotDF : : no visible binding for global variable ‘clustB’ getBarplotDF : : no visible binding for global variable ‘int.type’ getBarplotDF : : no visible binding for global variable ‘score’ getBarplotDF2: no visible binding for global variable ‘clustA’ getBarplotDF2: no visible binding for global variable ‘clustB’ getClusterNetwork: no visible binding for global variable ‘clustA’ getClusterNetwork: no visible binding for global variable ‘clustB’ getClusterNetwork: no visible binding for global variable ‘score’ getClusterSize: no visible binding for global variable ‘clustA’ getClusterSize: no visible binding for global variable ‘clustB’ getDistinctCouplets: no visible binding for global variable ‘clustA’ getDistinctCouplets: no visible binding for global variable ‘clustB’ getDistinctCouplets: no visible binding for global variable ‘int_pair’ getDistinctCouplets: no visible binding for global variable ‘cluster_pair’ getDotPlot_selInt: no visible binding for global variable ‘clustA’ getDotPlot_selInt: no visible binding for global variable ‘clustB’ getDotPlot_selInt: no visible binding for global variable ‘int_pair’ getDotPlot_selInt: no visible binding for global variable ‘cluster_pair’ getDotPlot_selInt: no visible binding for global variable ‘score’ getGeneTable: no visible binding for global variable ‘int_pair’ getGeneTable: no visible binding for global variable ‘geneA’ getGeneTable: no visible binding for global variable ‘geneB’ getGeneTable: no visible binding for global variable ‘typeA’ getGeneTable: no visible binding for global variable ‘typeB’ getGeneTable: no visible binding for global variable ‘annotation_strategy’ getGeneTable: no visible binding for global variable ‘pathway_cellchat’ getGeneTable: no visible binding for global variable ‘annotation_cellchat’ getGeneTable: no visible binding for global variable ‘evidence_cellchat’ getGeneTable: no visible binding for global variable ‘uniprotswissprot’ getGeneTable: no visible binding for global variable ‘ensembl_gene_id’ getGeneTable: no visible binding for global variable ‘hgnc_symbol’ getIntFlow: no visible binding for global variable ‘typeA’ getIntFlow: no visible binding for global variable ‘typeB’ getIntFlow: no visible binding for global variable ‘clustA’ getIntFlow: no visible binding for global variable ‘clustB’ getPieChart: no visible binding for global variable ‘condition’ getPieChart: no visible binding for global variable ‘value’ getPieChart: no visible binding for global variable ‘prop’ getPieChart: no visible binding for global variable ‘ypos’ getPieChart: no visible binding for global variable ‘perc’ getRankedTerms: no visible binding for global variable ‘functional_term’ getRankedTerms: no visible binding for global variable ‘int_pair’ getRankedTerms: no visible binding for global variable ‘n_occurrence’ getSignif_table: no visible binding for global variable ‘n_int_pair’ getSignif_table: no visible binding for global variable ‘n_cond’ getSunburst: no visible binding for global variable ‘clustA’ getSunburst: no visible binding for global variable ‘int_pair’ getSunburst: no visible binding for global variable ‘clustB’ getSunburst: no visible binding for global variable ‘score’ getSunburst: no visible binding for global variable ‘weightedInt’ getUniqueDotplot: no visible binding for global variable ‘int_pair’ getUniqueDotplot: no visible binding for global variable ‘cluster_pair’ getUniqueDotplot: no visible binding for global variable ‘condition’ getUniqueIntpairs_byCond: no visible binding for global variable ‘int_pair’ getUniqueIntpairs_byCond: no visible binding for global variable ‘condition’ getUniqueIntpairs_byCond: no visible binding for global variable ‘n_cond’ getUniqueIntpairs_byCond: no visible binding for global variable ‘clustA’ getUniqueIntpairs_byCond: no visible binding for global variable ‘clustB’ getUniqueIntpairs_byCond: no visible binding for global variable ‘clust_pair’ mod_cluster_verse_server : : no visible binding for global variable ‘clustA’ mod_cluster_verse_server : : no visible binding for global variable ‘clustB’ mod_cluster_verse_server : : no visible binding for global variable ‘score’ mod_cluster_verse_server : : no visible binding for global variable ‘int.type’ mod_function_verse_server : : no visible binding for global variable ‘GO_id’ mod_function_verse_server : : no visible binding for global variable ‘int_pair’ mod_gene_verse_server : : no visible binding for global variable ‘scSignalR_specific’ mod_gene_verse_server : : no visible binding for global variable ‘annotation_cellchat’ mod_gene_verse_server : : no visible binding for global variable ‘pathway_cellchat’ mod_gene_verse_server : : no visible binding for global variable ‘int_pair’ mod_gene_verse_server : : no visible binding for global variable ‘clustA’ mod_gene_verse_server : : no visible binding for global variable ‘int.type’ mod_int_pair_modules_server : : no visible binding for global variable ‘int_pair’ mod_int_pair_modules_server : : no visible binding for global variable ‘int_pairModule’ mod_int_pair_modules_server : : no visible binding for global variable ‘p_value’ mod_multi_cond_server : : no visible global function definition for ‘legend’ mod_multi_cond_server : : no visible binding for global variable ‘clustA’ mod_multi_cond_server : : no visible binding for global variable ‘p_value’ mod_multi_cond_server : : no visible binding for global variable ‘condition’ mod_multi_cond_server : : no visible binding for global variable ‘int_pair’ read.CPDBv2: no visible binding for global variable ‘cluster_pair’ read.CPDBv2: no visible binding for global variable ‘mean_value’ read.CPDBv2: no visible binding for global variable ‘interacting_pair’ read.CPDBv2: no visible binding for global variable ‘p_value’ read.icellnet: no visible binding for global variable ‘X’ read.icellnet: no visible binding for global variable ‘score’ updateInputLR: no visible binding for global variable ‘typeA’ updateInputLR: no visible binding for global variable ‘typeB’ updateInputLR: no visible binding for global variable ‘int_pair’ Undefined global functions or variables: Clusters GO_id Num_int X annotation_cellchat annotation_strategy clustA clustB clust_pair cluster_names cluster_pair condition diff_c1_c2 domain ensembl_gene_id evidence_cellchat functional_term geneA geneA.1 geneB geneB.4 gene_symbol go_id go_linkage_type hgnc_symbol int.type int_pair int_pairModule interacting_pair legend mean_value n_cond n_int n_int_pair n_occurrence p_value pathway_cellchat perc prop scSignalR_specific score type typeA typeB uniprotswissprot value weightedInt ypos Consider adding importFrom("graphics", "legend") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) getRadar_df.Rd:20-70: Lost braces 20 | cell_name){ | ^ checkRd: (-1) getRadar_df.Rd:21-24: Lost braces 21 | if(is.null(tab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:24-28: Lost braces 24 | } else { | ^ checkRd: (-1) getRadar_df.Rd:40-42: Lost braces 40 | if(is.null(lab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:42-44: Lost braces 42 | } else { | ^ checkRd: (-1) getRadar_df.Rd:107-157: Lost braces 107 | cell_name){ | ^ checkRd: (-1) getRadar_df.Rd:108-111: Lost braces 108 | if(is.null(tab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:111-115: Lost braces 111 | } else { | ^ checkRd: (-1) getRadar_df.Rd:127-129: Lost braces 127 | if(is.null(lab_c3)){ | ^ checkRd: (-1) getRadar_df.Rd:129-131: Lost braces 129 | } else { | ^ * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck/00check.log’ for details.