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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InterCellar.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings InterCellar_2.13.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 ... 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:
  .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 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 : <anonymous>: no visible binding for global variable
  'clustA'
getBarplotDF : <anonymous>: no visible binding for global variable
  'clustB'
getBarplotDF : <anonymous>: no visible binding for global variable
  'int.type'
getBarplotDF : <anonymous>: 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 : <anonymous>: no visible binding for global
  variable 'clustA'
mod_cluster_verse_server : <anonymous>: no visible binding for global
  variable 'clustB'
mod_cluster_verse_server : <anonymous>: no visible binding for global
  variable 'score'
mod_cluster_verse_server : <anonymous>: no visible binding for global
  variable 'int.type'
mod_function_verse_server : <anonymous>: no visible binding for global
  variable 'GO_id'
mod_function_verse_server : <anonymous>: no visible binding for global
  variable 'int_pair'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'scSignalR_specific'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'annotation_cellchat'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'pathway_cellchat'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'int_pair'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'clustA'
mod_gene_verse_server : <anonymous>: no visible binding for global
  variable 'int.type'
mod_int_pair_modules_server : <anonymous>: no visible binding for
  global variable 'int_pair'
mod_int_pair_modules_server : <anonymous>: no visible binding for
  global variable 'int_pairModule'
mod_int_pair_modules_server : <anonymous>: no visible binding for
  global variable 'p_value'
mod_multi_cond_server : <anonymous>: no visible global function
  definition for 'legend'
mod_multi_cond_server : <anonymous>: no visible binding for global
  variable 'clustA'
mod_multi_cond_server : <anonymous>: no visible binding for global
  variable 'p_value'
mod_multi_cond_server : <anonymous>: no visible binding for global
  variable 'condition'
mod_multi_cond_server : <anonymous>: 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
  'E:/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck/00check.log'
for details.