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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:InterCellar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings InterCellar_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/InterCellar.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 ‘InterCellar/DESCRIPTION’ ... OK
* this is package ‘InterCellar’ version ‘1.0.0’
* 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 ‘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 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
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
  ‘clusters’
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 ‘condition’
getBack2BackBarplot: no visible binding for global variable ‘n_int’
getBack2BackBarplot: no visible binding for global variable ‘clusters’
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’
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’
getClusterSize: no visible binding for global variable ‘clustA’
getClusterSize: no visible binding for global variable ‘clustB’
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 ‘uniprotswissprot’
getGeneTable: no visible binding for global variable ‘ensembl_gene_id’
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’
getRadarPlot: no visible global function definition for ‘legend’
getRankedTerms: no visible binding for global variable
  ‘functional_term’
getRankedTerms: no visible binding for global variable ‘uniq_score’
getRankedTerms: no visible binding for global variable ‘int_pair’
getRankedTerms: no visible binding for global variable ‘avg_uniqueness’
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’
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’
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 ‘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 ‘clustB’
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’
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’
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 annotation_strategy avg_uniqueness clustA
  clustB cluster_pair clusters condition diff_c1_c2 domain
  ensembl_gene_id functional_term geneA geneA.1 geneB geneB.4
  gene_symbol go_id go_linkage_type int.type int_pair int_pairModule
  interacting_pair legend mean_value n_int p_value scSignalR_specific
  score type typeA typeB uniprotswissprot uniq_score
Consider adding
  importFrom("graphics", "legend")
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 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 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/InterCellar.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL InterCellar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘InterCellar’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (InterCellar)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(InterCellar)
> 
> test_check("InterCellar")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• interactive() is not TRUE (1)

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 11.864   0.667  12.520