##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:InterCellar.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings InterCellar_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 5 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/InterCellar.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL InterCellar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘InterCellar’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (InterCellar)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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)
Warning: program compiled against libxml 212 using older 211
> 
> test_check("InterCellar")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• interactive() is not TRUE (1): 'test-golem-recommended.R:24:5'

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  9.940   0.403  10.354