Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4349
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1034/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterCellar 2.13.0  (landing page)
Marta Interlandi
Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024)
git_url: https://git.bioconductor.org/packages/InterCellar
git_branch: devel
git_last_commit: e86c244
git_last_commit_date: 2024-10-29 10:56:51 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for InterCellar on palomino7

To the developers/maintainers of the InterCellar package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/InterCellar.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: InterCellar
Version: 2.13.0
Command: 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
StartedAt: 2024-11-25 01:46:16 -0500 (Mon, 25 Nov 2024)
EndedAt: 2024-11-25 01:49:40 -0500 (Mon, 25 Nov 2024)
EllapsedTime: 204.0 seconds
RetCode: 0
Status:   OK  
CheckDir: InterCellar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* 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.


Installation output

InterCellar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL InterCellar
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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)

Tests output

InterCellar.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
[ 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 
   8.56    0.71    9.43 

Example timings

InterCellar.Rcheck/InterCellar-Ex.timings

nameusersystemelapsed
checkLL_RR0.070.230.31
getClusterNames0.040.210.25
getGeneTable0.280.220.50
getIntFlow0.140.260.41
run_app000