Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:37 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for InterCellar on palomino4


To the developers/maintainers of the InterCellar package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 984/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterCellar 2.4.0  (landing page)
Marta Interlandi
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/InterCellar
git_branch: RELEASE_3_16
git_last_commit: 884f4d6
git_last_commit_date: 2022-11-01 11:24:14 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: InterCellar
Version: 2.4.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InterCellar.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings InterCellar_2.4.0.tar.gz
StartedAt: 2023-04-11 02:33:17 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 02:36:33 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 195.4 seconds
RetCode: 0
Status:   OK  
CheckDir: InterCellar.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:InterCellar.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings InterCellar_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/InterCellar.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'InterCellar/DESCRIPTION' ... OK
* this is package 'InterCellar' version '2.4.0'
* 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 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
  '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 ... 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/InterCellar.Rcheck/00check.log'
for details.



Installation output

InterCellar.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL InterCellar
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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 version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• interactive() is not TRUE (1)

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
   7.59    0.68    8.28 

Example timings

InterCellar.Rcheck/InterCellar-Ex.timings

nameusersystemelapsed
checkLL_RR0.140.230.37
getClusterNames0.030.280.31
getGeneTable0.220.240.46
getIntFlow0.110.220.32
run_app000