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This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4827
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4600
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4564
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 608/2325HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dominoSignal 1.5.0  (landing page)
Jacob T Mitchell
Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025)
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: devel
git_last_commit: a76eebf
git_last_commit_date: 2025-10-29 11:31:35 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for dominoSignal on lconway

To the developers/maintainers of the dominoSignal package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dominoSignal.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: dominoSignal
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dominoSignal_1.5.0.tar.gz
StartedAt: 2025-11-18 20:44:51 -0500 (Tue, 18 Nov 2025)
EndedAt: 2025-11-18 20:48:16 -0500 (Tue, 18 Nov 2025)
EllapsedTime: 205.2 seconds
RetCode: 0
Status:   OK  
CheckDir: dominoSignal.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dominoSignal_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/dominoSignal.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dominoSignal/DESCRIPTION’ ... OK
* this is package ‘dominoSignal’ version ‘1.5.0’
* 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 ‘dominoSignal’ 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 ... OK
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  sysdata.rda    132Kb     30Kb       xz
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/dominoSignal.Rcheck/00check.log’
for details.


Installation output

dominoSignal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dominoSignal
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘dominoSignal’ ...
** this is package ‘dominoSignal’ version ‘1.5.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dominoSignal)

Tests output

dominoSignal.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("dominoSignal")
> 
> test_check("dominoSignal")
2025-11-18 20:48:03.336 R[57657:32070984] XType: Using static font registry.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
  9.977   0.681  10.760 

Example timings

dominoSignal.Rcheck/dominoSignal-Ex.timings

nameusersystemelapsed
add_rl_column0.0350.0070.042
build_domino0.1660.0190.188
circos_ligand_receptor0.6560.0400.701
cor_heatmap4.0670.0634.156
cor_scatter0.5650.0290.600
count_linkage0.0040.0000.004
create_domino0.0970.0110.109
create_regulon_list_scenic0.0110.0010.013
create_rl_map_cellphonedb0.0120.0010.014
dom_clusters0.2160.0130.231
dom_correlations0.1080.0110.121
dom_counts0.6560.0150.675
dom_database0.1000.0130.114
dom_de0.1040.0130.119
dom_info0.1010.0140.116
dom_linkages0.1070.0120.120
dom_network_items0.1220.0110.134
dom_signaling0.1070.0120.121
dom_tf_activation0.1030.0130.117
dom_zscores0.1080.0110.120
feat_heatmap1.0930.0481.149
gene_network0.1870.0280.220
incoming_signaling_heatmap0.2740.0270.303
mean_ligand_expression0.1140.0130.129
obtain_circos_expression0.1040.0130.118
plot_differential_linkages0.3020.0150.319
print-domino-method0.1160.0120.131
rename_clusters0.1390.0130.153
render_circos_ligand_receptor0.3140.0150.332
show-domino-method0.1100.0120.123
signaling_heatmap0.4790.0170.499
signaling_network0.1580.0130.173
summarize_linkages0.1780.0170.199
test_differential_linkages0.0090.0000.009