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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 611/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dominoSignal 1.3.0  (landing page)
Jacob T Mitchell
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: devel
git_last_commit: 57750dd
git_last_commit_date: 2025-04-15 13:39:14 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2025-09-26 20:50:53 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 20:54:13 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 200.2 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/dominoSignal.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dominoSignal/DESCRIPTION’ ... OK
* this is package ‘dominoSignal’ version ‘1.3.0’
* 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-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘dominoSignal’ ...
** this is package ‘dominoSignal’ version ‘1.3.0’
** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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")
2025-09-26 20:54:01.415 R[6043:391910527] XType: com.apple.fonts is not accessible.
2025-09-26 20:54:01.416 R[6043:391910527] XType: XTFontStaticRegistry is enabled.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ]
> 
> proc.time()
   user  system elapsed 
 10.390   0.604  11.049 

Example timings

dominoSignal.Rcheck/dominoSignal-Ex.timings

nameusersystemelapsed
add_rl_column0.0370.0040.042
build_domino0.1690.0170.188
circos_ligand_receptor0.7020.0230.728
cor_heatmap4.6350.1174.770
cor_scatter0.5500.0270.582
count_linkage0.0040.0000.005
create_domino0.0970.0100.108
create_regulon_list_scenic0.0100.0020.011
create_rl_map_cellphonedb0.0130.0010.014
dom_clusters0.1470.0110.160
dom_correlations0.1200.0110.132
dom_counts0.1170.0110.130
dom_database0.1040.0100.117
dom_de0.1210.0110.133
dom_info0.1230.0100.135
dom_linkages0.1090.0110.122
dom_network_items0.1160.0110.127
dom_signaling0.1040.0090.116
dom_tf_activation0.1260.0110.140
dom_zscores0.1130.0100.124
feat_heatmap1.0970.0181.119
gene_network0.1730.0130.190
incoming_signaling_heatmap0.2610.0130.276
mean_ligand_expression0.1170.0100.130
obtain_circos_expression0.1150.0100.127
plot_differential_linkages0.3180.0140.335
print-domino-method0.1110.0090.122
rename_clusters0.1220.0110.134
render_circos_ligand_receptor0.3260.0120.341
show-domino-method0.1120.0090.123
signaling_heatmap0.5220.0150.541
signaling_network0.1510.0130.166
summarize_linkages0.1680.0110.181
test_differential_linkages0.0080.0000.009