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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 598/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dominoSignal 1.0.0  (landing page)
Jacob T Mitchell
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: RELEASE_3_20
git_last_commit: b8fea56
git_last_commit_date: 2024-10-29 11:33:15 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for dominoSignal on merida1

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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-12-20 02:44:36 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:51:03 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 386.3 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/dominoSignal.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.0.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
cor_heatmap 9.804  0.103  11.299
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘dominoSignal’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
 15.307   0.948  18.587 

Example timings

dominoSignal.Rcheck/dominoSignal-Ex.timings

nameusersystemelapsed
add_rl_column0.0760.0060.083
build_domino0.2910.0230.328
circos_ligand_receptor1.5310.0891.864
cor_heatmap 9.804 0.10311.299
cor_scatter0.8020.0420.963
count_linkage0.0090.0010.011
create_domino0.2200.0140.267
create_regulon_list_scenic0.0220.0030.032
create_rl_map_cellphonedb0.0400.0030.049
dom_clusters0.3260.0220.397
dom_correlations0.2440.0170.294
dom_counts0.2490.0190.305
dom_database0.2740.0170.329
dom_de0.2450.0190.302
dom_info0.2660.0190.332
dom_linkages0.2500.0180.313
dom_network_items0.2430.0160.296
dom_signaling0.2670.0170.320
dom_tf_activation0.2430.0170.302
dom_zscores0.2730.0170.332
feat_heatmap2.6930.0313.141
gene_network0.3600.0190.436
incoming_signaling_heatmap0.5680.0180.676
mean_ligand_expression0.2530.0170.302
plot_differential_linkages1.2010.0241.410
print-domino-method0.2470.0170.305
rename_clusters0.2490.0170.306
show-domino-method0.2520.0290.328
signaling_heatmap1.1200.0991.415
signaling_network0.2980.0210.384
summarize_linkages0.3860.0260.481
test_differential_linkages0.0200.0000.026