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This page was generated on 2025-03-22 11:46 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4547
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4458
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 603/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dominoSignal 1.1.5  (landing page)
Jacob T Mitchell
Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025)
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: devel
git_last_commit: ee1b992
git_last_commit_date: 2025-03-17 11:48:55 -0400 (Mon, 17 Mar 2025)
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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for dominoSignal on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: dominoSignal
Version: 1.1.5
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dominoSignal_1.1.5.tar.gz
StartedAt: 2025-03-22 05:56:49 -0000 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 06:00:28 -0000 (Sat, 22 Mar 2025)
EllapsedTime: 219.3 seconds
RetCode: 0
Status:   OK  
CheckDir: dominoSignal.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings dominoSignal_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/dominoSignal.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dominoSignal/DESCRIPTION’ ... OK
* this is package ‘dominoSignal’ version ‘1.1.5’
* 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 loading without being on the library search path ... 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 5.334    0.1   5.446
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/dominoSignal.Rcheck/00check.log’
for details.


Installation output

dominoSignal.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL dominoSignal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘dominoSignal’ ...
** this is package ‘dominoSignal’ version ‘1.1.5’
** 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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 65 ]
> 
> proc.time()
   user  system elapsed 
 12.012   0.851  12.908 

Example timings

dominoSignal.Rcheck/dominoSignal-Ex.timings

nameusersystemelapsed
add_rl_column0.0430.0000.044
build_domino0.1780.0040.183
circos_ligand_receptor0.8620.0320.896
cor_heatmap5.3340.1005.446
cor_scatter0.4920.0080.501
count_linkage0.0050.0000.005
create_domino0.1190.0040.123
create_regulon_list_scenic0.0120.0000.012
create_rl_map_cellphonedb0.020.000.02
dom_clusters0.2190.0040.224
dom_correlations0.1380.0040.142
dom_counts0.7880.0200.809
dom_database0.1350.0040.139
dom_de0.1370.0000.137
dom_info0.1330.0080.141
dom_linkages0.1430.0040.147
dom_network_items0.1560.0080.164
dom_signaling0.1320.0040.136
dom_tf_activation0.1300.0040.135
dom_zscores0.1400.0070.148
feat_heatmap1.4130.0601.475
gene_network0.1990.0200.219
incoming_signaling_heatmap0.3260.0200.347
mean_ligand_expression0.140.000.14
obtain_circos_expression0.1390.0040.143
plot_differential_linkages0.3950.0240.420
print-domino-method0.1610.0080.169
rename_clusters0.1470.0040.151
render_circos_ligand_receptor0.4160.0160.432
show-domino-method0.1390.0000.140
signaling_heatmap0.6690.0040.674
signaling_network0.180.000.18
summarize_linkages0.2210.0040.225
test_differential_linkages0.010.000.01