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This page was generated on 2024-09-07 15:39 -0400 (Sat, 07 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4711
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 593/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dominoSignal 0.99.4  (landing page)
Jacob T Mitchell
Snapshot Date: 2024-09-06 14:00 -0400 (Fri, 06 Sep 2024)
git_url: https://git.bioconductor.org/packages/dominoSignal
git_branch: devel
git_last_commit: 4daf6c5
git_last_commit_date: 2024-08-05 14:07:20 -0400 (Mon, 05 Aug 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  


CHECK results for dominoSignal on nebbiolo2

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: 0.99.4
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings dominoSignal_0.99.4.tar.gz
StartedAt: 2024-09-06 21:42:01 -0400 (Fri, 06 Sep 2024)
EndedAt: 2024-09-06 21:46:45 -0400 (Fri, 06 Sep 2024)
EllapsedTime: 284.5 seconds
RetCode: 0
Status:   OK  
CheckDir: dominoSignal.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:dominoSignal.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings dominoSignal_0.99.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/dominoSignal.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘dominoSignal/DESCRIPTION’ ... OK
* this is package ‘dominoSignal’ version ‘0.99.4’
* 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/dominoSignal.Rcheck/00check.log’
for details.


Installation output

dominoSignal.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL dominoSignal
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 53 ]
> 
> proc.time()
   user  system elapsed 
  7.384   0.368   7.742 

Example timings

dominoSignal.Rcheck/dominoSignal-Ex.timings

nameusersystemelapsed
add_rl_column0.0320.0000.033
build_domino0.1230.0040.127
circos_ligand_receptor0.5750.0320.607
cor_heatmap3.4090.0723.481
cor_scatter0.3890.0040.393
count_linkage0.0050.0000.005
create_domino0.0820.0040.086
create_regulon_list_scenic0.0090.0000.009
create_rl_map_cellphonedb0.0050.0080.012
dom_clusters0.1610.0040.165
dom_correlations0.0980.0000.098
dom_counts0.0970.0000.097
dom_database0.1160.0000.116
dom_de0.1040.0000.104
dom_info0.1170.0160.133
dom_linkages0.0950.0040.099
dom_network_items0.1030.0000.103
dom_signaling0.1060.0040.110
dom_tf_activation0.0880.0080.096
dom_zscores0.1060.0040.110
feat_heatmap1.6050.0921.697
gene_network0.1610.0000.161
incoming_signaling_heatmap0.2140.0160.230
mean_ligand_expression0.0930.0200.114
plot_differential_linkages0.2550.0280.283
print-domino-method0.0960.0000.096
rename_clusters0.0950.0000.094
show-domino-method0.0940.0040.099
signaling_heatmap0.4370.0360.474
signaling_network0.1160.0000.116
summarize_linkages0.1560.0080.164
test_differential_linkages0.0070.0000.008