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This page was generated on 2023-09-23 11:37:08 -0400 (Sat, 23 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 1961/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SOMNiBUS 1.8.0  (landing page)
Audrey Lemaçon
Snapshot Date: 2023-09-22 14:00:14 -0400 (Fri, 22 Sep 2023)
git_url: https://git.bioconductor.org/packages/SOMNiBUS
git_branch: RELEASE_3_17
git_last_commit: ff0c9b8
git_last_commit_date: 2023-04-25 11:26:20 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    TIMEOUT    NA  

CHECK results for SOMNiBUS on merida1


To the developers/maintainers of the SOMNiBUS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SOMNiBUS.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: SOMNiBUS
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.8.0.tar.gz
StartedAt: 2023-09-23 08:25:38 -0400 (Sat, 23 Sep 2023)
EndedAt: 2023-09-23 09:05:38 -0400 (Sat, 23 Sep 2023)
EllapsedTime: 2400.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: SOMNiBUS.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SOMNiBUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SOMNiBUS_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/SOMNiBUS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SOMNiBUS/DESCRIPTION’ ... OK
* this is package ‘SOMNiBUS’ version ‘1.8.0’
* 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 ‘SOMNiBUS’ 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 R 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 startup messages can be suppressed ... 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 ... NOTE
testStat: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pf
Consider adding
  importFrom("stats", "pf")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
binomRegMethModel     294.176 18.150 389.692
runSOMNiBUS           242.110 16.862 334.686
binomRegMethModelPlot  39.954  3.804  53.954
binomRegMethModelPred  39.769  3.722  54.989
binomRegMethPredPlot   39.148  3.100  56.949
splitDataByGene        23.436  3.160  34.510
splitDataByChromatin   24.937  1.048  32.592
splitDataByDensity      5.751  0.066   7.503
formatFromBismark       5.208  0.594   7.597
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

SOMNiBUS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘SOMNiBUS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (SOMNiBUS)

Tests output

SOMNiBUS.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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(SOMNiBUS)
Package SOMNiBUS version 1.8.0 
NOTE: - Logging level is set to INFO 
      - Output file is /tmp/RtmpRNvtON/somnibus.log 
      - See 'package?SOMNiBUS' for help.
> library(mgcv)
Loading required package: nlme
This is mgcv 1.9-0. For overview type 'help("mgcv-package")'.
> library(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:nlme':

    collapse

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> test_check("SOMNiBUS")
2023-09-23 08:55:09.581 R[25318:810034798] XType: com.apple.fonts is not accessible.
2023-09-23 08:55:09.582 R[25318:810034798] XType: XTFontStaticRegistry is enabled.

Example timings

SOMNiBUS.Rcheck/SOMNiBUS-Ex.timings

nameusersystemelapsed
binomRegMethModel294.176 18.150389.692
binomRegMethModelPlot39.954 3.80453.954
binomRegMethModelPred39.769 3.72254.989
binomRegMethModelSim2.6880.2693.868
binomRegMethPredPlot39.148 3.10056.949
formatFromBSmooth0.5570.0200.871
formatFromBSseq0.1150.0020.165
formatFromBismark5.2080.5947.597
runSOMNiBUS242.110 16.862334.686
splitDataByChromatin24.937 1.04832.592
splitDataByDensity5.7510.0667.503
splitDataByGRanges0.4360.0160.617
splitDataByGene23.436 3.16034.510
splitDataByRegion0.0260.0090.049