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This page was generated on 2025-09-06 12:04 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 967/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiContacts 1.11.0  (landing page)
Jacques Serizay
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/HiContacts
git_branch: devel
git_last_commit: cbff73b
git_last_commit_date: 2025-04-15 12:56:29 -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    ERROR  skipped


CHECK results for HiContacts on nebbiolo2

To the developers/maintainers of the HiContacts package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.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: HiContacts
Version: 1.11.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiContacts_1.11.0.tar.gz
StartedAt: 2025-09-06 00:31:21 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 00:44:42 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 800.9 seconds
RetCode: 0
Status:   OK  
CheckDir: HiContacts.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiContacts.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiContacts_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiContacts.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HiContacts/DESCRIPTION’ ... OK
* this is package ‘HiContacts’ version ‘1.11.0’
* 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 ‘HiContacts’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
arithmetics          54.775  3.772  58.293
Contacts             18.604  1.135  20.637
getCompartments      14.514  2.303  12.434
tracks               13.035  1.083  14.350
plotMatrix           12.840  0.580  13.641
plotPs                9.205  0.562  10.447
scalogram             6.929  0.276   7.661
getDiamondInsulation  4.814  2.370   6.091
plotScalogram         6.767  0.312   7.442
* 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: OK


Installation output

HiContacts.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiContacts
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘HiContacts’ ...
** this is package ‘HiContacts’ version ‘1.11.0’
** using staged installation
** R
** 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 (HiContacts)

Tests output

HiContacts.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(HiContacts)
Loading required package: HiCExperiment
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
> 
> test_check("HiContacts")

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 51 ]
> 
> proc.time()
   user  system elapsed 
150.103  14.467 159.806 

Example timings

HiContacts.Rcheck/HiContacts-Ex.timings

nameusersystemelapsed
Contacts18.604 1.13520.637
Ps4.0180.1354.415
arithmetics54.775 3.77258.293
cisTransRatio3.1080.1593.519
getCompartments14.514 2.30312.434
getDiamondInsulation4.8142.3706.091
palettes0.0010.0000.001
plot4C3.3130.5514.095
plotMatrix12.840 0.58013.641
plotPs 9.205 0.56210.447
plotScalogram6.7670.3127.442
scalogram6.9290.2767.661
tracks13.035 1.08314.350
virtual4C3.7750.1654.192