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This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 968/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: 71e4813
git_last_commit_date: 2025-07-22 20:39:06 -0400 (Tue, 22 Jul 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    OK    OK  


CHECK results for HiCBricks on nebbiolo2

To the developers/maintainers of the HiCBricks package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCBricks.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: HiCBricks
Version: 1.27.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz
StartedAt: 2025-09-20 00:41:52 -0400 (Sat, 20 Sep 2025)
EndedAt: 2025-09-20 00:45:30 -0400 (Sat, 20 Sep 2025)
EllapsedTime: 217.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.27.1’
* 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 ‘HiCBricks’ 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
* 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

HiCBricks.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘HiCBricks’ ...
** this is package ‘HiCBricks’ version ‘1.27.1’
** 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 (HiCBricks)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.6900.0321.725
BrickContainer_change_output_directory1.1580.0151.176
BrickContainer_get_path_to_file1.0820.0231.128
BrickContainer_list_chromosomes1.0780.0181.098
BrickContainer_list_experiment_name1.1400.0191.163
BrickContainer_list_files1.0230.0131.039
BrickContainer_list_output_directory1.0140.0181.034
BrickContainer_list_resolutions0.9520.0130.968
BrickContainer_unlink_resolution2.1780.0312.215
Brick_add_ranges2.3560.1662.531
Brick_call_compartments1.4420.0481.583
Brick_export_to_sparse2.6710.0572.733
Brick_fetch_range_index0.9990.0081.014
Brick_fetch_row_vector1.4640.0241.491
Brick_get_bintable1.4550.0601.584
Brick_get_chrominfo0.7460.0290.780
Brick_get_entire_matrix1.0770.0721.153
Brick_get_matrix1.0520.0231.078
Brick_get_matrix_mcols1.0670.0531.199
Brick_get_matrix_within_coords1.4360.0421.491
Brick_get_ranges0.8810.0350.926
Brick_get_values_by_distance1.1240.0321.159
Brick_get_vector_values1.0220.0251.050
Brick_list_matrices0.8130.0080.934
Brick_list_matrix_mcols0.7040.0120.719
Brick_list_mcool_normalisations0.0010.0000.000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.7190.0120.734
Brick_list_ranges_mcols0.7310.0130.746
Brick_load_cis_matrix_till_distance1.0270.0221.114
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix0.9680.0311.003
Brick_local_score_differentiator1.5850.0401.628
Brick_make_ranges0.0090.0000.008
Brick_matrix_dimensions0.9810.0140.997
Brick_matrix_exists1.1070.0201.211
Brick_matrix_filename1.0140.0141.031
Brick_matrix_isdone1.0350.0301.068
Brick_matrix_issparse1.0410.0371.081
Brick_matrix_maxdist1.0170.0211.041
Brick_matrix_minmax1.0150.0211.041
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.7410.0130.760
Brick_return_region_position0.9240.0571.065
Brick_vizart_plot_heatmap2.0670.0402.112
Create_many_Bricks0.8300.0140.847
Create_many_Bricks_from_mcool0.0010.0000.000
load_BrickContainer0.8240.0190.850