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This page was generated on 2025-12-22 12:07 -0500 (Mon, 22 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4883
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4673
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4607
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4671
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 978/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.28.0  (landing page)
Koustav Pal
Snapshot Date: 2025-12-18 13:45 -0500 (Thu, 18 Dec 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_22
git_last_commit: 3296656
git_last_commit_date: 2025-10-29 10:48:17 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 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 taishan

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

raw results


Summary

Package: HiCBricks
Version: 1.28.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.28.0.tar.gz
StartedAt: 2025-12-19 10:32:57 -0000 (Fri, 19 Dec 2025)
EndedAt: 2025-12-19 10:36:19 -0000 (Fri, 19 Dec 2025)
EllapsedTime: 202.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.28.0’
* 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 ‘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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

HiCBricks.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘HiCBricks’ ...
** this is package ‘HiCBricks’ version ‘1.28.0’
** 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 (HiCBricks)

Tests output


Example timings

HiCBricks.Rcheck/HiCBricks-Ex.timings

nameusersystemelapsed
BrickContainer_change_experiment_name1.7500.0982.143
BrickContainer_change_output_directory1.2670.0281.300
BrickContainer_get_path_to_file1.2160.0961.315
BrickContainer_list_chromosomes1.2260.0401.270
BrickContainer_list_experiment_name1.1790.0351.252
BrickContainer_list_files1.1800.0711.695
BrickContainer_list_output_directory1.1920.0241.220
BrickContainer_list_resolutions1.1720.0561.233
BrickContainer_unlink_resolution2.5310.0803.107
Brick_add_ranges2.5640.1232.698
Brick_call_compartments2.2030.1122.623
Brick_export_to_sparse3.4380.1913.972
Brick_fetch_range_index1.3780.0241.605
Brick_fetch_row_vector2.2280.0882.321
Brick_get_bintable1.1850.0121.200
Brick_get_chrominfo1.1350.0201.538
Brick_get_entire_matrix1.5820.0431.731
Brick_get_matrix1.5360.0561.598
Brick_get_matrix_mcols1.5450.0361.935
Brick_get_matrix_within_coords2.2100.0362.256
Brick_get_ranges1.2640.0521.321
Brick_get_values_by_distance1.7080.0322.071
Brick_get_vector_values1.5370.0991.642
Brick_list_matrices1.1670.0001.315
Brick_list_matrix_mcols1.1050.0321.356
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.1380.0561.197
Brick_list_ranges_mcols1.1560.0121.514
Brick_load_cis_matrix_till_distance1.3830.0441.430
Brick_load_data_from_mcool0.0010.0000.001
Brick_load_data_from_sparse000
Brick_load_matrix1.5000.0241.528
Brick_local_score_differentiator2.3830.0752.934
Brick_make_ranges0.0130.0000.014
Brick_matrix_dimensions1.5060.0441.555
Brick_matrix_exists1.5190.1041.630
Brick_matrix_filename1.4920.0281.874
Brick_matrix_isdone1.4660.0311.503
Brick_matrix_issparse1.4820.0361.525
Brick_matrix_maxdist1.5000.0601.905
Brick_matrix_minmax1.4820.0361.533
Brick_mcool_normalisation_exists0.0010.0000.000
Brick_rangekey_exists1.2140.0201.238
Brick_return_region_position1.3370.0361.377
Brick_vizart_plot_heatmap3.0460.0523.532
Create_many_Bricks1.1670.0511.223
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.2620.0401.307