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This page was generated on 2025-09-30 12:06 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 970/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-09-29 13:45 -0400 (Mon, 29 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 kjohnson3

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.27.1.tar.gz
StartedAt: 2025-09-29 19:50:42 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 19:51:41 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 58.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.27.1’
* 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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_name0.3330.0400.376
BrickContainer_change_output_directory0.2810.0330.319
BrickContainer_get_path_to_file0.2200.0320.256
BrickContainer_list_chromosomes0.2130.0270.251
BrickContainer_list_experiment_name0.2090.0290.251
BrickContainer_list_files0.2230.0350.269
BrickContainer_list_output_directory0.2100.0250.237
BrickContainer_list_resolutions0.2100.0310.246
BrickContainer_unlink_resolution0.4510.0620.611
Brick_add_ranges0.5490.0430.594
Brick_call_compartments0.4060.0560.481
Brick_export_to_sparse0.6650.0700.760
Brick_fetch_range_index0.2460.0320.280
Brick_fetch_row_vector0.4300.0570.507
Brick_get_bintable0.3620.0320.409
Brick_get_chrominfo0.2050.0270.342
Brick_get_entire_matrix0.3400.0600.416
Brick_get_matrix0.3300.0500.389
Brick_get_matrix_mcols0.3310.0540.389
Brick_get_matrix_within_coords0.4590.0520.542
Brick_get_ranges0.2270.0320.261
Brick_get_values_by_distance0.3700.0630.445
Brick_get_vector_values0.3420.0580.486
Brick_list_matrices0.2050.0290.235
Brick_list_matrix_mcols0.2090.0300.240
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.2000.0230.223
Brick_list_ranges_mcols0.2040.0290.233
Brick_load_cis_matrix_till_distance0.2960.0450.341
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix0.3320.0520.389
Brick_local_score_differentiator0.5340.1080.677
Brick_make_ranges0.0020.0000.002
Brick_matrix_dimensions0.3340.0530.403
Brick_matrix_exists0.3320.0560.392
Brick_matrix_filename0.3250.0500.497
Brick_matrix_isdone0.3250.0480.383
Brick_matrix_issparse0.3300.0520.383
Brick_matrix_maxdist0.3280.0460.390
Brick_matrix_minmax0.3320.0550.421
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.2020.0290.235
Brick_return_region_position0.2360.0300.267
Brick_vizart_plot_heatmap0.6830.0990.921
Create_many_Bricks0.2120.0250.242
Create_many_Bricks_from_mcool000
load_BrickContainer0.2250.0280.252