Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

This page was generated on 2025-11-24 12:06 -0500 (Mon, 24 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4873
merida1macOS 12.7.6 Montereyx86_644.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" 4654
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4668
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: 2025-11-20 15:01 -0500 (Thu, 20 Nov 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 kjohnson1

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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-11-22 06:59:18 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 07:03:23 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 245.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* 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 13.7.8
* 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 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 ‘1.28.0’
** 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_name1.3180.1322.053
BrickContainer_change_output_directory0.8630.1021.374
BrickContainer_get_path_to_file0.7560.0911.187
BrickContainer_list_chromosomes0.7720.0991.175
BrickContainer_list_experiment_name0.7910.0951.268
BrickContainer_list_files0.8050.0951.299
BrickContainer_list_output_directory0.7890.0941.253
BrickContainer_list_resolutions0.7860.0981.188
BrickContainer_unlink_resolution1.7560.2082.840
Brick_add_ranges1.9070.1352.852
Brick_call_compartments1.3270.2342.082
Brick_export_to_sparse2.6080.3304.049
Brick_fetch_range_index1.4040.1282.097
Brick_fetch_row_vector1.5200.2222.457
Brick_get_bintable0.8210.1061.242
Brick_get_chrominfo0.7670.0961.189
Brick_get_entire_matrix1.1960.2182.043
Brick_get_matrix1.1740.1861.864
Brick_get_matrix_mcols1.1590.1831.963
Brick_get_matrix_within_coords1.6250.2692.661
Brick_get_ranges0.8240.1051.332
Brick_get_values_by_distance1.2880.2242.251
Brick_get_vector_values1.2270.2382.181
Brick_list_matrices0.7650.1461.302
Brick_list_matrix_mcols0.7600.1371.123
Brick_list_mcool_normalisations0.0010.0010.001
Brick_list_mcool_resolutions0.0000.0010.001
Brick_list_rangekeys0.7770.1061.059
Brick_list_ranges_mcols0.7430.1001.220
Brick_load_cis_matrix_till_distance0.9940.2321.681
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0000.0010.001
Brick_load_matrix1.1390.2151.781
Brick_local_score_differentiator1.8290.2893.063
Brick_make_ranges0.0090.0000.010
Brick_matrix_dimensions1.1750.2212.089
Brick_matrix_exists1.1260.1941.758
Brick_matrix_filename1.1340.2001.937
Brick_matrix_isdone1.1480.2281.819
Brick_matrix_issparse1.1420.1821.740
Brick_matrix_maxdist1.1250.1541.799
Brick_matrix_minmax1.1380.1791.710
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.8100.1171.380
Brick_return_region_position0.8800.1101.322
Brick_vizart_plot_heatmap2.3280.2883.663
Create_many_Bricks0.8110.1071.250
Create_many_Bricks_from_mcool0.0000.0010.000
load_BrickContainer0.8240.1011.204