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

This page was generated on 2025-09-25 12:05 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 969/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 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 lconway

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: 2025-09-24 21:41:33 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 21:44:38 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 184.6 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_1.27.1.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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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-x86_64/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_name1.3100.1281.456
BrickContainer_change_output_directory1.0570.0881.149
BrickContainer_get_path_to_file0.8270.0760.908
BrickContainer_list_chromosomes0.8780.0790.966
BrickContainer_list_experiment_name0.8790.0780.963
BrickContainer_list_files0.9190.0801.009
BrickContainer_list_output_directory0.8450.0770.932
BrickContainer_list_resolutions0.8690.0790.960
BrickContainer_unlink_resolution1.8480.1712.048
Brick_add_ranges2.0460.1232.192
Brick_call_compartments1.4760.2311.727
Brick_export_to_sparse2.6560.2662.944
Brick_fetch_range_index1.0020.0811.108
Brick_fetch_row_vector1.5070.1901.713
Brick_get_bintable1.1800.0791.264
Brick_get_chrominfo0.7850.0750.872
Brick_get_entire_matrix1.1820.2291.426
Brick_get_matrix1.1730.1691.354
Brick_get_matrix_mcols1.1480.1661.327
Brick_get_matrix_within_coords1.6810.2411.953
Brick_get_ranges0.8990.0850.999
Brick_get_values_by_distance1.3700.2581.647
Brick_get_vector_values1.2690.2441.544
Brick_list_matrices0.8250.0800.918
Brick_list_matrix_mcols0.8320.0830.958
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions0.0010.0010.000
Brick_list_rangekeys0.8320.0770.917
Brick_list_ranges_mcols0.8260.0800.914
Brick_load_cis_matrix_till_distance1.0690.2041.283
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0000.0000.001
Brick_load_matrix1.1150.2001.324
Brick_local_score_differentiator1.9140.3502.354
Brick_make_ranges0.0120.0000.012
Brick_matrix_dimensions1.2310.2421.491
Brick_matrix_exists1.1650.1921.371
Brick_matrix_filename1.1390.2011.351
Brick_matrix_isdone1.1400.2161.392
Brick_matrix_issparse1.2290.2531.497
Brick_matrix_maxdist1.2840.2901.604
Brick_matrix_minmax1.3100.2121.545
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.8910.0910.998
Brick_return_region_position1.0310.0921.139
Brick_vizart_plot_heatmap2.3970.3032.734
Create_many_Bricks0.8760.0850.978
Create_many_Bricks_from_mcool0.0010.0000.000
load_BrickContainer0.8630.0850.953