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This page was generated on 2025-08-21 11:41 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 970/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.26.0  (landing page)
Koustav Pal
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_21
git_last_commit: 773bb6b
git_last_commit_date: 2025-04-15 11:38:17 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (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: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2025-08-19 23:58:57 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-20 00:01:38 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 161.4 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_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.26.0’
* 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 ‘1.26.0’
** 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_name1.0460.1311.189
BrickContainer_change_output_directory0.8470.0970.980
BrickContainer_get_path_to_file0.6730.0820.784
BrickContainer_list_chromosomes0.6900.0820.779
BrickContainer_list_experiment_name0.6710.0790.753
BrickContainer_list_files0.6880.0850.795
BrickContainer_list_output_directory0.6560.0800.737
BrickContainer_list_resolutions0.6590.0760.747
BrickContainer_unlink_resolution1.4280.1701.612
Brick_add_ranges1.7230.1491.889
Brick_call_compartments1.3130.2041.559
Brick_export_to_sparse2.2690.2462.553
Brick_fetch_range_index0.5170.0700.603
Brick_fetch_row_vector1.1760.1571.413
Brick_get_bintable0.7400.0880.856
Brick_get_chrominfo0.6580.0790.742
Brick_get_entire_matrix1.0870.1731.277
Brick_get_matrix1.4710.1491.653
Brick_get_matrix_mcols0.7080.1260.886
Brick_get_matrix_within_coords1.3850.1421.564
Brick_get_ranges0.7170.0830.810
Brick_get_values_by_distance1.1280.1651.296
Brick_get_vector_values1.0620.1621.257
Brick_list_matrices0.6850.0940.782
Brick_list_matrix_mcols0.6420.0870.731
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys0.6740.0910.770
Brick_list_ranges_mcols0.6640.0860.755
Brick_load_cis_matrix_till_distance0.9130.1281.048
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0000.0010.001
Brick_load_matrix1.0100.1491.213
Brick_local_score_differentiator1.6330.2201.858
Brick_make_ranges0.0080.0000.009
Brick_matrix_dimensions1.0290.1441.179
Brick_matrix_exists0.9980.1311.151
Brick_matrix_filename1.0010.1351.143
Brick_matrix_isdone1.0180.1521.173
Brick_matrix_issparse1.0420.1631.238
Brick_matrix_maxdist1.0710.1771.271
Brick_matrix_minmax1.0330.1911.243
Brick_mcool_normalisation_exists0.0000.0010.001
Brick_rangekey_exists0.6930.1130.828
Brick_return_region_position0.7840.1160.918
Brick_vizart_plot_heatmap2.0490.2872.422
Create_many_Bricks0.7060.1140.844
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer0.7220.1130.858