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This page was generated on 2025-09-01 11:41 -0400 (Mon, 01 Sep 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" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
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: 2025-08-28 13:40 -0400 (Thu, 28 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: 2025-08-29 23:56:48 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 23:59:35 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 167.5 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_name1.1290.1261.281
BrickContainer_change_output_directory0.8540.0880.948
BrickContainer_get_path_to_file0.7140.0920.812
BrickContainer_list_chromosomes0.7040.0880.796
BrickContainer_list_experiment_name0.7040.0840.798
BrickContainer_list_files0.7340.0910.854
BrickContainer_list_output_directory0.7220.0950.837
BrickContainer_list_resolutions0.7140.0820.804
BrickContainer_unlink_resolution1.5180.1781.713
Brick_add_ranges1.7510.1251.884
Brick_call_compartments1.3230.2031.562
Brick_export_to_sparse2.4240.2822.762
Brick_fetch_range_index0.8880.1081.043
Brick_fetch_row_vector1.4360.1921.681
Brick_get_bintable0.7530.0890.855
Brick_get_chrominfo0.6940.0850.782
Brick_get_entire_matrix1.1140.1821.314
Brick_get_matrix1.5090.1521.704
Brick_get_matrix_mcols1.0730.1461.230
Brick_get_matrix_within_coords1.5070.1641.684
Brick_get_ranges0.7320.0940.849
Brick_get_values_by_distance1.1900.2011.400
Brick_get_vector_values1.0840.1581.248
Brick_list_matrices0.6720.0810.760
Brick_list_matrix_mcols0.6820.0790.764
Brick_list_mcool_normalisations0.0000.0010.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.6800.0950.798
Brick_list_ranges_mcols0.7060.0820.797
Brick_load_cis_matrix_till_distance0.9880.1421.202
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0000.0010.000
Brick_load_matrix0.6760.1510.883
Brick_local_score_differentiator1.6140.2852.015
Brick_make_ranges0.0080.0000.008
Brick_matrix_dimensions1.0390.1481.204
Brick_matrix_exists1.0380.1951.269
Brick_matrix_filename1.0690.1631.249
Brick_matrix_isdone1.0610.2121.285
Brick_matrix_issparse1.0980.2201.348
Brick_matrix_maxdist1.0880.2711.386
Brick_matrix_minmax1.0930.2271.359
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.7260.1130.870
Brick_return_region_position0.8280.1240.984
Brick_vizart_plot_heatmap2.1330.3572.586
Create_many_Bricks0.6230.1080.781
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer0.5460.0720.695