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This page was generated on 2025-09-29 11:40 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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: 2025-09-25 13:40 -0400 (Thu, 25 Sep 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: 2025-09-26 23:41:11 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 23:44:01 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 170.5 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_name1.2160.1221.376
BrickContainer_change_output_directory0.7210.0810.808
BrickContainer_get_path_to_file0.6740.0760.766
BrickContainer_list_chromosomes0.6340.0780.713
BrickContainer_list_experiment_name0.6820.0980.780
BrickContainer_list_files0.6860.0820.771
BrickContainer_list_output_directory0.6660.0840.752
BrickContainer_list_resolutions0.6730.0880.764
BrickContainer_unlink_resolution1.4470.1901.639
Brick_add_ranges1.7490.1571.910
Brick_call_compartments1.2770.1931.491
Brick_export_to_sparse2.3160.2502.612
Brick_fetch_range_index0.8220.0960.945
Brick_fetch_row_vector1.3350.1521.502
Brick_get_bintable1.1380.0941.234
Brick_get_chrominfo0.6840.0900.780
Brick_get_entire_matrix1.1140.3101.434
Brick_get_matrix1.0560.2051.278
Brick_get_matrix_mcols1.0810.2141.323
Brick_get_matrix_within_coords1.5430.2501.844
Brick_get_ranges0.7530.1050.870
Brick_get_values_by_distance1.1940.2811.496
Brick_get_vector_values1.1110.2051.331
Brick_list_matrices0.7150.1060.839
Brick_list_matrix_mcols0.6970.1150.820
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.7070.1100.826
Brick_list_ranges_mcols0.6930.1080.817
Brick_load_cis_matrix_till_distance0.9750.1571.143
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0000.0010.000
Brick_load_matrix1.0680.1941.298
Brick_local_score_differentiator1.7020.2411.962
Brick_make_ranges0.0090.0000.009
Brick_matrix_dimensions1.0720.1571.242
Brick_matrix_exists1.0600.1831.278
Brick_matrix_filename1.0840.1411.239
Brick_matrix_isdone1.0550.1951.264
Brick_matrix_issparse1.0510.1521.225
Brick_matrix_maxdist1.0780.1581.246
Brick_matrix_minmax1.0490.1581.230
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.7010.0870.793
Brick_return_region_position0.7700.0930.866
Brick_vizart_plot_heatmap2.2030.3402.580
Create_many_Bricks0.5060.0690.631
Create_many_Bricks_from_mcool000
load_BrickContainer0.5240.0770.637