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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-13 13:40 -0400 (Mon, 13 Oct 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 12.7.6 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: HiCBricks
Version: 1.26.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.26.0.tar.gz
StartedAt: 2025-10-14 10:07:18 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 10:10:48 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 210.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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_name1.8940.0321.931
BrickContainer_change_output_directory1.3590.0361.399
BrickContainer_get_path_to_file1.2860.0081.297
BrickContainer_list_chromosomes1.2940.0081.305
BrickContainer_list_experiment_name1.2990.0321.334
BrickContainer_list_files1.2740.0201.298
BrickContainer_list_output_directory1.2770.0081.289
BrickContainer_list_resolutions1.2490.0121.264
BrickContainer_unlink_resolution2.7130.0442.768
Brick_add_ranges2.8810.0802.968
Brick_call_compartments2.3810.0482.444
Brick_export_to_sparse3.7870.0953.892
Brick_fetch_range_index1.5000.0161.523
Brick_fetch_row_vector2.1870.0882.279
Brick_get_bintable1.7650.0321.804
Brick_get_chrominfo1.2740.0121.289
Brick_get_entire_matrix1.7000.0601.765
Brick_get_matrix1.6800.0241.708
Brick_get_matrix_mcols1.6790.0281.711
Brick_get_matrix_within_coords2.4550.0432.504
Brick_get_ranges1.3540.0201.377
Brick_get_values_by_distance1.8620.0481.914
Brick_get_vector_values1.7010.0361.741
Brick_list_matrices1.3120.0241.342
Brick_list_matrix_mcols1.3150.0361.354
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.2770.0321.313
Brick_list_ranges_mcols1.2640.0281.295
Brick_load_cis_matrix_till_distance1.5580.0241.590
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.6110.0241.638
Brick_local_score_differentiator2.6510.0602.720
Brick_make_ranges0.0140.0000.014
Brick_matrix_dimensions1.6810.0161.701
Brick_matrix_exists1.6820.0241.711
Brick_matrix_filename1.6540.0271.692
Brick_matrix_isdone1.6700.0281.702
Brick_matrix_issparse1.6890.0561.749
Brick_matrix_maxdist1.6660.0281.698
Brick_matrix_minmax1.6200.0281.652
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.3210.0041.328
Brick_return_region_position1.4610.0081.472
Brick_vizart_plot_heatmap3.3250.0483.382
Create_many_Bricks1.3360.0081.347
Create_many_Bricks_from_mcool000
load_BrickContainer1.3420.0241.369