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This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4903
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4668
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 978/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.28.0  (landing page)
Koustav Pal
Snapshot Date: 2025-11-14 13:45 -0500 (Fri, 14 Nov 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_22
git_last_commit: 3296656
git_last_commit_date: 2025-10-29 10:48:17 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on taishan

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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-11-14 10:27:38 -0000 (Fri, 14 Nov 2025)
EndedAt: 2025-11-14 10:30:54 -0000 (Fri, 14 Nov 2025)
EllapsedTime: 196.2 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_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.28.0’
* 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

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘HiCBricks’ ...
** this is package ‘HiCBricks’ version ‘1.28.0’
** 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_name1.6810.1141.801
BrickContainer_change_output_directory1.2580.0271.290
BrickContainer_get_path_to_file1.2060.0401.262
BrickContainer_list_chromosomes1.1720.0361.212
BrickContainer_list_experiment_name1.1950.0321.235
BrickContainer_list_files1.2430.0321.283
BrickContainer_list_output_directory1.1980.0231.229
BrickContainer_list_resolutions1.1800.0241.209
BrickContainer_unlink_resolution2.5030.1082.620
Brick_add_ranges2.5550.0682.633
Brick_call_compartments2.2130.1112.335
Brick_export_to_sparse3.4670.0723.552
Brick_fetch_range_index1.3730.0321.409
Brick_fetch_row_vector2.2590.0442.310
Brick_get_bintable1.1920.0271.224
Brick_get_chrominfo1.1460.0241.174
Brick_get_entire_matrix1.5540.0641.623
Brick_get_matrix1.5340.0401.580
Brick_get_matrix_mcols1.5130.0711.594
Brick_get_matrix_within_coords2.1660.0562.234
Brick_get_ranges1.2210.0161.242
Brick_get_values_by_distance1.7260.0361.771
Brick_get_vector_values1.5750.0351.617
Brick_list_matrices1.1920.0281.224
Brick_list_matrix_mcols1.1350.0281.167
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions0.0010.0000.000
Brick_list_rangekeys1.1610.0121.178
Brick_list_ranges_mcols1.2080.0321.244
Brick_load_cis_matrix_till_distance1.4130.0401.458
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse0.0010.0000.000
Brick_load_matrix1.5010.0201.526
Brick_local_score_differentiator2.3860.0522.449
Brick_make_ranges0.0110.0040.015
Brick_matrix_dimensions1.4880.0511.546
Brick_matrix_exists1.4700.0321.508
Brick_matrix_filename1.4940.0201.520
Brick_matrix_isdone1.4950.0241.533
Brick_matrix_issparse1.4870.0441.536
Brick_matrix_maxdist1.4680.0881.560
Brick_matrix_minmax1.4950.0401.541
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.1910.0001.198
Brick_return_region_position1.3100.0271.345
Brick_vizart_plot_heatmap3.0540.0283.153
Create_many_Bricks1.2470.0201.272
Create_many_Bricks_from_mcool000
load_BrickContainer1.2920.0241.320