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This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 974/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: 71e4813
git_last_commit_date: 2025-07-22 20:39:06 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    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: 1.27.1
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_1.27.1.tar.gz
StartedAt: 2025-10-17 10:03:01 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 10:06:32 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 211.2 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_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* 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 ‘1.27.1’
* 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-4.5.0/site-library’
* installing *source* package ‘HiCBricks’ ...
** this is package ‘HiCBricks’ version ‘1.27.1’
** 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_name1.8130.0891.911
BrickContainer_change_output_directory1.2880.0281.324
BrickContainer_get_path_to_file1.2000.0721.276
BrickContainer_list_chromosomes1.2000.0601.265
BrickContainer_list_experiment_name1.2430.0281.280
BrickContainer_list_files1.2020.0511.259
BrickContainer_list_output_directory1.1960.0481.249
BrickContainer_list_resolutions1.1900.0441.238
BrickContainer_unlink_resolution2.5150.0842.612
Brick_add_ranges2.5890.1352.734
Brick_call_compartments2.2150.0632.295
Brick_export_to_sparse3.4410.1163.570
Brick_fetch_range_index1.4050.0401.450
Brick_fetch_row_vector1.9880.0472.043
Brick_get_bintable1.6080.0881.706
Brick_get_chrominfo1.1650.0161.186
Brick_get_entire_matrix1.6050.0791.691
Brick_get_matrix1.5100.0201.535
Brick_get_matrix_mcols1.4860.0281.520
Brick_get_matrix_within_coords2.1960.0872.292
Brick_get_ranges1.2210.0281.253
Brick_get_values_by_distance1.7070.0801.796
Brick_get_vector_values1.5590.0281.592
Brick_list_matrices1.1980.0321.234
Brick_list_matrix_mcols1.1690.0351.211
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.1840.0591.247
Brick_list_ranges_mcols1.1540.0161.175
Brick_load_cis_matrix_till_distance1.4140.0281.448
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0010.0000.001
Brick_load_matrix1.4860.0401.535
Brick_local_score_differentiator2.3630.0752.450
Brick_make_ranges0.0130.0000.013
Brick_matrix_dimensions1.4930.0551.556
Brick_matrix_exists1.5050.0321.543
Brick_matrix_filename1.4700.0521.528
Brick_matrix_isdone1.5450.0601.611
Brick_matrix_issparse1.5100.0401.559
Brick_matrix_maxdist1.5020.0321.541
Brick_matrix_minmax1.5100.0201.536
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.1960.0151.217
Brick_return_region_position1.3290.0401.374
Brick_vizart_plot_heatmap3.0040.0723.090
Create_many_Bricks1.2340.0201.258
Create_many_Bricks_from_mcool000
load_BrickContainer1.2220.0121.239