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This page was generated on 2025-10-13 12:07 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 971/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-10-12 13:45 -0400 (Sun, 12 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 12.7.1 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: 2025-10-10 09:50:09 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 09:53:32 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 203.2 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_name1.7430.0691.822
BrickContainer_change_output_directory1.2620.0201.286
BrickContainer_get_path_to_file1.2060.0401.251
BrickContainer_list_chromosomes1.2190.0601.284
BrickContainer_list_experiment_name1.2270.0591.293
BrickContainer_list_files1.2420.0511.299
BrickContainer_list_output_directory1.1650.0751.244
BrickContainer_list_resolutions1.1970.0321.233
BrickContainer_unlink_resolution2.5370.0592.610
Brick_add_ranges2.5840.0762.669
Brick_call_compartments2.1860.0522.246
Brick_export_to_sparse3.5280.1323.726
Brick_fetch_range_index1.4430.0401.487
Brick_fetch_row_vector2.0950.0442.146
Brick_get_bintable1.5950.0481.652
Brick_get_chrominfo1.2230.0401.268
Brick_get_entire_matrix1.6400.0631.710
Brick_get_matrix1.5790.0321.617
Brick_get_matrix_mcols1.5740.0481.628
Brick_get_matrix_within_coords2.2500.0242.281
Brick_get_ranges1.2540.0321.293
Brick_get_values_by_distance1.6910.0481.745
Brick_get_vector_values1.5570.0441.607
Brick_list_matrices1.1790.0591.245
Brick_list_matrix_mcols1.1860.0281.219
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.1570.0151.177
Brick_list_ranges_mcols1.1830.0241.211
Brick_load_cis_matrix_till_distance1.4590.0721.536
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse000
Brick_load_matrix1.4960.0361.538
Brick_local_score_differentiator2.3120.0762.413
Brick_make_ranges0.0120.0000.012
Brick_matrix_dimensions1.4820.0401.527
Brick_matrix_exists1.5220.0681.595
Brick_matrix_filename1.5060.0231.544
Brick_matrix_isdone1.5060.0321.543
Brick_matrix_issparse1.5120.0241.541
Brick_matrix_maxdist1.5540.0521.610
Brick_matrix_minmax1.4980.0281.531
Brick_mcool_normalisation_exists0.0010.0000.001
Brick_rangekey_exists1.1830.0281.215
Brick_return_region_position1.3160.0081.328
Brick_vizart_plot_heatmap2.8730.0672.950
Create_many_Bricks1.2040.0521.261
Create_many_Bricks_from_mcool000
load_BrickContainer1.2510.0361.292