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This page was generated on 2025-08-16 12:07 -0400 (Sat, 16 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 959/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-08-15 13:45 -0400 (Fri, 15 Aug 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: 2025-08-15 07:25:25 -0000 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 07:29:46 -0000 (Fri, 15 Aug 2025)
EllapsedTime: 261.2 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_name1.6770.0711.754
BrickContainer_change_output_directory1.2350.0401.279
BrickContainer_get_path_to_file1.1980.0161.216
BrickContainer_list_chromosomes1.1950.0201.218
BrickContainer_list_experiment_name1.2100.0121.226
BrickContainer_list_files1.2500.0081.301
BrickContainer_list_output_directory1.1090.0441.349
BrickContainer_list_resolutions1.1790.0241.206
BrickContainer_unlink_resolution2.4560.0602.525
Brick_add_ranges2.5670.0392.614
Brick_call_compartments2.2760.0602.345
Brick_export_to_sparse3.3860.0963.495
Brick_fetch_range_index1.4030.0161.643
Brick_fetch_row_vector2.0000.0322.038
Brick_get_bintable1.2350.0441.283
Brick_get_chrominfo1.1890.0201.215
Brick_get_entire_matrix1.5840.0431.631
Brick_get_matrix1.8130.0161.834
Brick_get_matrix_mcols1.5510.0481.604
Brick_get_matrix_within_coords2.1870.0442.335
Brick_get_ranges1.2810.0121.296
Brick_get_values_by_distance1.6720.0441.721
Brick_get_vector_values1.6320.0401.676
Brick_list_matrices1.1360.0201.160
Brick_list_matrix_mcols1.1800.0081.192
Brick_list_mcool_normalisations0.0010.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.1890.0241.217
Brick_list_ranges_mcols1.1730.0081.201
Brick_load_cis_matrix_till_distance1.4490.0161.557
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0000.0000.001
Brick_load_matrix1.5410.0591.605
Brick_local_score_differentiator2.2930.0722.413
Brick_make_ranges0.0120.0000.012
Brick_matrix_dimensions1.4450.0281.478
Brick_matrix_exists1.4350.0121.724
Brick_matrix_filename1.4400.0161.460
Brick_matrix_isdone1.4510.0401.697
Brick_matrix_issparse1.5140.0241.542
Brick_matrix_maxdist1.5100.0521.566
Brick_matrix_minmax1.4440.0241.485
Brick_mcool_normalisation_exists0.0010.0000.000
Brick_rangekey_exists1.1000.0121.116
Brick_return_region_position1.2050.0121.221
Brick_vizart_plot_heatmap2.5710.1072.687
Create_many_Bricks1.1130.0681.436
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.2150.0441.263