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This page was generated on 2025-08-18 11:41 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-14 13:40 -0400 (Thu, 14 Aug 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 palomino7

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.

raw results


Summary

Package: HiCBricks
Version: 1.26.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HiCBricks_1.26.0.tar.gz
StartedAt: 2025-08-15 03:04:49 -0400 (Fri, 15 Aug 2025)
EndedAt: 2025-08-15 03:10:10 -0400 (Fri, 15 Aug 2025)
EllapsedTime: 320.8 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings HiCBricks_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 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
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
Brick_export_to_sparse           3.22   0.35    6.31
Brick_local_score_differentiator 2.43   0.41    5.30
Brick_vizart_plot_heatmap        2.42   0.33   13.04
Brick_add_ranges                 2.44   0.15    6.44
BrickContainer_unlink_resolution 2.14   0.38    6.36
Brick_get_matrix_within_coords   1.79   0.29    5.54
Brick_get_matrix                 1.79   0.26    5.04
Brick_get_matrix_mcols           1.38   0.21    6.99
Create_many_Bricks               1.10   0.11    6.07
* 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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_name1.580.204.03
BrickContainer_change_output_directory1.220.113.08
BrickContainer_get_path_to_file1.000.173.51
BrickContainer_list_chromosomes0.990.153.00
BrickContainer_list_experiment_name0.960.193.73
BrickContainer_list_files1.020.123.30
BrickContainer_list_output_directory0.910.182.77
BrickContainer_list_resolutions1.140.113.22
BrickContainer_unlink_resolution2.140.386.36
Brick_add_ranges2.440.156.44
Brick_call_compartments1.780.254.58
Brick_export_to_sparse3.220.356.31
Brick_fetch_range_index1.170.143.71
Brick_fetch_row_vector1.890.284.59
Brick_get_bintable1.140.193.55
Brick_get_chrominfo0.930.234.23
Brick_get_entire_matrix1.500.223.99
Brick_get_matrix1.790.265.04
Brick_get_matrix_mcols1.380.216.99
Brick_get_matrix_within_coords1.790.295.54
Brick_get_ranges1.080.183.02
Brick_get_values_by_distance1.580.174.16
Brick_get_vector_values1.380.173.76
Brick_list_matrices1.090.223.00
Brick_list_matrix_mcols0.970.193.27
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.940.153.00
Brick_list_ranges_mcols0.980.213.04
Brick_load_cis_matrix_till_distance1.140.313.75
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.560.264.24
Brick_local_score_differentiator2.430.415.30
Brick_make_ranges000
Brick_matrix_dimensions1.360.114.44
Brick_matrix_exists1.610.224.72
Brick_matrix_filename1.190.423.95
Brick_matrix_isdone1.490.144.67
Brick_matrix_issparse1.500.243.98
Brick_matrix_maxdist1.450.174.00
Brick_matrix_minmax1.410.184.03
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.930.152.88
Brick_return_region_position1.220.123.19
Brick_vizart_plot_heatmap 2.42 0.3313.04
Create_many_Bricks1.100.116.07
Create_many_Bricks_from_mcool000
load_BrickContainer0.970.154.06