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This page was generated on 2025-08-07 12:05 -0400 (Thu, 07 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 959/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.27.1  (landing page)
Koustav Pal
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for HiCBricks on nebbiolo2

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: 1.27.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz
StartedAt: 2025-08-06 23:19:21 -0400 (Wed, 06 Aug 2025)
EndedAt: 2025-08-06 23:22:35 -0400 (Wed, 06 Aug 2025)
EllapsedTime: 194.2 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings HiCBricks_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/HiCBricks.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

HiCBricks.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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_name1.2520.0421.297
BrickContainer_change_output_directory0.9290.0250.957
BrickContainer_get_path_to_file0.8210.0610.884
BrickContainer_list_chromosomes0.9000.0220.946
BrickContainer_list_experiment_name0.7470.0120.761
BrickContainer_list_files0.7460.0400.789
BrickContainer_list_output_directory0.7430.0140.759
BrickContainer_list_resolutions0.7260.0140.743
BrickContainer_unlink_resolution1.6520.0391.699
Brick_add_ranges1.7280.0411.772
Brick_call_compartments1.1860.0561.245
Brick_export_to_sparse2.2040.0462.253
Brick_fetch_range_index0.8800.0130.896
Brick_fetch_row_vector1.3470.0221.373
Brick_get_bintable0.7620.0120.872
Brick_get_chrominfo0.7230.0170.743
Brick_get_entire_matrix1.1710.0311.206
Brick_get_matrix1.3980.0271.429
Brick_get_matrix_mcols0.9680.0351.006
Brick_get_matrix_within_coords1.4090.0221.434
Brick_get_ranges0.8430.0180.886
Brick_get_values_by_distance1.0770.0171.096
Brick_get_vector_values1.0060.0621.071
Brick_list_matrices0.7310.0180.752
Brick_list_matrix_mcols0.7120.0110.725
Brick_list_mcool_normalisations0.0010.0000.000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.7600.0090.771
Brick_list_ranges_mcols0.8160.0170.861
Brick_load_cis_matrix_till_distance0.9080.0240.934
Brick_load_data_from_mcool0.0010.0000.000
Brick_load_data_from_sparse000
Brick_load_matrix0.9760.0261.004
Brick_local_score_differentiator1.6420.0501.696
Brick_make_ranges0.0090.0000.009
Brick_matrix_dimensions0.9930.0531.049
Brick_matrix_exists0.9810.0231.006
Brick_matrix_filename0.9940.0141.011
Brick_matrix_isdone1.0130.0231.038
Brick_matrix_issparse0.9550.0201.020
Brick_matrix_maxdist0.9920.0161.010
Brick_matrix_minmax0.9840.0201.006
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.7130.0110.727
Brick_return_region_position0.8080.0130.823
Brick_vizart_plot_heatmap1.8840.0771.963
Create_many_Bricks0.7520.0110.765
Create_many_Bricks_from_mcool000
load_BrickContainer0.7650.0070.774