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This page was generated on 2025-08-09 12:07 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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: 2025-08-08 13:45 -0400 (Fri, 08 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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings HiCBricks_1.27.1.tar.gz
StartedAt: 2025-08-09 02:56:46 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 03:02:07 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 321.0 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCBricks.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings HiCBricks_1.27.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-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 '1.27.1'
* 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 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   0.50    5.89
Brick_vizart_plot_heatmap              2.49   0.36    5.64
Brick_add_ranges                       2.50   0.19    6.39
BrickContainer_unlink_resolution       2.21   0.26   10.50
Brick_local_score_differentiator       2.01   0.35    5.12
Brick_get_matrix                       1.94   0.27    5.24
BrickContainer_change_experiment_name  1.60   0.22    6.44
BrickContainer_change_output_directory 1.35   0.14    7.86
Brick_matrix_dimensions                1.34   0.15    5.81
BrickContainer_list_output_directory   1.18   0.10    5.12
* 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:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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_name1.600.226.44
BrickContainer_change_output_directory1.350.147.86
BrickContainer_get_path_to_file1.100.144.01
BrickContainer_list_chromosomes1.070.143.69
BrickContainer_list_experiment_name1.140.093.86
BrickContainer_list_files1.040.093.11
BrickContainer_list_output_directory1.180.105.12
BrickContainer_list_resolutions1.220.194.86
BrickContainer_unlink_resolution 2.21 0.2610.50
Brick_add_ranges2.500.196.39
Brick_call_compartments1.630.224.32
Brick_export_to_sparse3.220.505.89
Brick_fetch_range_index1.390.154.34
Brick_fetch_row_vector1.870.214.31
Brick_get_bintable1.180.092.83
Brick_get_chrominfo0.900.093.25
Brick_get_entire_matrix1.450.254.17
Brick_get_matrix1.940.275.24
Brick_get_matrix_mcols1.410.334.45
Brick_get_matrix_within_coords1.970.334.53
Brick_get_ranges1.250.113.08
Brick_get_values_by_distance1.650.254.32
Brick_get_vector_values1.390.244.80
Brick_list_matrices1.110.142.88
Brick_list_matrix_mcols1.100.063.43
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.060.162.94
Brick_list_ranges_mcols1.080.073.38
Brick_load_cis_matrix_till_distance1.190.183.37
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.530.294.30
Brick_local_score_differentiator2.010.355.12
Brick_make_ranges0.020.000.02
Brick_matrix_dimensions1.340.155.81
Brick_matrix_exists1.280.273.86
Brick_matrix_filename1.420.343.56
Brick_matrix_isdone1.400.243.88
Brick_matrix_issparse1.640.254.00
Brick_matrix_maxdist1.380.233.99
Brick_matrix_minmax1.290.203.79
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.050.243.43
Brick_return_region_position1.090.093.53
Brick_vizart_plot_heatmap2.490.365.64
Create_many_Bricks1.050.132.98
Create_many_Bricks_from_mcool000
load_BrickContainer1.070.123.25