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This page was generated on 2025-02-26 11:46 -0500 (Wed, 26 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4663
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4493
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4504
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4458
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4313
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 959/2302HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.25.0  (landing page)
Koustav Pal
Snapshot Date: 2025-02-25 13:40 -0500 (Tue, 25 Feb 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: 51b1cc8
git_last_commit_date: 2024-10-29 10:32:24 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 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
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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on kjohnson3

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: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.25.0.tar.gz
StartedAt: 2025-02-25 20:23:01 -0500 (Tue, 25 Feb 2025)
EndedAt: 2025-02-25 20:23:55 -0500 (Tue, 25 Feb 2025)
EllapsedTime: 54.7 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCBricks_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.25.0’
* 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 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 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘HiCBricks’ ...
** this is package ‘HiCBricks’ version ‘1.25.0’
** 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_name0.3330.0430.500
BrickContainer_change_output_directory0.2510.0320.282
BrickContainer_get_path_to_file0.2070.0260.233
BrickContainer_list_chromosomes0.2060.0270.234
BrickContainer_list_experiment_name0.2090.0330.243
BrickContainer_list_files0.2120.0290.241
BrickContainer_list_output_directory0.2060.0280.235
BrickContainer_list_resolutions0.2060.0300.242
BrickContainer_unlink_resolution0.4350.0610.494
Brick_add_ranges0.5280.0430.687
Brick_call_compartments0.3970.0560.453
Brick_export_to_sparse0.6710.0850.767
Brick_fetch_range_index0.2480.0330.287
Brick_fetch_row_vector0.4120.0710.486
Brick_get_bintable0.2140.0310.246
Brick_get_chrominfo0.2010.0290.229
Brick_get_entire_matrix0.3400.0610.400
Brick_get_matrix0.4640.0540.649
Brick_get_matrix_mcols0.3340.0520.391
Brick_get_matrix_within_coords0.4590.0580.518
Brick_get_ranges0.2130.0330.247
Brick_get_values_by_distance0.3580.0830.443
Brick_get_vector_values0.3400.0560.394
Brick_list_matrices0.2060.0340.270
Brick_list_matrix_mcols0.1990.0280.317
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.1980.0280.226
Brick_list_ranges_mcols0.2000.0270.227
Brick_load_cis_matrix_till_distance0.2820.0420.325
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0000.0000.001
Brick_load_matrix0.3260.0560.382
Brick_local_score_differentiator0.5160.0840.604
Brick_make_ranges0.0020.0000.002
Brick_matrix_dimensions0.3210.0570.380
Brick_matrix_exists0.3280.0600.397
Brick_matrix_filename0.3200.0690.396
Brick_matrix_isdone0.3160.0560.476
Brick_matrix_issparse0.3310.0550.387
Brick_matrix_maxdist0.3230.0490.384
Brick_matrix_minmax0.3200.0520.373
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.2020.0290.239
Brick_return_region_position0.2340.0310.266
Brick_vizart_plot_heatmap0.6210.0760.699
Create_many_Bricks0.2040.0290.345
Create_many_Bricks_from_mcool000
load_BrickContainer0.2150.0300.245