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This page was generated on 2025-03-28 11:51 -0400 (Fri, 28 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4783
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4552
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4581
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4518
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 962/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.25.0  (landing page)
Koustav Pal
Snapshot Date: 2025-03-27 13:40 -0400 (Thu, 27 Mar 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 -0400 (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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HiCBricks_1.25.0.tar.gz
StartedAt: 2025-03-27 22:58:57 -0400 (Thu, 27 Mar 2025)
EndedAt: 2025-03-27 23:02:30 -0400 (Thu, 27 Mar 2025)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HiCBricks_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘1.25.0’
* 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 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-3.21-bioc/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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_name1.4160.0321.447
BrickContainer_change_output_directory1.3000.0171.318
BrickContainer_get_path_to_file0.9340.0140.948
BrickContainer_list_chromosomes0.9140.0090.925
BrickContainer_list_experiment_name0.8790.0130.892
BrickContainer_list_files0.8980.0170.916
BrickContainer_list_output_directory0.8600.0090.870
BrickContainer_list_resolutions0.9440.0781.023
BrickContainer_unlink_resolution1.9270.0982.096
Brick_add_ranges2.4020.0652.467
Brick_call_compartments1.6680.0841.756
Brick_export_to_sparse2.9000.1023.004
Brick_fetch_range_index1.1780.0251.266
Brick_fetch_row_vector1.9250.0301.955
Brick_get_bintable1.0660.0531.119
Brick_get_chrominfo0.9590.0180.977
Brick_get_entire_matrix1.4770.0291.561
Brick_get_matrix2.1080.1502.258
Brick_get_matrix_mcols1.3760.1081.485
Brick_get_matrix_within_coords1.9860.1022.088
Brick_get_ranges1.0340.0251.060
Brick_get_values_by_distance1.4600.0591.519
Brick_get_vector_values1.1300.0711.201
Brick_list_matrices0.7640.0210.785
Brick_list_matrix_mcols0.7440.0140.757
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.7760.0150.791
Brick_list_ranges_mcols0.7780.0140.792
Brick_load_cis_matrix_till_distance1.0110.0161.027
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0010.0000.000
Brick_load_matrix1.0080.0191.027
Brick_local_score_differentiator1.8310.2102.132
Brick_make_ranges0.0090.0000.009
Brick_matrix_dimensions1.0320.2221.254
Brick_matrix_exists0.9460.0210.967
Brick_matrix_filename0.9850.0581.045
Brick_matrix_isdone1.0470.0211.069
Brick_matrix_issparse0.9540.0471.002
Brick_matrix_maxdist0.9550.0220.978
Brick_matrix_minmax0.9480.0190.968
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.7110.0070.719
Brick_return_region_position0.7970.0080.807
Brick_vizart_plot_heatmap1.8200.0731.894
Create_many_Bricks0.6980.0130.711
Create_many_Bricks_from_mcool000
load_BrickContainer0.7390.0100.749