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This page was generated on 2025-03-06 12:12 -0500 (Thu, 06 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4769
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4504
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4527
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4480
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4416
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 953/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.24.0  (landing page)
Koustav Pal
Snapshot Date: 2025-03-03 13:00 -0500 (Mon, 03 Mar 2025)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_20
git_last_commit: 989054d
git_last_commit_date: 2024-10-29 10:32:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: HiCBricks
Version: 1.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.24.0.tar.gz
StartedAt: 2025-03-04 07:18:16 -0000 (Tue, 04 Mar 2025)
EndedAt: 2025-03-04 07:21:10 -0000 (Tue, 04 Mar 2025)
EllapsedTime: 174.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HiCBricks_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.24.0’
* 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 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘HiCBricks’ ...
** 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_name1.5650.0541.622
BrickContainer_change_output_directory1.2070.0481.257
BrickContainer_get_path_to_file1.0680.0181.090
BrickContainer_list_chromosomes1.0760.0141.092
BrickContainer_list_experiment_name1.0640.0121.080
BrickContainer_list_files1.0930.0151.113
BrickContainer_list_output_directory1.0720.0161.092
BrickContainer_list_resolutions1.0990.0121.118
BrickContainer_unlink_resolution2.3090.0242.339
Brick_add_ranges2.3340.0282.368
Brick_call_compartments2.1340.0362.182
Brick_export_to_sparse3.1970.1003.306
Brick_fetch_range_index1.3500.0561.410
Brick_fetch_row_vector1.9140.0281.947
Brick_get_bintable1.1580.0121.173
Brick_get_chrominfo1.1750.0241.205
Brick_get_entire_matrix1.4650.0551.525
Brick_get_matrix1.7280.0401.773
Brick_get_matrix_mcols1.4320.0281.466
Brick_get_matrix_within_coords2.0600.0762.141
Brick_get_ranges1.1700.0281.200
Brick_get_values_by_distance1.6260.0201.652
Brick_get_vector_values1.4670.0441.514
Brick_list_matrices1.1540.0521.209
Brick_list_matrix_mcols1.0820.0201.105
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.0620.0161.081
Brick_list_ranges_mcols1.0570.0241.084
Brick_load_cis_matrix_till_distance1.3340.0321.370
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0010.0000.000
Brick_load_matrix1.3690.0311.406
Brick_local_score_differentiator2.1690.0682.251
Brick_make_ranges0.0110.0000.011
Brick_matrix_dimensions1.3880.0361.429
Brick_matrix_exists1.3860.0281.418
Brick_matrix_filename1.4090.0361.449
Brick_matrix_isdone1.3850.0321.420
Brick_matrix_issparse1.3810.0361.421
Brick_matrix_maxdist1.4730.0321.509
Brick_matrix_minmax1.4250.0321.462
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.0820.0111.097
Brick_return_region_position1.1680.0321.203
Brick_vizart_plot_heatmap2.5030.0402.552
Create_many_Bricks1.0620.0241.089
Create_many_Bricks_from_mcool0.0010.0000.000
load_BrickContainer1.1100.0241.136