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This page was generated on 2025-01-30 12:11 -0500 (Thu, 30 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4400
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: 2025-01-27 13:00 -0500 (Mon, 27 Jan 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: 2025-01-28 07:56:53 -0000 (Tue, 28 Jan 2025)
EndedAt: 2025-01-28 08:01:13 -0000 (Tue, 28 Jan 2025)
EllapsedTime: 259.2 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_name1.4870.0821.595
BrickContainer_change_output_directory1.2090.0771.319
BrickContainer_get_path_to_file1.0610.0551.149
BrickContainer_list_chromosomes1.1060.0511.175
BrickContainer_list_experiment_name1.1170.0231.157
BrickContainer_list_files1.0790.0471.146
BrickContainer_list_output_directory1.1010.0381.152
BrickContainer_list_resolutions1.1230.0511.200
BrickContainer_unlink_resolution2.3180.1012.457
Brick_add_ranges2.3110.1042.455
Brick_call_compartments2.1450.0512.230
Brick_export_to_sparse3.0360.1863.268
Brick_fetch_range_index1.2740.0891.392
Brick_fetch_row_vector1.8090.0661.997
Brick_get_bintable1.1160.0781.214
Brick_get_chrominfo1.0320.0551.103
Brick_get_entire_matrix1.4360.0901.562
Brick_get_matrix1.6860.1061.848
Brick_get_matrix_mcols1.4350.0361.475
Brick_get_matrix_within_coords2.0230.0442.074
Brick_get_ranges1.1430.0641.214
Brick_get_values_by_distance1.5840.0361.624
Brick_get_vector_values1.4680.0471.521
Brick_list_matrices1.0990.0281.130
Brick_list_matrix_mcols1.1140.0121.185
Brick_list_mcool_normalisations0.0010.0000.001
Brick_list_mcool_resolutions0.0010.0000.000
Brick_list_rangekeys1.1030.0001.105
Brick_list_ranges_mcols1.0880.0241.115
Brick_load_cis_matrix_till_distance1.3690.0401.413
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.4440.0361.484
Brick_local_score_differentiator2.2570.0642.332
Brick_make_ranges0.0110.0000.011
Brick_matrix_dimensions1.4290.0361.470
Brick_matrix_exists1.4480.0081.461
Brick_matrix_filename1.4430.0521.500
Brick_matrix_isdone1.4250.0511.481
Brick_matrix_issparse1.4640.0251.588
Brick_matrix_maxdist1.4620.0231.491
Brick_matrix_minmax1.3840.0481.436
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.0950.0121.110
Brick_return_region_position1.2300.0441.279
Brick_vizart_plot_heatmap2.6640.0602.788
Create_many_Bricks1.1920.0081.203
Create_many_Bricks_from_mcool0.0010.0000.000
load_BrickContainer1.1830.0201.209