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This page was generated on 2025-01-23 12:08 -0500 (Thu, 23 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" 4493
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" 4394
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: 2025-01-20 13:00 -0500 (Mon, 20 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 merida1

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: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2025-01-21 05:04:30 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 05:10:13 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 343.1 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 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    5.683  0.488   6.211
Brick_vizart_plot_heatmap 4.688  0.695   6.491
* 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/4.4-x86_64/Resources/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_name2.6990.1712.948
BrickContainer_change_output_directory2.1450.1172.326
BrickContainer_get_path_to_file1.9780.1102.131
BrickContainer_list_chromosomes1.9090.1122.066
BrickContainer_list_experiment_name1.9310.1102.077
BrickContainer_list_files1.9420.1092.101
BrickContainer_list_output_directory1.9260.1142.077
BrickContainer_list_resolutions1.9150.1092.077
BrickContainer_unlink_resolution4.1410.2334.430
Brick_add_ranges4.0740.1794.311
Brick_call_compartments3.0420.4473.545
Brick_export_to_sparse5.6830.4886.211
Brick_fetch_range_index2.1860.1152.316
Brick_fetch_row_vector3.2960.3823.704
Brick_get_bintable1.9520.1142.081
Brick_get_chrominfo1.8180.0971.925
Brick_get_entire_matrix3.0320.3843.463
Brick_get_matrix2.5310.3332.880
Brick_get_matrix_mcols2.5590.3492.927
Brick_get_matrix_within_coords3.6130.3393.993
Brick_get_ranges1.9640.1122.104
Brick_get_values_by_distance2.8330.4413.320
Brick_get_vector_values2.6160.3212.964
Brick_list_matrices1.8550.1042.005
Brick_list_matrix_mcols1.8600.1062.114
Brick_list_mcool_normalisations0.0010.0010.001
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys1.8300.1022.021
Brick_list_ranges_mcols1.8760.1102.088
Brick_load_cis_matrix_till_distance2.4260.3432.969
Brick_load_data_from_mcool0.0010.0000.001
Brick_load_data_from_sparse0.0000.0020.002
Brick_load_matrix2.5940.5693.361
Brick_local_score_differentiator4.0880.5764.999
Brick_make_ranges0.0210.0010.021
Brick_matrix_dimensions2.5650.4013.531
Brick_matrix_exists2.5840.4643.538
Brick_matrix_filename2.5470.3753.799
Brick_matrix_isdone2.5790.3573.343
Brick_matrix_issparse2.5750.4413.726
Brick_matrix_maxdist2.5930.3843.541
Brick_matrix_minmax2.5630.4353.357
Brick_mcool_normalisation_exists0.0010.0010.003
Brick_rangekey_exists1.8780.1152.108
Brick_return_region_position2.1010.1222.847
Brick_vizart_plot_heatmap4.6880.6956.491
Create_many_Bricks1.8950.1132.167
Create_many_Bricks_from_mcool0.0000.0020.002
load_BrickContainer2.0150.1202.298