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This page was generated on 2025-03-19 11:44 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 962/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.25.0  (landing page)
Koustav Pal
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 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
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 lconway

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: 2025-03-18 21:24:30 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 21:27:29 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 178.6 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-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 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 ‘1.25.0’
* 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-x86_64/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_name1.2170.1191.354
BrickContainer_change_output_directory0.9960.0921.090
BrickContainer_get_path_to_file0.8650.0830.954
BrickContainer_list_chromosomes0.8690.0810.966
BrickContainer_list_experiment_name0.8710.0800.959
BrickContainer_list_files0.8840.0770.968
BrickContainer_list_output_directory0.8620.0770.949
BrickContainer_list_resolutions0.8420.0810.932
BrickContainer_unlink_resolution1.8030.1711.996
Brick_add_ranges1.9680.1302.113
Brick_call_compartments1.4190.2481.690
Brick_export_to_sparse2.6630.2822.966
Brick_fetch_range_index1.0050.0821.100
Brick_fetch_row_vector1.5320.2171.776
Brick_get_bintable0.8900.0850.984
Brick_get_chrominfo0.8380.0800.931
Brick_get_entire_matrix1.2560.2941.578
Brick_get_matrix1.6150.2421.878
Brick_get_matrix_mcols1.2500.2311.513
Brick_get_matrix_within_coords1.7480.2372.000
Brick_get_ranges0.8660.0830.958
Brick_get_values_by_distance1.3430.2421.608
Brick_get_vector_values1.2420.2331.499
Brick_list_matrices0.8290.0810.920
Brick_list_matrix_mcols0.8130.0740.893
Brick_list_mcool_normalisations0.0010.0010.001
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys0.8060.0770.894
Brick_list_ranges_mcols0.8500.0840.945
Brick_load_cis_matrix_till_distance1.1310.1741.327
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0000.0010.001
Brick_load_matrix1.1920.2111.437
Brick_local_score_differentiator1.9680.4252.434
Brick_make_ranges0.0110.0000.011
Brick_matrix_dimensions1.2320.2061.453
Brick_matrix_exists1.1860.1981.400
Brick_matrix_filename1.1310.2041.363
Brick_matrix_isdone1.1740.2171.418
Brick_matrix_issparse1.2560.2461.520
Brick_matrix_maxdist1.2120.3021.534
Brick_matrix_minmax1.2300.2371.496
Brick_mcool_normalisation_exists0.0000.0000.001
Brick_rangekey_exists0.8680.0830.962
Brick_return_region_position0.9530.0911.062
Brick_vizart_plot_heatmap2.3410.3702.754
Create_many_Bricks0.8870.0890.988
Create_many_Bricks_from_mcool000
load_BrickContainer0.9180.0911.015