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This page was generated on 2025-02-11 11:43 -0500 (Tue, 11 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4444
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 955/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.25.0  (landing page)
Koustav Pal
Snapshot Date: 2025-02-10 13:40 -0500 (Mon, 10 Feb 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 -0500 (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


CHECK results for HiCBricks on kjohnson3

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: 2025-02-10 19:38:40 -0500 (Mon, 10 Feb 2025)
EndedAt: 2025-02-10 19:39:35 -0500 (Mon, 10 Feb 2025)
EllapsedTime: 54.7 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) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* 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-arm64/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_name0.3330.0430.380
BrickContainer_change_output_directory0.2600.0330.291
BrickContainer_get_path_to_file0.2020.0250.334
BrickContainer_list_chromosomes0.2000.0260.226
BrickContainer_list_experiment_name0.2020.0300.232
BrickContainer_list_files0.2080.0290.239
BrickContainer_list_output_directory0.2010.0320.233
BrickContainer_list_resolutions0.2030.0270.232
BrickContainer_unlink_resolution0.4390.0700.509
Brick_add_ranges0.5250.0470.576
Brick_call_compartments0.4030.0780.593
Brick_export_to_sparse0.6530.0670.721
Brick_fetch_range_index0.2470.0330.279
Brick_fetch_row_vector0.4150.1220.536
Brick_get_bintable0.2170.0360.258
Brick_get_chrominfo0.2010.0320.233
Brick_get_entire_matrix0.3430.0680.411
Brick_get_matrix0.4710.1190.594
Brick_get_matrix_mcols0.3220.0560.481
Brick_get_matrix_within_coords0.4440.0560.501
Brick_get_ranges0.2090.0330.243
Brick_get_values_by_distance0.3560.0700.427
Brick_get_vector_values0.3300.0580.386
Brick_list_matrices0.1990.0330.233
Brick_list_matrix_mcols0.1970.0310.228
Brick_list_mcool_normalisations000
Brick_list_mcool_resolutions000
Brick_list_rangekeys0.1970.0280.226
Brick_list_ranges_mcols0.2010.0280.323
Brick_load_cis_matrix_till_distance0.2880.0650.358
Brick_load_data_from_mcool0.0000.0010.000
Brick_load_data_from_sparse000
Brick_load_matrix0.3230.0770.416
Brick_local_score_differentiator0.5080.0880.599
Brick_make_ranges0.0020.0000.002
Brick_matrix_dimensions0.3230.0630.390
Brick_matrix_exists0.3250.0550.380
Brick_matrix_filename0.3250.0590.393
Brick_matrix_isdone0.3220.0700.396
Brick_matrix_issparse0.3380.1190.574
Brick_matrix_maxdist0.3270.0610.392
Brick_matrix_minmax0.3220.0550.377
Brick_mcool_normalisation_exists000
Brick_rangekey_exists0.2040.0400.247
Brick_return_region_position0.2400.0350.277
Brick_vizart_plot_heatmap0.6100.1290.743
Create_many_Bricks0.2070.0310.270
Create_many_Bricks_from_mcool000
load_BrickContainer0.2190.0290.359