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This page was generated on 2025-01-11 11:46 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 949/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.25.0  (landing page)
Koustav Pal
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for HiCBricks on kunpeng2

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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2025-01-11 07:30:24 -0000 (Sat, 11 Jan 2025)
EndedAt: 2025-01-11 07:33:35 -0000 (Sat, 11 Jan 2025)
EllapsedTime: 191.2 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HiCBricks.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.25.0’
* 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 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-4.5.0-devel_2024-11-24/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_name1.5710.0521.626
BrickContainer_change_output_directory1.2700.0361.309
BrickContainer_get_path_to_file1.1490.0361.188
BrickContainer_list_chromosomes1.1070.0441.155
BrickContainer_list_experiment_name1.1310.0151.226
BrickContainer_list_files1.1410.0321.176
BrickContainer_list_output_directory1.1410.0401.183
BrickContainer_list_resolutions1.1110.0081.121
BrickContainer_unlink_resolution2.3970.0482.604
Brick_add_ranges2.4530.0722.529
Brick_call_compartments2.2350.0762.320
Brick_export_to_sparse3.4320.1193.700
Brick_fetch_range_index1.3940.0121.409
Brick_fetch_row_vector1.9840.0362.092
Brick_get_bintable1.1660.0241.193
Brick_get_chrominfo1.1200.0441.167
Brick_get_entire_matrix1.5380.0281.569
Brick_get_matrix1.5630.0361.602
Brick_get_matrix_mcols1.8950.0562.058
Brick_get_matrix_within_coords2.2160.0562.277
Brick_get_ranges1.2100.0201.233
Brick_get_values_by_distance1.7240.0242.033
Brick_get_vector_values1.5120.0401.555
Brick_list_matrices1.1490.0401.192
Brick_list_matrix_mcols1.1230.0271.153
Brick_list_mcool_normalisations0.0010.0000.000
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.1420.0121.228
Brick_list_ranges_mcols1.1240.0121.259
Brick_load_cis_matrix_till_distance1.4450.0471.497
Brick_load_data_from_mcool000
Brick_load_data_from_sparse000
Brick_load_matrix1.5080.0201.531
Brick_local_score_differentiator2.3430.0482.543
Brick_make_ranges0.0130.0000.012
Brick_matrix_dimensions1.5270.0241.554
Brick_matrix_exists1.4680.0121.495
Brick_matrix_filename1.4860.0321.522
Brick_matrix_isdone1.5080.0321.545
Brick_matrix_issparse1.5090.0281.753
Brick_matrix_maxdist1.5110.0521.624
Brick_matrix_minmax1.5030.0281.534
Brick_mcool_normalisation_exists0.0010.0000.000
Brick_rangekey_exists1.1340.0121.147
Brick_return_region_position1.3010.0311.336
Brick_vizart_plot_heatmap2.7510.0122.769
Create_many_Bricks1.1610.0121.176
Create_many_Bricks_from_mcool0.0000.0000.001
load_BrickContainer1.2150.0401.257