Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFG[H]IJKLMNOPQRSTUVWXYZ

This page was generated on 2024-07-03 11:44 -0400 (Wed, 03 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4413
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4356
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 (2024-04-24) -- "Puppy Cup" 4407
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 937/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.23.0  (landing page)
Koustav Pal
Snapshot Date: 2024-07-02 14:00 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: f7d7911
git_last_commit_date: 2024-04-30 11:10:16 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 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: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2024-07-03 05:54:13 -0000 (Wed, 03 Jul 2024)
EndedAt: 2024-07-03 05:57:52 -0000 (Wed, 03 Jul 2024)
EllapsedTime: 219.4 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.23.0’
* 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-4.4.0/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_name1.5000.1181.619
BrickContainer_change_output_directory1.2680.0361.305
BrickContainer_get_path_to_file1.1290.0111.144
BrickContainer_list_chromosomes1.1000.0281.137
BrickContainer_list_experiment_name1.1190.0321.154
BrickContainer_list_files1.1410.0391.183
BrickContainer_list_output_directory1.1170.0201.140
BrickContainer_list_resolutions1.1250.0161.151
BrickContainer_unlink_resolution2.3930.0842.479
Brick_add_ranges2.5130.0482.568
Brick_call_compartments2.2600.0642.330
Brick_export_to_sparse3.3450.0803.436
Brick_fetch_range_index1.3420.0201.365
Brick_fetch_row_vector1.9210.0601.986
Brick_get_bintable1.1590.0081.174
Brick_get_chrominfo1.0970.0431.144
Brick_get_entire_matrix1.4920.0751.570
Brick_get_matrix1.8560.0401.900
Brick_get_matrix_mcols1.4640.0681.535
Brick_get_matrix_within_coords2.0880.0362.129
Brick_get_ranges1.2000.0281.231
Brick_get_values_by_distance1.6630.0321.698
Brick_get_vector_values1.5290.0311.562
Brick_list_matrices1.1210.0081.131
Brick_list_matrix_mcols1.1060.0481.161
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions0.0000.0000.001
Brick_list_rangekeys1.0980.0241.124
Brick_list_ranges_mcols1.1080.0161.127
Brick_load_cis_matrix_till_distance1.3750.0281.407
Brick_load_data_from_mcool0.0000.0000.001
Brick_load_data_from_sparse000
Brick_load_matrix1.4910.0241.518
Brick_local_score_differentiator2.2190.0842.311
Brick_make_ranges0.0120.0000.012
Brick_matrix_dimensions1.4710.0201.494
Brick_matrix_exists1.4800.0161.499
Brick_matrix_filename1.4920.0481.543
Brick_matrix_isdone1.4640.0161.483
Brick_matrix_issparse1.5300.0241.557
Brick_matrix_maxdist1.5040.0631.571
Brick_matrix_minmax1.5500.0601.614
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.1690.0201.445
Brick_return_region_position1.2800.0161.298
Brick_vizart_plot_heatmap2.6430.0282.678
Create_many_Bricks1.1230.0161.141
Create_many_Bricks_from_mcool000
load_BrickContainer1.1640.0401.204