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This page was generated on 2024-05-09 11:40:57 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 962/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.22.0  (landing page)
Koustav Pal
Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_19
git_last_commit: dceb449
git_last_commit_date: 2024-04-30 11:10:16 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.22.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HiCBricks_1.22.0.tar.gz
StartedAt: 2024-05-09 08:18:32 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 08:23:11 -0000 (Thu, 09 May 2024)
EllapsedTime: 278.5 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HiCBricks_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HiCBricks.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘1.22.0’
* 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-beta-2024-04-15_r86425/bin/R CMD INSTALL HiCBricks
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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_name1.5360.0361.573
BrickContainer_change_output_directory1.2800.0161.298
BrickContainer_get_path_to_file1.0970.0161.277
BrickContainer_list_chromosomes1.1330.0281.164
BrickContainer_list_experiment_name1.1290.0121.143
BrickContainer_list_files1.1800.0121.194
BrickContainer_list_output_directory1.1240.0001.135
BrickContainer_list_resolutions1.1820.0281.211
BrickContainer_unlink_resolution2.4180.0402.467
Brick_add_ranges2.4910.0282.524
Brick_call_compartments2.3010.0392.357
Brick_export_to_sparse3.3740.0723.503
Brick_fetch_range_index1.4030.0241.431
Brick_fetch_row_vector1.9510.0282.319
Brick_get_bintable1.1570.0121.170
Brick_get_chrominfo1.1120.0281.142
Brick_get_entire_matrix1.5570.0401.600
Brick_get_matrix1.9470.0602.010
Brick_get_matrix_mcols1.5320.0081.543
Brick_get_matrix_within_coords2.1230.0352.284
Brick_get_ranges1.1660.0241.193
Brick_get_values_by_distance1.6560.0121.671
Brick_get_vector_values1.5710.0361.611
Brick_list_matrices1.1120.0281.142
Brick_list_matrix_mcols1.1520.0081.163
Brick_list_mcool_normalisations0.0000.0000.001
Brick_list_mcool_resolutions000
Brick_list_rangekeys1.0810.0201.103
Brick_list_ranges_mcols1.1320.0161.150
Brick_load_cis_matrix_till_distance1.3950.0321.430
Brick_load_data_from_mcool000
Brick_load_data_from_sparse0.0010.0000.000
Brick_load_matrix1.4650.0281.650
Brick_local_score_differentiator2.2860.0882.381
Brick_make_ranges0.0120.0000.012
Brick_matrix_dimensions1.5270.0161.546
Brick_matrix_exists1.5110.0241.734
Brick_matrix_filename1.4810.0321.516
Brick_matrix_isdone1.4410.0321.476
Brick_matrix_issparse1.4810.0161.499
Brick_matrix_maxdist1.4890.0321.525
Brick_matrix_minmax1.4990.0201.624
Brick_mcool_normalisation_exists0.0010.0000.000
Brick_rangekey_exists1.1730.0081.183
Brick_return_region_position1.2310.0161.248
Brick_vizart_plot_heatmap2.7040.0112.726
Create_many_Bricks1.1790.0241.237
Create_many_Bricks_from_mcool0.0010.0000.000
load_BrickContainer1.2660.0201.287