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This page was generated on 2023-06-06 11:00:33 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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

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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 913/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HiCBricks 1.19.0  (landing page)
Koustav Pal
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: devel
git_last_commit: 127412f
git_last_commit_date: 2023-04-25 15:05:30 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: HiCBricks
Version: 1.19.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings HiCBricks_1.19.0.tar.gz
StartedAt: 2023-06-06 00:01:53 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 00:06:15 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 261.4 seconds
RetCode: 0
Status:   OK  
CheckDir: HiCBricks.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:HiCBricks.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings HiCBricks_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HiCBricks.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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
* checking for file ‘HiCBricks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCBricks’ version ‘1.19.0’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘IntroductionToHiCBricks.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

HiCBricks.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL HiCBricks
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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_name1.6820.0361.719
BrickContainer_change_output_directory1.3320.0201.352
BrickContainer_get_path_to_file1.2170.0121.232
BrickContainer_list_chromosomes1.1950.0481.246
BrickContainer_list_experiment_name1.2160.0241.243
BrickContainer_list_files1.2540.0321.289
BrickContainer_list_output_directory1.1960.0201.218
BrickContainer_list_resolutions1.2130.0321.247
BrickContainer_unlink_resolution2.6400.0562.697
Brick_add_ranges2.6900.0592.755
Brick_call_compartments2.4430.0402.489
Brick_export_to_sparse3.5480.1043.659
Brick_fetch_range_index1.4390.0441.486
Brick_fetch_row_vector2.0450.0402.089
Brick_get_bintable1.6170.0321.652
Brick_get_chrominfo1.2050.0041.212
Brick_get_entire_matrix1.6710.0601.733
Brick_get_matrix1.6080.0121.623
Brick_get_matrix_mcols1.6060.0441.653
Brick_get_matrix_within_coords2.2650.0362.305
Brick_get_ranges1.3030.0041.310
Brick_get_values_by_distance1.7660.0361.806
Brick_get_vector_values1.6640.0161.682
Brick_list_matrices1.2260.0121.240
Brick_list_matrix_mcols1.2580.0271.291
Brick_list_mcool_normalisations0.0010.0000.001
Brick_list_mcool_resolutions0.0010.0000.001
Brick_list_rangekeys1.1990.0201.222
Brick_list_ranges_mcols1.2290.0041.236
Brick_load_cis_matrix_till_distance1.5250.0321.559
Brick_load_data_from_mcool0.0010.0000.000
Brick_load_data_from_sparse000
Brick_load_matrix1.5660.0521.621
Brick_local_score_differentiator2.4480.0402.494
Brick_make_ranges0.0130.0000.013
Brick_matrix_dimensions1.5970.0281.628
Brick_matrix_exists1.5590.0321.594
Brick_matrix_filename1.5680.0241.595
Brick_matrix_isdone1.5680.0201.591
Brick_matrix_issparse1.5440.0241.574
Brick_matrix_maxdist1.6010.0321.635
Brick_matrix_minmax1.5620.0161.581
Brick_mcool_normalisation_exists000
Brick_rangekey_exists1.2140.0081.224
Brick_return_region_position1.3330.0241.360
Brick_vizart_plot_heatmap2.7850.0562.848
Create_many_Bricks1.2480.0081.258
Create_many_Bricks_from_mcool000
load_BrickContainer1.2680.0161.284